rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
74411,SRR23929935,SRX19740082,SRS17106156,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 029  10 dy post single ablation,GSM7085299,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation,10X 22 029  10 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation,GSM7085299,GSM7085299: 10X 22 029  10 dy post single ablation; Danio rerio; RNA Seq,GSM7085299 r1,GSM7085299,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_5005_S5_L002_R1_001.fastq.gz P25452_5005_S5_L002_R2_001.fastq.gz,fastq fastq,15981848610.0,135439395.0,GSM7085299 r1,0:28 1:90,A:4477963598;C:3506223270;G:3720138896;T:4272649273;N:4873573,28,90,,,4477963598,3506223270,3720138896,4272649273,4873573,SRX19740082,SRS17106156,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.04362,0.92756,0.00827,0.05019,0.96735,0.82235,0.52602,0.51548,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74412,SRR23929936,SRX19740082,SRS17106156,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 029  10 dy post single ablation,GSM7085299,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation,10X 22 029  10 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation,GSM7085299,GSM7085299: 10X 22 029  10 dy post single ablation; Danio rerio; RNA Seq,GSM7085299 r1,GSM7085299,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_5005_S5_L001_R1_001.fastq.gz P25452_5005_S5_L001_R2_001.fastq.gz,fastq fastq,15668510938.0,132783991.0,GSM7085299 r2,0:28 1:90,A:4395565570;C:3432293178;G:3641398206;T:4194659976;N:4594008,28,90,,,4395565570,3432293178,3641398206,4194659976,4594008,SRX19740082,SRS17106156,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.04195,0.92568,0.00791,0.05081,0.96907,0.82457,0.52113,0.50458,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74413,SRR23929937,SRX19740081,SRS17106155,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 028  10 dy post single ablation,GSM7085298,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation,10X 22 028  10 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation,GSM7085298,GSM7085298: 10X 22 028  10 dy post single ablation; Danio rerio; RNA Seq,GSM7085298 r1,GSM7085298,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_5004_S4_L002_R1_001.fastq.gz P25452_5004_S4_L002_R2_001.fastq.gz,fastq fastq,19699197418.0,166942351.0,GSM7085298 r1,0:28 1:90,A:5698419662;C:4261860362;G:4502693367;T:5230229242;N:5994785,28,90,,,5698419662,4261860362,4502693367,5230229242,5994785,SRX19740081,SRS17106155,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.01071,0.90569,0.00273,0.11561,0.98654,0.78792,0.40331,0.53787,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74414,SRR23929938,SRX19740081,SRS17106155,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 028  10 dy post single ablation,GSM7085298,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation,10X 22 028  10 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:10 dy post single ablation,GSM7085298,GSM7085298: 10X 22 028  10 dy post single ablation; Danio rerio; RNA Seq,GSM7085298 r1,GSM7085298,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_5004_S4_L001_R1_001.fastq.gz P25452_5004_S4_L001_R2_001.fastq.gz,fastq fastq,19264495566.0,163258437.0,GSM7085298 r2,0:28 1:90,A:5579106248;C:4162230591;G:4396617008;T:5120939377;N:5602342,28,90,,,5579106248,4162230591,4396617008,5120939377,5602342,SRX19740081,SRS17106155,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.01049,0.9064,0.00254,0.11668,0.98802,0.78819,0.38795,0.5416,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74415,SRR23929939,SRX19740080,SRS17106154,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 023  2 dy post double ablation,GSM7085297,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation,10X 22 023  2 dy post double ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation,GSM7085297,GSM7085297: 10X 22 023  2 dy post double ablation; Danio rerio; RNA Seq,GSM7085297 r1,GSM7085297,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_5002_S2_L002_R1_001.fastq.gz P25452_5002_S2_L002_R2_001.fastq.gz,fastq fastq,21576552402.0,182852139.0,GSM7085297 r1,0:28 1:90,A:6042712664;C:4829068008;G:5090500060;T:5607976659;N:6295011,28,90,,,6042712664,4829068008,5090500060,5607976659,6295011,SRX19740080,SRS17106154,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00738,0.92586,0.00228,0.09935,0.99121,0.79484,0.3212,0.51367,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74416,SRR23929940,SRX19740080,SRS17106154,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 023  2 dy post double ablation,GSM7085297,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation,10X 22 023  2 dy post double ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation,GSM7085297,GSM7085297: 10X 22 023  2 dy post double ablation; Danio rerio; RNA Seq,GSM7085297 r1,GSM7085297,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_5002_S2_L001_R1_001.fastq.gz P25452_5002_S2_L001_R2_001.fastq.gz,fastq fastq,21225949858.0,179880931.0,GSM7085297 r2,0:28 1:90,A:5950173859;C:4745833170;G:5001820306;T:5522228778;N:5893745,28,90,,,5950173859,4745833170,5001820306,5522228778,5893745,SRX19740080,SRS17106154,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00726,0.92674,0.00215,0.10093,0.99176,0.79527,0.29771,0.53423,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74417,SRR23929941,SRX19740079,SRS17106153,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 022  2 dy post double ablation,GSM7085296,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation,10X 22 022  2 dy post double ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation,GSM7085296,GSM7085296: 10X 22 022  2 dy post double ablation; Danio rerio; RNA Seq,GSM7085296 r1,GSM7085296,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_5001_S1_L002_R1_001.fastq.gz P25452_5001_S1_L002_R2_001.fastq.gz,fastq fastq,44183541338.0,374436791.0,GSM7085296 r1,0:28 1:90,A:12516849477;C:9732461815;G:10343631784;T:11577097367;N:13500895,28,90,,,12516849477,9732461815,10343631784,11577097367,13500895,SRX19740079,SRS17106153,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00804,0.91216,0.00229,0.10832,0.9906,0.79539,0.33148,0.51054,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74418,SRR23929942,SRX19740079,SRS17106153,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 022  2 dy post double ablation,GSM7085296,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation,10X 22 022  2 dy post double ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post double ablation,GSM7085296,GSM7085296: 10X 22 022  2 dy post double ablation; Danio rerio; RNA Seq,GSM7085296 r1,GSM7085296,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_5001_S1_L001_R1_001.fastq.gz P25452_5001_S1_L001_R2_001.fastq.gz,fastq fastq,43501281740.0,368654930.0,GSM7085296 r2,0:28 1:90,A:12337254735;C:9571145572;G:10170136596;T:11410054623;N:12690214,28,90,,,12337254735,9571145572,10170136596,11410054623,12690214,SRX19740079,SRS17106153,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00811,0.91214,0.00243,0.10798,0.99042,0.79299,0.27117,0.51073,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74419,SRR23929943,SRX19740078,SRS17106152,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 021  2 dy post single ablation,GSM7085295,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation,10X 22 021  2 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation,GSM7085295,GSM7085295: 10X 22 021  2 dy post single ablation; Danio rerio; RNA Seq,GSM7085295 r1,GSM7085295,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2008_S8_L001_R1_001.fastq.gz P25452_2008_S8_L001_R2_001.fastq.gz,fastq fastq,10399611282.0,88132299.0,GSM7085295 r1,0:28 1:90,A:2977005008;C:2261455885;G:2402621333;T:2758168947;N:360109,28,90,,,2977005008,2261455885,2402621333,2758168947,360109,SRX19740078,SRS17106152,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00664,0.91101,0.00219,0.14269,0.9903,0.71492,0.31124,0.52378,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74420,SRR23929944,SRX19740078,SRS17106152,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 021  2 dy post single ablation,GSM7085295,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation,10X 22 021  2 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation,GSM7085295,GSM7085295: 10X 22 021  2 dy post single ablation; Danio rerio; RNA Seq,GSM7085295 r1,GSM7085295,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2008_S8_L002_R1_001.fastq.gz P25452_2008_S8_L002_R2_001.fastq.gz,fastq fastq,10469509172.0,88724654.0,GSM7085295 r2,0:28 1:90,A:2996060103;C:2277562123;G:2419801341;T:2775787165;N:298440,28,90,,,2996060103,2277562123,2419801341,2775787165,298440,SRX19740078,SRS17106152,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00668,0.91267,0.00218,0.14377,0.98942,0.71571,0.30058,0.51379,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74421,SRR23929945,SRX19740077,SRS17106151,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 020  2 dy post single ablation,GSM7085294,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation,10X 22 020  2 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation,GSM7085294,GSM7085294: 10X 22 020  2 dy post single ablation; Danio rerio; RNA Seq,GSM7085294 r1,GSM7085294,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2007_S7_L002_R1_001.fastq.gz P25452_2007_S7_L002_R2_001.fastq.gz,fastq fastq,12171375736.0,103147252.0,GSM7085294 r1,0:28 1:90,A:3516523748;C:2630891316;G:2846235380;T:3177374207;N:351085,28,90,,,3516523748,2630891316,2846235380,3177374207,351085,SRX19740077,SRS17106151,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00723,0.88579,0.00253,0.14244,0.98955,0.73241,0.30415,0.52544,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74422,SRR23929946,SRX19740077,SRS17106151,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 020  2 dy post single ablation,GSM7085294,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation,10X 22 020  2 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:2 dy post single ablation,GSM7085294,GSM7085294: 10X 22 020  2 dy post single ablation; Danio rerio; RNA Seq,GSM7085294 r1,GSM7085294,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2007_S7_L001_R1_001.fastq.gz P25452_2007_S7_L001_R2_001.fastq.gz,fastq fastq,12113839290.0,102659655.0,GSM7085294 r2,0:28 1:90,A:3500990622;C:2617308142;G:2831547053;T:3163575276;N:418197,28,90,,,3500990622,2617308142,2831547053,3163575276,418197,SRX19740077,SRS17106151,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00769,0.88714,0.00281,0.14223,0.98904,0.73127,0.27861,0.53047,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74423,SRR23929947,SRX19740076,SRS17106150,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 