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
33294,SRR29920543,SRX25414719,SRS22075127,SRP521426,PRJNA1138768,Gonadotropin releasing hormone 3 and gonadotropes relationships in female zebrafish pituitary revealed by single cell transcriptomics,GSE272806,Transcriptome Analysis,Gonadotropin releasing hormone GnRH governs reproduction in vertebrates by regulating pituitary gonadotropins. Zebrafish  however  is an exception as gnrh3–/– fish  which lack the hypophysiotropic GnRH3  are fertile  suggesting that zebrafish utilizes a Gnrh independent mechanism to regulate reproduction. To elucidate the role of Gnrh3 and the Gnrh independent mechanisms that regulate the pituitary gonadotropes  we profiled the gene expression in individual pituitary cells of wild type and gnrh–/– adult female zebrafish and identified transcriptionally defined cell types. The classical Lh and Fsh gonadotropes expressed both gonadotropin beta subunits with a ratio of 13:1 lhb:fshb and 40:1 fshb:lhb  respectively. We discovered that Lh gonadotropes predominantly express genes encoding receptors for Gnrh gnrhr2  thyroid hormone  estrogen  dopamine  and steroidogenic factor 1 SF1. No Gnrh receptor expression was enriched in Fsh gonadotropes  instead  the expression of cholecystokinin receptor cckrb and galanin receptor gal1rb were enriched in these cells. The hereditary loss of Gnrh3 gene resulted in downregulation of fshb in Lh gonadotropes. Likewise  targeted chemogenetic ablation of Gnrh3 neurons led to a decrease in the number of fshb+/lhb+ cells. Our studies suggest that Gnrh3 directly acts on Lh gonadotropes through Gnrhr2  but the outcome of this interaction is still unknown. Gnrh3 also regulates fshb expression  probably via a non Gnrh receptor route. Altogether  while Lh secretion and synthesis are likely regulated by multiple factors in a Gnrh independent manner  Gnrh3 seems to play a role in the cellular organization of the pituitary in zebrafish. Overall design: Pituitaries of WT and Gnrh3 knockout female zebrafish were dissociated and analyzed using single cell RNA sequencing,,pubmed:39499852,,gnrh3 knockout  scRNAseq,GSM8412848,,source name:Pituitary|tissue:Pituitary|age:Adult 3 mpf|genotype:gnrh3 / |Sex:female|geo loc name:missing|collection date:missing,gnrh3 knockout  scRNAseq,Barcode processing and gene counting were made using the 10×Genomics Cell Ranger v6.0.2 software. Quality control  normalization  data integration  and clustering were performed using Seurat v4 R package. Assembly: GRCz11/danRer11 Supplementary files format and content: Tab separated values files  matrix file  and comma separated values file,Pituitary,,Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly  the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C  then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded  then 1 mL Accumax working solution 30% Accumax in PBS was added  and the cells were gently resuspended. post incubation at room temperature for 5 minutes  the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C  the supernatant was removed  and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer’s manual for a target of 4 000 cells per sample.,,tissue:Pituitary|age:Adult 3 mpf|genotype:gnrh3 / |Sex:female,GSM8412848,GSM8412848: gnrh3 knockout  scRNAseq; Danio rerio; RNA Seq,GSM8412848 r1,GSM8412848,1,Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly  the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C  then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded  then 1 mL Accumax working solution 30% Accumax in PBS was added  and the cells were gently resuspended. post incubation at room temperature for 5 minutes  the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C  the supernatant was removed  and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP521426,,loader:fastq load.py,KO_20210616_A00904_IL100185604_S1_L001_I1_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_I2_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_R1_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,27063230346.0,121906443.0,GSM8412848 r1,0:10 1:10 2:101 3:101,A:6434793761;C:4051189285;G:4401327014;T:9737249538;N:541888,10,10,101,101,6434793761,4051189285,4401327014,9737249538,541888,SRX25414719,SRS22075127,SRA1930291,Stanford University,Stanford University,2,0.10559,0.92046,0.02334,0.15386,0.97879,0.81732,0.68611,0.62975,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-07-22,Adult,Adult,Pituitary Gland,Endocrine System