019  no ablation,GSM7085293,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation,10X 22 019  no ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation,GSM7085293,GSM7085293: 10X 22 019  no ablation; Danio rerio; RNA Seq,GSM7085293 r1,GSM7085293,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2006_S6_L002_R1_001.fastq.gz P25452_2006_S6_L002_R2_001.fastq.gz,fastq fastq,26823163746.0,227314947.0,GSM7085293 r1,0:28 1:90,A:7462514069;C:6054472155;G:6429173301;T:6876229429;N:774792,28,90,,,7462514069,6054472155,6429173301,6876229429,774792,SRX19740076,SRS17106150,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00659,0.91951,0.0022,0.12919,0.99222,0.78677,0.35595,0.57041,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74424,SRR23929948,SRX19740076,SRS17106150,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 019  no ablation,GSM7085293,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation,10X 22 019  no ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation,GSM7085293,GSM7085293: 10X 22 019  no ablation; Danio rerio; RNA Seq,GSM7085293 r1,GSM7085293,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2006_S6_L001_R1_001.fastq.gz P25452_2006_S6_L001_R2_001.fastq.gz,fastq fastq,26613584654.0,225538853.0,GSM7085293 r2,0:28 1:90,A:7408899229;C:6002907526;G:6374299140;T:6826557518;N:921241,28,90,,,7408899229,6002907526,6374299140,6826557518,921241,SRX19740076,SRS17106150,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00675,0.91914,0.00208,0.12941,0.99172,0.78711,0.31131,0.54926,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74425,SRR23929949,SRX19740075,SRS17106149,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 018  no ablation,GSM7085292,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation,10X 22 018  no ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation,GSM7085292,GSM7085292: 10X 22 018  no ablation; Danio rerio; RNA Seq,GSM7085292 r1,GSM7085292,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2005_S5_L001_R1_001.fastq.gz P25452_2005_S5_L001_R2_001.fastq.gz,fastq fastq,28788320170.0,243968815.0,GSM7085292 r1,0:28 1:90,A:8028169272;C:6492038211;G:6870412969;T:7396707337;N:992381,28,90,,,8028169272,6492038211,6870412969,7396707337,992381,SRX19740075,SRS17106149,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00685,0.91809,0.00218,0.13019,0.99186,0.78374,0.33856,0.54827,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74426,SRR23929950,SRX19740075,SRS17106149,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 018  no ablation,GSM7085292,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation,10X 22 018  no ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:no ablation|time:no ablation,GSM7085292,GSM7085292: 10X 22 018  no ablation; Danio rerio; RNA Seq,GSM7085292 r1,GSM7085292,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2005_S5_L002_R1_001.fastq.gz P25452_2005_S5_L002_R2_001.fastq.gz,fastq fastq,29018537226.0,245919807.0,GSM7085292 r2,0:28 1:90,A:8087164697;C:6548645987;G:6930820281;T:7451072090;N:834171,28,90,,,8087164697,6548645987,6930820281,7451072090,834171,SRX19740075,SRS17106149,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00688,0.91748,0.00228,0.13154,0.99184,0.78344,0.35287,0.56374,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74427,SRR23929951,SRX19740074,SRS17106148,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 017  5 dy post single ablation,GSM7085291,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post single ablation,10X 22 017  5 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post single ablation,GSM7085291,GSM7085291: 10X 22 017  5 dy post single ablation; Danio rerio; RNA Seq,GSM7085291 r1,GSM7085291,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2004_S4_L002_R1_001.fastq.gz P25452_2004_S4_L002_R2_001.fastq.gz,fastq fastq,13492044952.0,114339364.0,GSM7085291 r1,0:28 1:90,A:3873940551;C:2926902171;G:3135095393;T:3555720987;N:385850,28,90,,,3873940551,2926902171,3135095393,3555720987,385850,SRX19740074,SRS17106148,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00505,0.91196,0.00151,0.10926,0.99172,0.74633,0.3125,0.50464,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74428,SRR23929952,SRX19740074,SRS17106148,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 017  5 dy post single ablation,GSM7085291,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post single ablation,10X 22 017  5 dy post single ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post single ablation,GSM7085291,GSM7085291: 10X 22 017  5 dy post single ablation; Danio rerio; RNA Seq,GSM7085291 r1,GSM7085291,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2004_S4_L001_R1_001.fastq.gz P25452_2004_S4_L001_R2_001.fastq.gz,fastq fastq,13406231340.0,113612130.0,GSM7085291 r2,0:28 1:90,A:3850846331;C:2906712145;G:3113344227;T:3534865936;N:462701,28,90,,,3850846331,2906712145,3113344227,3534865936,462701,SRX19740074,SRS17106148,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00522,0.91073,0.00161,0.11013,0.99172,0.74665,0.2884,0.52618,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74429,SRR23929953,SRX19740073,SRS17106147,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 016  5 dy post double ablation,GSM7085290,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post double ablation,10X 22 016  5 dy post double ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post double ablation,GSM7085290,GSM7085290: 10X 22 016  5 dy post double ablation; Danio rerio; RNA Seq,GSM7085290 r1,GSM7085290,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2003_S3_L002_R1_001.fastq.gz P25452_2003_S3_L002_R2_001.fastq.gz,fastq fastq,29520641622.0,250174929.0,GSM7085290 r1,0:28 1:90,A:8496409320;C:6362210704;G:6766268604;T:7894905763;N:847231,28,90,,,8496409320,6362210704,6766268604,7894905763,847231,SRX19740073,SRS17106147,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00483,0.91059,0.00152,0.09736,0.99362,0.81937,0.31545,0.52536,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74430,SRR23929954,SRX19740073,SRS17106147,SRP428435,PRJNA941866,Decoding pancreatic endocrine cell differentiation and beta cell regeneration in zebrafish,GSE226841,Transcriptome Analysis,The aim of the study is to investigate the endocrinogenesis process in zebrafish pancreas during normal development and regenerative condition. Overall design: Using lineage tracing methodology TgKIkrt4 p2a mNeonGreen t2a iCre; ubb:loxp CFP stop loxp H2BmCherry  we used FACS to sort out mCherry positive cells in adult zebrafish pancreas  indicating cells in the krt4+ cell lineage,,pubmed:37595046,,10X 22 016  5 dy post double ablation,GSM7085290,,source name:krt4 lineage traced cells in adult zebrafish pancreas|genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post double ablation,10X 22 016  5 dy post double ablation,The raw sequencing data was then processed with the ‘count’ command of the Cell Ranger software v5.0.1 10× Genomics with the option ‘  expect cells’ set to 7000 all other options were used as per default. Assembly: danRer11 Supplementary files format and content: matrix files,krt4 lineage traced cells in adult zebrafish pancreas,We selected 6 mpf 9 mpf fish with 8 10 fish in each condition  We sacrificed the adult fish by putting each one into ice cold Hanks' Balanced Salt Solution HBSS  no calcium  no magnesium for 10 minutes. Next  we used blunt forceps to carefully remove the skin  kidney  eggs in females  liver and gallbladder to expose the pancreata. This step is critical for avoiding krt4 + cell contamination from other organs. We also removed adipose tissue as much as possible. Then  we cut at the anterior region of the intestinal bulb and hindgut  and transferred the intestine and pancreas together to a new dish. We used blunt dissection tools to carefully separate the pancreata from the intestine. Meanwhile  we also removed the spleen appearing in dark red  which is also attached to the intestine. We moved and immersed the whole pancreata into 5 mL HBSS kept on ice. For each condition  we pooled 4 8 samples together for an enzymatic digestion with 600 μL 1×TrypLE™ Thermofisher supplemented with 60 μL 100× Pluronic™ F68 Thermofisher at 37 °C on a shaker at 125 rpm for 45 – 60 minutes to prevent tissue adhesion. We also pipetted the tissue up and down every 5 minutes for better digestion. We added 6 mL precooled 2% BSA to end the digestion and centrifuged the sample at 500 g for 5 minutes. post removing the supernatant  we washed the pellets with 300 μL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning™ Falcon™ cell strainer Corning™ 352235 to filter out not fully digested tissues. During FACS  we selected single cell populations based on forward scatter and side scatter signals. Next  we performed negative selection with the DAPI channel to remove dead cells and cell debris. Lastly  we used the Cherry channel for the subsequent gating to collect all cells of the krt4 derived lineage in a new tube as the single cell suspension.,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer’s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,genotype:WT|tissue:pancreas|cell type:krt4 lineage traced cells|treatment:ablation|time:5 dy post double ablation,GSM7085290,GSM7085290: 10X 22 016  5 dy post double ablation; Danio rerio; RNA Seq,GSM7085290 r1,GSM7085290,1,Droplet based scRNA seq was performed using the Chromium Single Cell 3′ Library and Gel Bead Kit v3 10× Genomics and Chromium Single Cell 3′ Chip G 10× Genomics. Approximately 8 000 10 000 cells from each condition were loaded and encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10× scRNA Seq libraries were PCR amplified 13 cycles  pooled  denatured  and diluted in prior to paired end sequencing on a NextSeq 500 according to manufacturer's recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10× Genomics to generate a gene by cell count matrix with default parameters.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP428435,,loader:fastq load.py,P25452_2003_S3_L001_R1_001.fastq.gz P25452_2003_S3_L001_R2_001.fastq.gz,fastq fastq,29361448176.0,248825832.0,GSM7085290 r2,0:28 1:90,A:8453733104;C:6324569877;G:6726263046;T:7855861357;N:1020792,28,90,,,8453733104,6324569877,6726263046,7855861357,1020792,SRX19740073,SRS17106147,SRA1608504,Karolinska Institute,Karolinska Institute,2,0.00488,0.91294,0.00158,0.09794,0.99306,0.8182,0.31803,0.52363,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Sweden,2023-03-07,Adult,Adult,Pancreas,Endocrine System
74472,SRR23824316,SRX19646193,SRS17014002,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas Ctrl replicate 2,GSM7092957,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092957,GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092957 r1,GSM7092957,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Pancreas-2_S8_L001_R2_001.fastq.gz Ctrl-Pancreas-2_S8_L001_R1_001.fastq.gz,fastq fastq,4689094030.0,39738085.0,GSM7092957 r1,0:28 1:90,A:1232747701;C:1087501739;G:1176854549;T:1191883874;N:106167,28,90,,,1232747701,1087501739,1176854549,1191883874,106167,SRX19646193,SRS17014002,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00515,0.93252,0.00155,0.06137,0.99648,0.88692,0.38705,0.60914,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74473,SRR23824317,SRX19646193,SRS17014002,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas Ctrl replicate 2,GSM7092957,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092957,GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092957 r1,GSM7092957,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Pancreas-2_S8_L002_R2_001.fastq.gz Ctrl-Pancreas-2_S8_L002_R1_001.fastq.gz,fastq fastq,4677907984.0,39643288.0,GSM7092957 r2,0:28 1:90,A:1227626448;C:1085304810;G:1174779891;T:1190095936;N:100899,28,90,,,1227626448,1085304810,1174779891,1190095936,100899,SRX19646193,SRS17014002,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00531,0.93306,0.00158,0.06221,0.99596,0.88749,0.37673,0.60528,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74474,SRR23824318,SRX19646193,SRS17014002,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas Ctrl replicate 2,GSM7092957,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092957,GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092957 r1,GSM7092957,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Pancreas-2_S8_L003_R1_001.fastq.gz Ctrl-Pancreas-2_S8_L003_R2_001.fastq.gz,fastq fastq,4761421422.0,40351029.0,GSM7092957 r3,0:28 1:90,A:1250348494;C:1104936433;G:1195812813;T:1210226243;N:97439,28,90,,,1250348494,1104936433,1195812813,1210226243,97439,SRX19646193,SRS17014002,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00518,0.93314,0.00149,0.06284,0.99596,0.88753,0.3933,0.60442,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74475,SRR23824319,SRX19646193,SRS17014002,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas Ctrl replicate 2,GSM7092957,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas Ctrl replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092957,GSM7092957: Pancreas Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092957 r1,GSM7092957,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Pancreas-2_S8_L004_R2_001.fastq.gz Ctrl-Pancreas-2_S8_L004_R1_001.fastq.gz,fastq fastq,4667970850.0,39559075.0,GSM7092957 r4,0:28 1:90,A:1226515454;C:1082416982;G:1171222300;T:1187726852;N:89262,28,90,,,1226515454,1082416982,1171222300,1187726852,89262,SRX19646193,SRS17014002,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00499,0.93259,0.00167,0.0614,0.9959,0.88755,0.38604,0.53191,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74476,SRR23824320,SRX19646192,SRS17014003,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas Ctrl replicate 1,GSM7092956,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092956,GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092956 r1,GSM7092956,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Pancreas-1_S4_L001_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L001_R2_001.fastq.gz,fastq fastq,4087782314.0,34642223.0,GSM7092956 r1,0:28 1:90,A:988379101;C:980631744;G:1075271505;T:1043407296;N:92668,28,90,,,988379101,980631744,1075271505,1043407296,92668,SRX19646192,SRS17014003,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00484,0.96438,0.00131,0.03915,0.99697,0.91311,0.4152,0.60907,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74477,SRR23824321,SRX19646192,SRS17014003,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas Ctrl replicate 1,GSM7092956,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092956,GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092956 r1,GSM7092956,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Pancreas-1_S4_L002_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L002_R2_001.fastq.gz,fastq fastq,4117642214.0,34895273.0,GSM7092956 r2,0:28 1:90,A:995176406;C:987675179;G:1083314338;T:1051387356;N:88935,28,90,,,995176406,987675179,1083314338,1051387356,88935,SRX19646192,SRS17014003,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0049,0.96448,0.00126,0.03869,0.99655,0.91151,0.42291,0.61172,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74478,SRR23824322,SRX19646192,SRS17014003,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas Ctrl replicate 1,GSM7092956,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092956,GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092956 r1,GSM7092956,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Pancreas-1_S4_L003_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L003_R2_001.fastq.gz,fastq fastq,4158634470.0,35242665.0,GSM7092956 r3,0:28 1:90,A:1004519785;C:998011643;G:1094510237;T:1061510107;N:82698,28,90,,,1004519785,998011643,1094510237,1061510107,82698,SRX19646192,SRS17014003,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00486,0.96439,0.00124,0.04007,0.99689,0.91064,0.40883,0.61125,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74479,SRR23824323,SRX19646192,SRS17014003,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas Ctrl replicate 1,GSM7092956,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas Ctrl replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092956,GSM7092956: Pancreas Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092956 r1,GSM7092956,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Pancreas-1_S4_L004_R1_001.fastq.gz Ctrl-Pancreas-1_S4_L004_R2_001.fastq.gz,fastq fastq,4084344502.0,34613089.0,GSM7092956 r4,0:28 1:90,A:988069108;C:979213026;G:1073790783;T:1043193951;N:77634,28,90,,,988069108,979213026,1073790783,1043193951,77634,SRX19646192,SRS17014003,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00479,0.96445,0.00132,0.0387,0.99701,0.91086,0.42113,0.61441,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74504,SRR23824344,SRX19646185,SRS17013995,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 7 dpi replicate 1,GSM7092948,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092948,GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092948 r1,GSM7092948,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Pancreas-1_S20_L001_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L001_R2_001.fastq.gz,fastq fastq,4549683756.0,38556642.0,GSM7092948 r1,0:28 1:90,A:1143775236;C:1105204092;G:1203189006;T:1097413006;N:102416,28,90,,,1143775236,1105204092,1203189006,1097413006,102416,SRX19646185,SRS17013995,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.02063,0.94539,0.00665,0.10755,0.99622,0.91309,0.32854,0.54953,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74505,SRR23824345,SRX19646185,SRS17013995,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 7 dpi replicate 1,GSM7092948,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092948,GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092948 r1,GSM7092948,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Pancreas-1_S20_L002_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L002_R2_001.fastq.gz,fastq fastq,4517687938.0,38285491.0,GSM7092948 r2,0:28 1:90,A:1134622351;C:1097536764;G:1194906587;T:1090524287;N:97949,28,90,,,1134622351,1097536764,1194906587,1090524287,97949,SRX19646185,SRS17013995,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.02109,0.94517,0.00676,0.10863,0.99628,0.91252,0.3052,0.54958,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74506,SRR23824346,SRX19646185,SRS17013995,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 7 dpi replicate 1,GSM7092948,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092948,GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092948 r1,GSM7092948,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Pancreas-1_S20_L003_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L003_R2_001.fastq.gz,fastq fastq,4636317940.0,39290830.0,GSM7092948 r3,0:28 1:90,A:1163890164;C:1127297116;G:1227016473;T:1118019811;N:94376,28,90,,,1163890164,1127297116,1227016473,1118019811,94376,SRX19646185,SRS17013995,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.02099,0.94599,0.00695,0.10973,0.99618,0.9123,0.34518,0.51887,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74507,SRR23824347,SRX19646185,SRS17013995,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 7 dpi replicate 1,GSM7092948,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 7 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092948,GSM7092948: Pancreas 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092948 r1,GSM7092948,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Pancreas-1_S20_L004_R1_001.fastq.gz 7dpi-Pancreas-1_S20_L004_R2_001.fastq.gz,fastq fastq,4497198064.0,38111848.0,GSM7092948 r4,0:28 1:90,A:1131098871;C:1091572129;G:1188115242;T:1086325472;N:86350,28,90,,,1131098871,1091572129,1188115242,1086325472,86350,SRX19646185,SRS17013995,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.02003,0.9465,0.00658,0.10877,0.99596,0.91171,0.34392,0.54247,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74508,SRR23824348,SRX19646184,SRS17013994,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 7 dpi replicate 2,GSM7092949,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092949,GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092949 r1,GSM7092949,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Pancreas-2_S24_L001_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L001_R2_001.fastq.gz,fastq fastq,3694404180.0,31308510.0,GSM7092949 r1,0:28 1:90,A:925642312;C:897963126;G:972697543;T:898017524;N:83675,28,90,,,925642312,897963126,972697543,898017524,83675,SRX19646184,SRS17013994,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01944,0.9386,0.00639,0.10031,0.99561,0.90763,0.34147,0.64485,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74509,SRR23824349,SRX19646184,SRS17013994,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 7 dpi replicate 2,GSM7092949,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092949,GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092949 