33295,SRR29920544,SRX25414718,SRS22075126,SRP521426,PRJNA1138768,Gonadotropin releasing hormone 3 and gonadotropes relationships in female zebrafish pituitary revealed by single cell transcriptomics,GSE272806,Transcriptome Analysis,Gonadotropin releasing hormone GnRH governs reproduction in vertebrates by regulating pituitary gonadotropins. Zebrafish  however  is an exception as gnrh3–/– fish  which lack the hypophysiotropic GnRH3  are fertile  suggesting that zebrafish utilizes a Gnrh independent mechanism to regulate reproduction. To elucidate the role of Gnrh3 and the Gnrh independent mechanisms that regulate the pituitary gonadotropes  we profiled the gene expression in individual pituitary cells of wild type and gnrh–/– adult female zebrafish and identified transcriptionally defined cell types. The classical Lh and Fsh gonadotropes expressed both gonadotropin beta subunits with a ratio of 13:1 lhb:fshb and 40:1 fshb:lhb  respectively. We discovered that Lh gonadotropes predominantly express genes encoding receptors for Gnrh gnrhr2  thyroid hormone  estrogen  dopamine  and steroidogenic factor 1 SF1. No Gnrh receptor expression was enriched in Fsh gonadotropes  instead  the expression of cholecystokinin receptor cckrb and galanin receptor gal1rb were enriched in these cells. The hereditary loss of Gnrh3 gene resulted in downregulation of fshb in Lh gonadotropes. Likewise  targeted chemogenetic ablation of Gnrh3 neurons led to a decrease in the number of fshb+/lhb+ cells. Our studies suggest that Gnrh3 directly acts on Lh gonadotropes through Gnrhr2  but the outcome of this interaction is still unknown. Gnrh3 also regulates fshb expression  probably via a non Gnrh receptor route. Altogether  while Lh secretion and synthesis are likely regulated by multiple factors in a Gnrh independent manner  Gnrh3 seems to play a role in the cellular organization of the pituitary in zebrafish. Overall design: Pituitaries of WT and Gnrh3 knockout female zebrafish were dissociated and analyzed using single cell RNA sequencing,,pubmed:39499852,,WT  scRNAseq,GSM8412847,,source name:Pituitary|tissue:Pituitary|age:Adult 3 mpf|genotype:wild type|Sex:female|geo loc name:missing|collection date:missing,WT  scRNAseq,Barcode processing and gene counting were made using the 10×Genomics Cell Ranger v6.0.2 software. Quality control  normalization  data integration  and clustering were performed using Seurat v4 R package. Assembly: GRCz11/danRer11 Supplementary files format and content: Tab separated values files  matrix file  and comma separated values file,Pituitary,,Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly  the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C  then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded  then 1 mL Accumax working solution 30% Accumax in PBS was added  and the cells were gently resuspended. post incubation at room temperature for 5 minutes  the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C  the supernatant was removed  and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer’s manual for a target of 4 000 cells per sample.,,tissue:Pituitary|age:Adult 3 mpf|genotype:wild type|Sex:female,GSM8412847,GSM8412847: WT  scRNAseq; Danio rerio; RNA Seq,GSM8412847 r1,GSM8412847,1,Five pituitaries were dissected from each gnrh3–/– and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly  the samples were centrifuged at 2 000 × rpm for 5 minutes at 4°C  then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 µm membrane filter at 28.5°C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 µL 6×Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 × rpm for 5 minutes at 4°C. The supernatant was gently discarded  then 1 mL Accumax working solution 30% Accumax in PBS was added  and the cells were gently resuspended. post incubation at room temperature for 5 minutes  the dissociated cells were filtered through 40 µm pore cell strainer. post centrifuging at 2 000 × rpm for 5 minutes at 4°C  the supernatant was removed  and the cell pellets were gently resuspended with 50 µL 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10×Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10×Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP521426,,loader:fastq