r1,GSM7092949,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Pancreas-2_S24_L002_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L002_R2_001.fastq.gz,fastq fastq,3695460280.0,31317460.0,GSM7092949 r2,0:28 1:90,A:924776645;C:898527265;G:973466829;T:898610296;N:79245,28,90,,,924776645,898527265,973466829,898610296,79245,SRX19646184,SRS17013994,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01959,0.93749,0.00645,0.10075,0.99571,0.90889,0.36214,0.64826,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74510,SRR23824350,SRX19646184,SRS17013994,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 7 dpi replicate 2,GSM7092949,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092949,GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092949 r1,GSM7092949,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Pancreas-2_S24_L003_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L003_R2_001.fastq.gz,fastq fastq,3765831586.0,31913827.0,GSM7092949 r3,0:28 1:90,A:942337142;C:916041305;G:992299130;T:915077569;N:76440,28,90,,,942337142,916041305,992299130,915077569,76440,SRX19646184,SRS17013994,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0193,0.93865,0.00649,0.1012,0.99614,0.9093,0.34282,0.63758,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74511,SRR23824351,SRX19646184,SRS17013994,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 7 dpi replicate 2,GSM7092949,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 7 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092949,GSM7092949: Pancreas 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092949 r1,GSM7092949,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Pancreas-2_S24_L004_R1_001.fastq.gz 7dpi-Pancreas-2_S24_L004_R2_001.fastq.gz,fastq fastq,3665890896.0,31066872.0,GSM7092949 r4,0:28 1:90,A:918497729;C:890554002;G:964737735;T:892032221;N:69209,28,90,,,918497729,890554002,964737735,892032221,69209,SRX19646184,SRS17013994,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01901,0.93844,0.0062,0.10108,0.99592,0.90796,0.32691,0.64748,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74544,SRR23824380,SRX19646175,SRS17013985,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 1 dpi replicate 2,GSM7092941,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092941,GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092941 r1,GSM7092941,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Pancreas-2_S16_L001_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L001_R2_001.fastq.gz,fastq fastq,4309260644.0,36519158.0,GSM7092941 r1,0:28 1:90,A:1046247537;C:1048122611;G:1162975668;T:1051816689;N:98139,28,90,,,1046247537,1048122611,1162975668,1051816689,98139,SRX19646175,SRS17013985,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00671,0.9366,0.00224,0.09388,0.99651,0.90189,0.37644,0.63945,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74545,SRR23824381,SRX19646175,SRS17013985,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 1 dpi replicate 2,GSM7092941,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092941,GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092941 r1,GSM7092941,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Pancreas-2_S16_L002_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L002_R2_001.fastq.gz,fastq fastq,4297639414.0,36420673.0,GSM7092941 r2,0:28 1:90,A:1043016765;C:1045256212;G:1159666945;T:1049606913;N:92579,28,90,,,1043016765,1045256212,1159666945,1049606913,92579,SRX19646175,SRS17013985,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00646,0.93715,0.00204,0.09343,0.99685,0.90327,0.38255,0.63012,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74546,SRR23824382,SRX19646175,SRS17013985,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 1 dpi replicate 2,GSM7092941,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092941,GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092941 r1,GSM7092941,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Pancreas-2_S16_L003_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L003_R2_001.fastq.gz,fastq fastq,4389542888.0,37199516.0,GSM7092941 r3,0:28 1:90,A:1064162384;C:1068512248;G:1185538637;T:1071241453;N:88166,28,90,,,1064162384,1068512248,1185538637,1071241453,88166,SRX19646175,SRS17013985,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00644,0.93752,0.0021,0.09439,0.99659,0.90382,0.37098,0.63183,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74547,SRR23824383,SRX19646175,SRS17013985,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 1 dpi replicate 2,GSM7092941,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 1 dpi replicate 2,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092941,GSM7092941: Pancreas 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092941 r1,GSM7092941,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Pancreas-2_S16_L004_R1_001.fastq.gz 1dpi-Pancreas-2_S16_L004_R2_001.fastq.gz,fastq fastq,4277274856.0,36248092.0,GSM7092941 r4,0:28 1:90,A:1039365242;C:1039483839;G:1153145758;T:1045198402;N:81615,28,90,,,1039365242,1039483839,1153145758,1045198402,81615,SRX19646175,SRS17013985,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00627,0.93724,0.00211,0.09386,0.99659,0.90262,0.4275,0.61845,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74548,SRR23824388,SRX19646174,SRS17013984,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 1 dpi replicate 1,GSM7092940,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 1 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092940,GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092940 r1,GSM7092940,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Pancreas-1_S12_L001_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L001_R2_001.fastq.gz,fastq fastq,5429558190.0,46013205.0,GSM7092940 r1,0:28 1:90,A:1303586809;C:1328725175;G:1505666398;T:1291455764;N:124044,28,90,,,1303586809,1328725175,1505666398,1291455764,124044,SRX19646174,SRS17013984,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00632,0.94424,0.00213,0.10919,0.99695,0.91936,0.36162,0.55183,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74549,SRR23824389,SRX19646174,SRS17013984,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 1 dpi replicate 1,GSM7092940,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 1 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092940,GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092940 r1,GSM7092940,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Pancreas-1_S12_L002_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L002_R2_001.fastq.gz,fastq fastq,5406650142.0,45819069.0,GSM7092940 r2,0:28 1:90,A:1297924443;C:1322864150;G:1498812275;T:1286932180;N:117094,28,90,,,1297924443,1322864150,1498812275,1286932180,117094,SRX19646174,SRS17013984,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00647,0.94374,0.00235,0.11112,0.99699,0.91816,0.3583,0.56118,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74550,SRR23824390,SRX19646174,SRS17013984,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 1 dpi replicate 1,GSM7092940,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 1 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092940,GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092940 r1,GSM7092940,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Pancreas-1_S12_L003_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L003_R2_001.fastq.gz,fastq fastq,5529750810.0,46862295.0,GSM7092940 r3,0:28 1:90,A:1325091638;C:1354598961;G:1534908275;T:1315039358;N:112578,28,90,,,1325091638,1354598961,1534908275,1315039358,112578,SRX19646174,SRS17013984,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00611,0.94576,0.00203,0.11108,0.99709,0.91863,0.38685,0.65557,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
74551,SRR23824391,SRX19646174,SRS17013984,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast  zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury  single cell transcriptomic analyses were performed on the heart  blood  liver  kidney  and pancreatic islets. Overall design: Upon heart cryoinjury  cells from multiple organs heart  liver  pancreas  and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,Pancreas 1 dpi replicate 1,GSM7092940,,source name:Pancreas|tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,Pancreas 1 dpi replicate 1,Demultiplexing  alignment  filtering  and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction  expression value normalization  clustering  cell type annotation and so on were done scater and scran. For more details and the cell type annotation information  see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Pancreas,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Pancreas|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092940,GSM7092940: Pancreas 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092940 r1,GSM7092940,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells  ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C  the pellet was resuspended in 500 l and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Pancreas-1_S12_L004_R1_001.fastq.gz 1dpi-Pancreas-1_S12_L004_R2_001.fastq.gz,fastq fastq,5383384318.0,45621901.0,GSM7092940 r4,0:28 1:90,A:1294350602;C:1316150189;G:1490887301;T:1281893201;N:103025,28,90,,,1294350602,1316150189,1490887301,1281893201,103025,SRX19646174,SRS17013984,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00616,0.94398,0.00206,0.10993,0.99715,0.91963,0.37232,0.65892,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Pancreas,Endocrine System
76740,SRR25374386,SRX21113512,SRS18382106,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 A10,GSM7655684,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 A10,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655684,GSM7655684: ExVi2Red 01 A10; Danio rerio; RNA Seq,GSM7655684 r1,GSM7655684,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21286_Track-51602_R1.fastq.gz,fastq,38304684.0,504009.0,GSM7655684 r1,0:76,A:10444153;C:8397210;G:8505443;T:10956830;N:1048,76,,,,10444153,8397210,8505443,10956830,1048,SRX21113512,SRS18382106,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.78167,,0.12085,,0.94621,,0.44883,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76741,SRR25374387,SRX21113511,SRS18382105,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 B10,GSM7655683,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 B10,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655683,GSM7655683: ExVi2Red 01 B10; Danio rerio; RNA Seq,GSM7655683 r1,GSM7655683,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21287_Track-51603_R1.fastq.gz,fastq,41818544.0,550244.0,GSM7655683 r1,0:76,A:11263718;C:9415229;G:9551199;T:11587507;N:891,76,,,,11263718,9415229,9551199,11587507,891,SRX21113511,SRS18382105,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.72269,,0.12564,,0.9542,,0.55822,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76742,SRR25374388,SRX21113510,SRS18382104,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 C10,GSM7655682,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 C10,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655682,GSM7655682: ExVi2Red 01 C10; Danio rerio; RNA Seq,GSM7655682 r1,GSM7655682,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21288_Track-51604_R1.fastq.gz,fastq,41119648.0,541048.0,GSM7655682 r1,0:76,A:10732270;C:9662921;G:9639944;T:11083600;N:913,76,,,,10732270,9662921,9639944,11083600,913,SRX21113510,SRS18382104,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.86963,,0.06809,,0.93292,,0.65489,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76743,SRR25374389,SRX21113509,SRS18382103,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 D10,GSM7655681,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 D10,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655681,GSM7655681: ExVi2Red 01 D10; Danio rerio; RNA Seq,GSM7655681 r1,GSM7655681,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21289_Track-51605_R1.fastq.gz,fastq,42475108.0,558883.0,GSM7655681 r1,0:76,A:11042198;C:9997401;G:9991867;T:11442635;N:1007,76,,,,11042198,9997401,9991867,11442635,1007,SRX21113509,SRS18382103,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.85259,,0.05736,,0.94223,,0.68549,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76744,SRR25374390,SRX21113508,SRS18382102,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 E10,GSM7655680,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 E10,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655680,GSM7655680: ExVi2Red 01 E10; Danio rerio; RNA Seq,GSM7655680 r1,GSM7655680,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21290_Track-51606_R1.fastq.gz,fastq,42190564.0,555139.0,GSM7655680 r1,0:76,A:10880720;C:9985936;G:9919117;T:11403588;N:1203,76,,,,10880720,9985936,9919117,11403588,1203,SRX21113508,SRS18382102,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.84883,,0.06243,,0.94387,,0.71713,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76745,SRR25374391,SRX21113507,SRS18382101,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 F10,GSM7655679,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 F10,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655679,GSM7655679: ExVi2Red 01 F10; Danio rerio; RNA Seq,GSM7655679 r1,GSM7655679,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21291_Track-51607_R1.fastq.gz,fastq,30276196.0,398371.0,GSM7655679 r1,0:76,A:7966868;C:7016730;G:7000707;T:8291155;N:736,76,,,,7966868,7016730,7000707,8291155,736,SRX21113507,SRS18382101,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.83303,,0.05427,,0.93785,,0.69443,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76746,SRR25374392,SRX21113506,SRS18382100,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 G10,GSM7655678,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 G10,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655678,GSM7655678: ExVi2Red 01 G10; Danio rerio; RNA Seq,GSM7655678 r1,GSM7655678,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21292_Track-51608_R1.fastq.gz,fastq,42697028.0,561803.0,GSM7655678 r1,0:76,A:11421256;C:9416456;G:9762806;T:12095440;N:1070,76,,,,11421256,9416456,9762806,12095440,1070,SRX21113506,SRS18382100,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.4772,,0.03926,,0.94742,,0.64918,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76747,SRR25374393,SRX21113505,SRS18382099,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 H01,GSM7655653,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 H01,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655653,GSM7655653: ExVi16Gr 02 H01; Danio rerio; RNA Seq,GSM7655653 r1,GSM7655653,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21317_Track-51633_R1.fastq.gz,fastq,39867624.0,524574.0,GSM7655653 r1,0:76,A:10664168;C:9072852;G:9105099;T:11024563;N:942,76,,,,10664168,9072852,9105099,11024563,942,SRX21113505,SRS18382099,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.83797,,0.06671,,0.94044,,0.62345,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76748,SRR25374394,SRX21113504,SRS18382098,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 A02,GSM7655652,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 A02,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655652,GSM7655652: ExVi16Gr 02 A02; Danio rerio; RNA Seq,GSM7655652 r1,GSM7655652,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21318_Track-51634_R1.fastq.gz,fastq,37836752.0,497852.0,GSM7655652 r1,0:76,A:10538160;C:8088084;G:8235430;T:10974153;N:925,76,,,,10538160,8088084,8235430,10974153,925,SRX21113504,SRS18382098,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.80039,,0.2249,,0.95392,,0.68704,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76749,SRR25374395,SRX21113503,SRS18382097,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 B02,GSM7655651,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 B02,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655651,GSM7655651: ExVi16Gr 02 B02; Danio rerio; RNA Seq,GSM7655651 r1,GSM7655651,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21319_Track-51635_R1.fastq.gz,fastq,37765464.0,496914.0,GSM7655651 r1,0:76,A:10327605;C:8440804;G:8513957;T:10482149;N:949,76,,,,10327605,8440804,8513957,10482149,949,SRX21113503,SRS18382097,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.79171,,0.10658,,0.93785,,0.57458,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76750,SRR25374396,SRX21113502,SRS18382096,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 C02,GSM7655650,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 C02,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655650,GSM7655650: ExVi16Gr 02 C02; Danio rerio; RNA Seq,GSM7655650 r1,GSM7655650,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21320_Track-51636_R1.fastq.gz,fastq,33616016.0,442316.0,GSM7655650 r1,0:76,A:9130691;C:7426220;G:7511228;T:9547023;N:854,76,,,,9130691,7426220,7511228,9547023,854,SRX21113502,SRS18382096,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.8161,,0.16087,,0.94282,,0.74593,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76751,SRR25374397,SRX21113501,SRS18382094,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 D02,GSM7655649,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 D02,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655649,GSM7655649: ExVi16Gr 02 D02; Danio rerio; RNA Seq,GSM7655649 r1,GSM7655649,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21321_Track-51637_R1.fastq.gz,fastq,48530712.0,638562.0,GSM7655649 r1,0:76,A:12706296;C:11286685;G:11268611;T:13267981;N:1139,76,,,,12706296,11286685,11268611,13267981,1139,SRX21113501,SRS18382094,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.87539,,0.05636,,0.94509,,0.67319,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76752,SRR25374398,SRX21113500,SRS18382095,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 E02,GSM7655648,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 E02,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655648,GSM7655648: ExVi16Gr 02 E02; Danio rerio; RNA Seq,GSM7655648 r1,GSM7655648,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21322_Track-51638_R1.fastq.gz,fastq,38063080.0,500830.0,GSM7655648 r1,0:76,A:10345224;C:8528904;G:8613676;T:10574273;N:1003,76,,,,10345224,8528904,8613676,10574273,1003,SRX21113500,SRS18382095,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.82962,,0.12581,,0.94334,,0.5417,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76753,SRR25374399,SRX21113499,SRS18382093,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 F02,GSM7655647,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 F02,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655647,GSM7655647: ExVi16Gr 02 F02; Danio rerio; RNA Seq,GSM7655647 r1,GSM7655647,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21323_Track-51639_R1.fastq.gz,fastq,33778504.0,444454.0,GSM7655647 r1,0:76,A:8715964;C:7998179;G:7952604;T:9110906;N:851,76,,,,8715964,7998179,7952604,9110906,851,SRX21113499,SRS18382093,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.86888,,0.04769,,0.9417,,0.71664,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76754,SRR25374400,SRX21113498,SRS18382091,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 G02,GSM7655646,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 G02,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655646,GSM7655646: ExVi16Gr 02 G02; Danio rerio; RNA Seq,GSM7655646 r1,GSM7655646,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21324_Track-51640_R1.fastq.gz,fastq,38434264.0,505714.0,GSM7655646 r1,0:76,A:10173498;C:8859852;G:8871249;T:10528740;N:925,76,,,,10173498,8859852,8871249,10528740,925,SRX21113498,SRS18382091,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.84613,,0.07553,,0.93839,,0.68257,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76755,SRR25374401,SRX21113497,SRS18382092,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 H04,GSM7655629,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 H04,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655629,GSM7655629: ExVi16Gr 02 H04; Danio rerio; RNA Seq,GSM7655629 r1,GSM7655629,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21341_Track-51657_R1.fastq.gz,fastq,30968860.0,407485.0,GSM7655629 r1,0:76,A:8289373;C:7104056;G:7130406;T:8444292;N:733,76,,,,8289373,7104056,7130406,8444292,733,SRX21113497,SRS18382092,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.89416,,0.07736,,0.9217,,0.52336,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76756,SRR25374402,SRX21113496,SRS18382090,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 A05,GSM7655628,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 A05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655628,GSM7655628: ExVi16Gr 02 A05; Danio rerio; RNA Seq,GSM7655628 r1,GSM7655628,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21342_Track-51658_R1.fastq.gz,fastq,77775132.0,1023357.0,GSM7655628 r1,0:76,A:20285912;C:17896974;G:18105934;T:21484315;N:1997,76,,,,20285912,17896974,18105934,21484315,1997,SRX21113496,SRS18382090,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.85173,,0.08581,,0.94923,,0.6598,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76757,SRR25374403,SRX21113495,SRS18382089,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 B05,GSM7655627,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 B05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655627,GSM7655627: ExVi16Gr 02 B05; Danio rerio; RNA Seq,GSM7655627 r1,GSM7655627,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21343_Track-51659_R1.fastq.gz,fastq,48071824.0,632524.0,GSM7655627 r1,0:76,A:13026880;C:10835674;G:10943843;T:13264257;N:1170,76,,,,13026880,10835674,10943843,13264257,1170,SRX21113495,SRS18382089,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.8831,,0.07207,,0.91881,,0.53229,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76758,SRR25374404,SRX21113494,SRS18382088,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 C05,GSM7655626,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 C05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655626,GSM7655626: ExVi16Gr 02 C05; Danio rerio; RNA Seq,GSM7655626 r1,GSM7655626,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21344_Track-51660_R1.fastq.gz,fastq,44401404.0,584229.0,GSM7655626 r1,0:76,A:11837676;C:10159931;G:10224645;T:12177927;N:1225,76,,,,11837676,10159931,10224645,12177927,1225,SRX21113494,SRS18382088,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.8662,,0.10475,,0.93939,,0.61495,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76759,SRR25374405,SRX21113493,SRS18382087,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 D05,GSM7655625,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 D05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655625,GSM7655625: ExVi16Gr 02 D05; Danio rerio; RNA Seq,GSM7655625 r1,GSM7655625,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21345_Track-51661_R1.fastq.gz,fastq,40097980.0,527605.0,GSM7655625 r1,0:76,A:10996482;C:8953433;G:9037603;T:11109378;N:1084,76,,,,10996482,8953433,9037603,11109378,1084,SRX21113493,SRS18382087,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.8426,,0.13642,,0.94245,,0.59961,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76760,SRR25374406,SRX21113492,SRS18382086,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,UHR 02 E05,GSM7655624,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,UHR 02 E05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655624,GSM7655624: UHR 02 E05; Danio rerio; RNA Seq,GSM7655624 r1,GSM7655624,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21346_Track-51662_R1.fastq.gz,fastq,73001572.0,960547.0,GSM7655624 r1,0:76,A:18801430;C:17125045;G:17615098;T:19458134;N:1865,76,,,,18801430,17125045,17615098,19458134,1865,SRX21113492,SRS18382086,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.00277,,0.00188,,0.99906,,0.73509,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76761,SRR25374407,SRX21113491,SRS18382085,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 F05,GSM7655623,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 F05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655623,GSM7655623: ExVi16Gr 02 F05; Danio rerio; RNA Seq,GSM7655623 r1,GSM7655623,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21347_Track-51663_R1.fastq.gz,fastq,27670764.0,364089.0,GSM7655623 r1,0:76,A:7066830;C:6632931;G:6548167;T:7422248;N:588,76,,,,7066830,6632931,6548167,7422248,588,SRX21113491,SRS18382085,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.87564,,0.03905,,0.92614,,0.74611,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76762,SRR25374408,SRX21113490,SRS18382083,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 G05,GSM7655622,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 G05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655622,GSM7655622: ExVi16Gr 02 G05; Danio rerio; RNA Seq,GSM7655622 r1,GSM7655622,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21348_Track-51664_R1.fastq.gz,fastq,42969260.0,565385.0,GSM7655622 r1,0:76,A:11590827;C:9713842;G:9805929;T:11857589;N:1073,76,,,,11590827,9713842,9805929,11857589,1073,SRX21113490,SRS18382083,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.84464,,0.11633,,0.94939,,0.6516,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76763,SRR25374409,SRX21113489,SRS18382084,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 H08,GSM7655597,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 H08,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655597,GSM7655597: ExVi16Gr 02 H08; Danio rerio; RNA Seq,GSM7655597 r1,GSM7655597,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21373_Track-51689_R1.fastq.gz,fastq,38007448.0,500098.0,GSM7655597 r1,0:76,A:10173426;C:8641625;G:8730744;T:10460660;N:993,76,,,,10173426,8641625,8730744,10460660,993,SRX21113489,SRS18382084,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.79669,,0.08276,,0.95067,,0.65876,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76764,SRR25374410,SRX21113488,SRS18382082,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 A09,GSM7655596,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 A09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655596,GSM7655596: ExVi16Gr 02 A09; Danio rerio; RNA Seq,GSM7655596 r1,GSM7655596,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21374_Track-51690_R1.fastq.gz,fastq,44346608.0,583508.0,GSM7655596 r1,0:76,A:11794284;C:10211396;G:10275551;T:12064327;N:1050,76,,,,11794284,10211396,10275551,12064327,1050,SRX21113488,SRS18382082,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.84786,,0.10747,,0.9432,,0.64267,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76765,SRR25374411,SRX21113487,SRS18382081,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 B09,GSM7655595,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 B09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655595,GSM7655595: ExVi16Gr 02 B09; Danio rerio; RNA Seq,GSM7655595 r1,GSM7655595,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21375_Track-51691_R1.fastq.gz,fastq,43404512.0,571112.0,GSM7655595 r1,0:76,A:11406215;C:10089747;G:10096444;T:11811131;N:975,76,,,,11406215,10089747,10096444,11811131,975,SRX21113487,SRS18382081,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.87723,,0.08948,,0.94365,,0.60874,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76766,SRR25374412,SRX21113486,SRS18382080,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 C09,GSM7655594,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 C09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655594,GSM7655594: ExVi16Gr 02 C09; Danio rerio; RNA Seq,GSM7655594 r1,GSM7655594,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21376_Track-51692_R1.fastq.gz,fastq,45027036.0,592461.0,GSM7655594 r1,0:76,A:11841919;C:10492780;G:10537256;T:12153887;N:1194,76,,,,11841919,10492780,10537256,12153887,1194,SRX21113486,SRS18382080,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.84983,,0.08729,,0.93584,,0.63209,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76767,SRR25374413,SRX21113485,SRS18382079,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 D09,GSM7655593,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 D09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655593,GSM7655593: ExVi16Gr 02 D09; Danio rerio; RNA Seq,GSM7655593 r1,GSM7655593,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21377_Track-51693_R1.fastq.gz,fastq,12382908.0,162933.0,GSM7655593 r1,0:76,A:3238636;C:2869308;G:2881983;T:3392821;N:160,76,,,,3238636,2869308,2881983,3392821,160,SRX21113485,SRS18382079,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.83061,,0.05654,,0.94558,,0.64901,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76768,SRR25374414,SRX21113484,SRS18382077,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 E09,GSM7655592,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 E09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655592,GSM7655592: ExVi16Gr 02 E09; Danio rerio; RNA Seq,GSM7655592 r1,GSM7655592,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21378_Track-51694_R1.fastq.gz,fastq,35251232.0,463832.0,GSM7655592 r1,0:76,A:9503812;C:8037895;G:8131353;T:9577315;N:857,76,,,,9503812,8037895,8131353,9577315,857,SRX21113484,SRS18382077,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.77275,,0.07657,,0.94836,,0.59607,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76769,SRR25374415,SRX21113483,SRS18382078,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 F09,GSM7655591,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 F09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655591,GSM7655591: ExVi16Gr 02 F09; Danio rerio; RNA Seq,GSM7655591 r1,GSM7655591,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21379_Track-51695_R1.fastq.gz,fastq,29051836.0,382261.0,GSM7655591 r1,0:76,A:7518130;C:6891176;G:6876887;T:7764943;N:700,76,,,,7518130,6891176,6876887,7764943,700,SRX21113483,SRS18382078,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.86709,,0.07623,,0.94495,,0.65172,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76770,SRR25374416,SRX21113482,SRS18382076,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 G09,GSM7655590,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 G09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655590,GSM7655590: ExVi16Gr 02 G09; Danio rerio; RNA Seq,GSM7655590 r1,GSM7655590,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21380_Track-51696_R1.fastq.gz,fastq,109516.0,1441.0,GSM7655590 r1,0:76,A:29131;C:25838;G:25349;T:29198;N:0,76,,,,29131,25838,25349,29198,0,SRX21113482,SRS18382076,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.76586,,0.05934,,0.99277,,0.74208,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76771,SRR25374417,SRX21113481,SRS18382075,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 A01,GSM7655755,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 A01,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655755,GSM7655755: ExVi2Red 01 A01; Danio rerio; RNA Seq,GSM7655755 r1,GSM7655755,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21214_Track-51531_R1.fastq.gz,fastq,45532968.0,599118.0,GSM7655755 r1,0:76,A:12246803;C:10349678;G:10361865;T:12573403;N:1219,76,,,,12246803,10349678,10361865,12573403,1219,SRX21113481,SRS18382075,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.87285,,0.0881,,0.90136,,0.6883,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76772,SRR25374418,SRX21113480,SRS18382074,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 B01,GSM7655754,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 B01,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655754,GSM7655754: ExVi2Red 01 B01; Danio rerio; RNA Seq,GSM7655754 r1,GSM7655754,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21215_Track-51532_R1.fastq.gz,fastq,34996100.0,460475.0,GSM7655754 r1,0:76,A:9331462;C:8037189;G:8071185;T:9555393;N:871,76,,,,9331462,8037189,8071185,9555393,871,SRX21113480,SRS18382074,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.84607,,0.05475,,0.92374,,0.60845,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76773,SRR25374419,SRX21113479,SRS18382073,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 C01,GSM7655753,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 C01,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655753,GSM7655753: ExVi2Red 01 C01; Danio rerio; RNA Seq,GSM7655753 r1,GSM7655753,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21216_Track-51533_R1.fastq.gz,fastq,35915548.0,472573.0,GSM7655753 r1,0:76,A:9876241;C:7948709;G:8031565;T:10058067;N:966,76,,,,9876241,7948709,8031565,10058067,966,SRX21113479,SRS18382073,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.83728,,0.10675,,0.94426,,0.70513,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76774,SRR25374420,SRX21113478,SRS18382072,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 D01,GSM7655752,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 D01,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655752,GSM7655752: ExVi2Red 01 D01; Danio rerio; RNA Seq,GSM7655752 r1,GSM7655752,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21217_Track-51534_R1.fastq.gz,fastq,40427896.0,531946.0,GSM7655752 r1,0:76,A:10795650;C:9203028;G:9208037;T:11220185;N:996,76,,,,10795650,9203028,9208037,11220185,996,SRX21113478,SRS18382072,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.82317,,0.05906,,0.93229,,0.65906,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76775,SRR25374421,SRX21113477,SRS18382071,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 E01,GSM7655751,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 E01,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655751,GSM7655751: ExVi2Red 01 E01; Danio rerio; RNA Seq,GSM7655751 r1,GSM7655751,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21218_Track-51535_R1.fastq.gz,fastq,44180016.0,581316.0,GSM7655751 r1,0:76,A:11920819;C:10035364;G:10070579;T:12151996;N:1258,76,,,,11920819,10035364,10070579,12151996,1258,SRX21113477,SRS18382071,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.87211,,0.08161,,0.9011,,0.58341,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76776,SRR25374422,SRX21113476,SRS18382069,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 F01,GSM7655750,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 F01,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655750,GSM7655750: ExVi2Red 01 F01; Danio rerio; RNA Seq,GSM7655750 r1,GSM7655750,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21219_Track-51536_R1.fastq.gz,fastq,33634636.0,442561.0,GSM7655750 r1,0:76,A:8955856;C:7717906;G:7739888;T:9220366;N:620,76,,,,8955856,7717906,7739888,9220366,620,SRX21113476,SRS18382069,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.79266,,0.0799,,0.93852,,0.6609,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76777,SRR25374423,SRX21113475,SRS18382070,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 G04,GSM7655725,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 G04,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655725,GSM7655725: ExVi2Red 01 G04; Danio rerio; RNA Seq,GSM7655725 r1,GSM7655725,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21244_Track-51561_R1.fastq.gz,fastq,28279068.0,372093.0,GSM7655725 r1,0:76,A:7573141;C:6458500;G:6502179;T:7744670;N:578,76,,,,7573141,6458500,6502179,7744670,578,SRX21113475,SRS18382070,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.82931,,0.07538,,0.93892,,0.57086,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76778,SRR25374424,SRX21113474,SRS18382068,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 H04,GSM7655724,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 H04,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655724,GSM7655724: ExVi2Red 01 H04; Danio rerio; RNA Seq,GSM7655724 r1,GSM7655724,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21245_Track-51562_R1.fastq.gz,fastq,33646188.0,442713.0,GSM7655724 r1,0:76,A:8914312;C:7724087;G:7709961;T:9296909;N:919,76,,,,8914312,7724087,7709961,9296909,919,SRX21113474,SRS18382068,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.83628,,0.07615,,0.94123,,0.62167,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76779,SRR25374425,SRX21113473,SRS18382067,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 A05,GSM7655723,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 A05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655723,GSM7655723: ExVi2Red 01 A05; Danio rerio; RNA Seq,GSM7655723 r1,GSM7655723,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21246_Track-51563_R1.fastq.gz,fastq,65374820.0,860195.0,GSM7655723 r1,0:76,A:17920811;C:14416412;G:14755021;T:18280774;N:1802,76,,,,17920811,14416412,14755021,18280774,1802,SRX21113473,SRS18382067,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.82654,,0.12154,,0.93517,,0.62121,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76780,SRR25374426,SRX21113472,SRS18382066,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 B05,GSM7655722,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 B05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655722,GSM7655722: ExVi2Red 01 B05; Danio rerio; RNA Seq,GSM7655722 r1,GSM7655722,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21247_Track-51564_R1.fastq.gz,fastq,39210908.0,515933.0,GSM7655722 r1,0:76,A:10287821;C:9187861;G:9206063;T:10528196;N:967,76,,,,10287821,9187861,9206063,10528196,967,SRX21113472,SRS18382066,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.86501,,0.0627,,0.91007,,0.61738,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76781,SRR25374427,SRX21113471,SRS18382065,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 C05,GSM7655721,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 C05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655721,GSM7655721: ExVi2Red 01 C05; Danio rerio; RNA Seq,GSM7655721 r1,GSM7655721,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21248_Track-51565_R1.fastq.gz,fastq,38625252.0,508227.0,GSM7655721 r1,0:76,A:10080873;C:9030644;G:8994423;T:10518327;N:985,76,,,,10080873,9030644,8994423,10518327,985,SRX21113471,SRS18382065,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.86695,,0.06747,,0.93837,,0.67272,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76782,SRR25374428,SRX21113470,SRS18382063,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 D05,GSM7655720,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 D05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655720,GSM7655720: ExVi2Red 01 D05; Danio rerio; RNA Seq,GSM7655720 r1,GSM7655720,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21249_Track-51566_R1.fastq.gz,fastq,38599488.0,507888.0,GSM7655720 r1,0:76,A:10171275;C:8965675;G:8953753;T:10507855;N:930,76,,,,10171275,8965675,8953753,10507855,930,SRX21113470,SRS18382063,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.84344,,0.069,,0.93519,,0.66364,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76783,SRR25374429,SRX21113469,SRS18382064,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,UHR 01 E05,GSM7655719,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,UHR 01 E05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655719,GSM7655719: UHR 01 E05; Danio rerio; RNA Seq,GSM7655719 r1,GSM7655719,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21250_Track-51567_R1.fastq.gz,fastq,37809468.0,497493.0,GSM7655719 r1,0:76,A:9802568;C:8894462;G:9020819;T:10090613;N:1006,76,,,,9802568,8894462,9020819,10090613,1006,SRX21113469,SRS18382064,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.00309,,0.00234,,0.99894,,0.71653,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76784,SRR25374430,SRX21113468,SRS18382062,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 F05,GSM7655718,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 F05,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655718,GSM7655718: ExVi2Red 01 F05; Danio rerio; RNA Seq,GSM7655718 r1,GSM7655718,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21251_Track-51568_R1.fastq.gz,fastq,27209672.0,358022.0,GSM7655718 r1,0:76,A:7189506;C:6365576;G:6376421;T:7277585;N:584,76,,,,7189506,6365576,6376421,7277585,584,SRX21113468,SRS18382062,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.89002,,0.05915,,0.8869,,0.58584,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76785,SRR25374431,SRX21113467,SRS18382061,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 H08,GSM7655693,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 H08,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655693,GSM7655693: ExVi2Red 01 H08; Danio rerio; RNA Seq,GSM7655693 r1,GSM7655693,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21277_Track-51593_R1.fastq.gz,fastq,35576816.0,468116.0,GSM7655693 r1,0:76,A:9738994;C:7920726;G:7964832;T:9951202;N:1062,76,,,,9738994,7920726,7964832,9951202,1062,SRX21113467,SRS18382061,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.82033,,0.12428,,0.92837,,0.61179,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76786,SRR25374432,SRX21113466,SRS18382060,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 A09,GSM7655692,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 A09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655692,GSM7655692: ExVi2Red 01 A09; Danio rerio; RNA Seq,GSM7655692 r1,GSM7655692,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21278_Track-51594_R1.fastq.gz,fastq,50878200.0,669450.0,GSM7655692 r1,0:76,A:13254053;C:11944278;G:11914998;T:13763637;N:1234,76,,,,13254053,11944278,11914998,13763637,1234,SRX21113466,SRS18382060,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.8501,,0.05515,,0.94221,,0.6349,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76787,SRR25374433,SRX21113465,SRS18382058,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 B09,GSM7655691,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 B09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655691,GSM7655691: ExVi2Red 01 B09; Danio rerio; RNA Seq,GSM7655691 r1,GSM7655691,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21279_Track-51595_R1.fastq.gz,fastq,37781120.0,497120.0,GSM7655691 r1,0:76,A:9776300;C:8939889;G:8924638;T:10139202;N:1091,76,,,,9776300,8939889,8924638,10139202,1091,SRX21113465,SRS18382058,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.86291,,0.05774,,0.95022,,0.66413,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76788,SRR25374434,SRX21113464,SRS18382059,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 C09,GSM7655690,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 C09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655690,GSM7655690: ExVi2Red 01 C09; Danio rerio; RNA Seq,GSM7655690 r1,GSM7655690,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21280_Track-51596_R1.fastq.gz,fastq,38501144.0,506594.0,GSM7655690 r1,0:76,A:10447266;C:8626827;G:8684790;T:10741285;N:976,76,,,,10447266,8626827,8684790,10741285,976,SRX21113464,SRS18382059,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.82592,,0.08168,,0.95213,,0.62373,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76789,SRR25374435,SRX21113463,SRS18382057,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 D09,GSM7655689,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 D09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655689,GSM7655689: ExVi2Red 01 D09; Danio rerio; RNA Seq,GSM7655689 r1,GSM7655689,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21281_Track-51597_R1.fastq.gz,fastq,37118476.0,488401.0,GSM7655689 r1,0:76,A:9991639;C:8479533;G:8508978;T:10137419;N:907,76,,,,9991639,8479533,8508978,10137419,907,SRX21113463,SRS18382057,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.85202,,0.06249,,0.94095,,0.56917,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76790,SRR25374436,SRX21113462,SRS18382055,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 E09,GSM7655688,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 E09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655688,GSM7655688: ExVi2Red 01 E09; Danio rerio; RNA Seq,GSM7655688 r1,GSM7655688,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21282_Track-51598_R1.fastq.gz,fastq,34346604.0,451929.0,GSM7655688 r1,0:76,A:9152214;C:7869775;G:7863371;T:9460406;N:838,76,,,,9152214,7869775,7863371,9460406,838,SRX21113462,SRS18382055,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.83557,,0.07471,,0.94657,,0.66911,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76791,SRR25374437,SRX21113461,SRS18382056,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 F09,GSM7655687,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 F09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655687,GSM7655687: ExVi2Red 01 F09; Danio rerio; RNA Seq,GSM7655687 r1,GSM7655687,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21283_Track-51599_R1.fastq.gz,fastq,38042484.0,500559.0,GSM7655687 r1,0:76,A:10115031;C:8815862;G:8847514;T:10263187;N:890,76,,,,10115031,8815862,8847514,10263187,890,SRX21113461,SRS18382056,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.88055,,0.0673,,0.91354,,0.60568,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76792,SRR25374438,SRX21113460,SRS18382054,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 G09,GSM7655686,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 G09,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655686,GSM7655686: ExVi2Red 01 G09; Danio rerio; RNA Seq,GSM7655686 r1,GSM7655686,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21284_Track-51600_R1.fastq.gz,fastq,39984968.0,526118.0,GSM7655686 r1,0:76,A:10493521;C:9293954;G:9265128;T:10931579;N:786,76,,,,10493521,9293954,9265128,10931579,786,SRX21113460,SRS18382054,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.86059,,0.06872,,0.94501,,0.67013,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76793,SRR25374439,SRX21113459,SRS18382053,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi2Red 01 H12,GSM7655661,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi2Red 01 H12,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655661,GSM7655661: ExVi2Red 01 H12; Danio rerio; RNA Seq,GSM7655661 r1,GSM7655661,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21309_Track-51625_R1.fastq.gz,fastq,42457552.0,558652.0,GSM7655661 r1,0:76,A:11537651;C:9525737;G:9537176;T:11855919;N:1069,76,,,,11537651,9525737,9537176,11855919,1069,SRX21113459,SRS18382053,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.84093,,0.07999,,0.94458,,0.51356,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76794,SRR25374440,SRX21113458,SRS18382052,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 A01,GSM7655660,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 A01,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655660,GSM7655660: ExVi16Gr 02 A01; Danio rerio; RNA Seq,GSM7655660 r1,GSM7655660,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21310_Track-51626_R1.fastq.gz,fastq,43953384.0,578334.0,GSM7655660 r1,0:76,A:12164178;C:9594866;G:9736597;T:12456729;N:1014,76,,,,12164178,9594866,9736597,12456729,1014,SRX21113458,SRS18382052,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.83108,,0.12766,,0.94734,,0.62985,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System
76795,SRR25374441,SRX21113457,SRS18382050,SRP450614,PRJNA996961,Single cell transcriptome profiling of zebrafish pancreatic beta cells segregated by CaMPARI based calcium labeling.,GSE237867,Transcriptome Analysis,Coordination of cell activity trough Ca2+ waves enables pancreatic ß cells to secrete precise quantities of insulin in response to blood sugar. However  how the coordinating Ca2+ waves are orchestrated in space and time remains unknown. By applying functional Ca2+ imaging  using CaMPARI and single molecule RNA detection  we reveal a gene signature depicting a molecularly and metabolically distinct state of first responder ß cells.  We highlight Vitamin B6 metabolism as a signature pathway associated with the first responder ß cells . Overall design: Ex vivo photoconversion of ins:CaMPARI islets and Fluorescence activated cell sorting FACS The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.  The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence.  Single cell RNA Sequencing For single cell RNA Seq  ß cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  ß cells were collected from two conditions: responsive ß cells displaying photoconversion at 2.5 mM; and non responsive ß cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5.,,pubmed:38924394,,ExVi16Gr 02 B01,GSM7655659,,source name:pancreas|tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion|geo loc name:missing|collection date:missing,ExVi16Gr 02 B01,Raw reads in fastq format were trimmed using trim galore with default parameters to remove adapter sequences.  Trimmed reads were aligned to the zebrafish genome  GRCz10  using HISAT2 with default parameters. htseq count was used to assign reads to exons thus eventually getting counts per gene. For analysis  cells with more than 800 detected genes were utilized.  Transcriptional profile of responsive and non responsive were compared using ROTS with default parameters.  Genes with false discovery rate FDR less than 0.05 were considered as differentially expressed. For gene ontology GO analysis of differentially expressed genes  FishEnrichR was utilized.  As background  genes expressed in at least 5 % of the cells were used. Assembly: GRCz10 Supplementary files format and content: csv,pancreas,The primary islets from 4 mpf Tgins:CaMPARI animals were dissected from the fish post euthanasia.  Each islet was placed in a well of 24 well plate with 5 ml of DPBS medium supplemented with calcium  magnesium ThermoFisher  14040141  along with the appropriate concentration of D Glucose.  The islets were allowed to equilibrate for 5 min.  Subsequently  the entire 24 well plate was photoconverted using a 405 nm LED array Loctite  1167593 for 3 seconds.  The LED array evenly illuminated the entire dish with an intensity of 400 mW/cm2 and was triggered using a foot pedal switch.  An internal timer using an LED controller Loctite  1359255 was utilized for precise timing of light exposure.,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,4 mpf Tgins:CaMPARI zebrafish,tissue:pancreas|age:4 mpf|cell type:beta cell|genotype:Tgins:CaMPARI|treatment:photoconversion,GSM7655659,GSM7655659: ExVi16Gr 02 B01; Danio rerio; RNA Seq,GSM7655659 r1,GSM7655659,1,The photoconverted islets were dissociated into single cells by incubation in TrypLE ThermoFisher  12563029 at 37°C in a benchtop shaker set at 450 rpm for 45 min.  Following dissociation  TrypLE was inactivated with 10% FBS  and the cells pelleted by centrifugation at 500 g for 10 min at 4°C.  The supernatant was carefully discarded  and the pellet re suspended in 500 µl of HBSS without xxx+  Mg2+.  To remove debris  the solution was passed over a 30 µm cell filter Miltenyi Biotec  130 041 407.  To remove dead cells  calcein violet ThermoFisher  C34858 was added at a final concentration of 1 µM and the cell suspension incubated at room temperature for 20 minutes.  The single cell preparation was sorted through 100 µm nozzle.  The following channels were utilized in FACS: Pacific Blue for calcein violet; FITC Fluorescein isothiocyanate for green fluorescence; and PE Phycoerythrin for red fluorescence. For single cell RNA Seq  β cells isolated from Tgins:CaMPARI islets were subjected to profiling using Smart Seq2 protocol from Takara.  For this  islets were isolated  photoconverted ex vivo  dissociated and FAC sorted as described above.  β cells were collected from two conditions: responsive β cells displaying photoconversion at 2.5 mM; and non responsive β cells without xxx at 16.5 mM.  Photoconversion was defined as a high red to green ratio.  For FACS of each condition  index sorting was utilized  and the cells were collected in 96 well plate containing lysis buffer 2 µl of nuclease free water with 0.2% Triton X 100 and 4 U murine RNase Inhibitor NEB.  For each condition a total of 93 cells were collected for profiling.  Preparation of cDNA library and sequencing was performed exactly as described in a previous publication Singh et al.  Scientific Reports  2018; doi: 10.1038/s41598 018 35218 5. Smart Seq2 from Takara,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP450614,,loader:fastq load.py,L21311_Track-51627_R1.fastq.gz,fastq,40255300.0,529675.0,GSM7655659 r1,0:76,A:11092819;C:8866166;G:9025334;T:11270055;N:926,76,,,,11092819,8866166,9025334,11270055,926,SRX21113457,SRS18382050,SRA1676813,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.82194,,0.10415,,0.91334,,0.64999,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Belgium,2023-07-20,Adult,Adult,Pancreas,Endocrine System