load.py,WT_20210616_A00904_IL100185603_S1_L001_I1_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_I2_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_R1_001.fastq.gz WT_20210616_A00904_IL100185603_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,26784946020.0,120652910.0,GSM8412847 r1,0:10 1:10 2:101 3:101,A:6396247260;C:3989076165;G:4295547390;T:9690479627;N:537378,10,10,101,101,6396247260,3989076165,4295547390,9690479627,537378,SRX25414718,SRS22075126,SRA1930291,Stanford University,Stanford University,2,0.10896,0.92399,0.02311,0.16455,0.97652,0.80377,0.67721,0.64804,101,101,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-07-22,Adult,Adult,Pituitary Gland,Endocrine System
34324,SRR31647630,SRX27010714,SRS23475005,SRP550229,PRJNA1195876,Anti Müllerian hormone signalling sustains circadian homeostasis in zebrafish [scRNA seq],GSE283840,Transcriptome Analysis,Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however  the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here  we report that anti Müllerian hormone Amh mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably  amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms  which were recapitulated in bmpr2a null mutants. Somatotropes and gonadotropes were identified as Amh positive pituitary cell populations. Single cell transcriptome analysis further revealed a lineage specific regulation of pituitary clock by Amh. Moreover  Amh induced effect on clock gene expression could be abolished by blocking Smad1/5/9 phosphorylation and bmpr2a knockout. Mechanistically  Amh binds to its receptors  Bmpr2a/Bmpr1bb  which in turn activate Smad1/5/9 by phosphorylation and promote circadian gene expression. Our findings reveal a key hormone signalling pathway for circadian homeostasis in zebrafish with implications for rhythmic organ functions and circadian health. Overall design: Molecular components of the circadian clock are known; however  the mechanisms by which long term circadian homeostasis and oscillation are achieved throughout complex systems and anatomical regions are poorly understood. We performed CUT&Tag and single cell RNA sequencing of wildtype  amh or bmpr2a knockout zebrafish pituitary to investigate the molecular mechanism by which Amh signaling sustains circadian homeostasis.,,pubmed:40348785,,pituitary gland  Amh KO,GSM8672964,,source name:pituitary gland|tissue:pituitary gland|genotype:knockout Amh|geo loc name:missing|collection date:missing,pituitary gland  Amh KO,Raw sequencing data were demultiplexed and aligned to the ENSEMBL GRCz11 zebrafish transcriptome to generate feature barcode matrices using CellRanger v5.0.1 with the default parameters. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,pituitary gland,,post dissection  zebrafish pituitaries from WT or amh /  females were washed with cold PBS or fresh Ringer’s solution for 5 10 min  followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies  400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer  centrifuged 2000 rpm  5 min  4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer’s instructions.,,tissue:pituitary gland|genotype:knockout Amh,GSM8672964,GSM8672964: pituitary gland  Amh KO; Danio rerio; RNA Seq,GSM8672964 r1,GSM8672964,1,post dissection  zebrafish pituitaries from WT or amh /  females were washed with cold PBS or fresh Ringer's solution for 5 10 min  followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies  400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer  centrifuged 2000 rpm  5 min  4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell three prime Library & Gel Bead Kit v3.1 according to the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP550229,,,Amh_KO_R1.fq.gz Amh_KO_R2.fq.gz,fastq fastq,154810080300.0,516033601.0,GSM8672964 r1,0:150 1:150,A:51891488591;C:26616629262;G:25307529846;T:50992970078;N:1462523,150,150,,,51891488591,26616629262,25307529846,50992970078,1462523,SRX27010714,SRS23475005,SRA2029986,"Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences","Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-12-09,Undetermined,Undetermined,Pituitary Gland,Endocrine System
34325,SRR31647631,SRX27010713,SRS23475006,SRP550229,PRJNA1195876,Anti Müllerian hormone signalling sustains circadian homeostasis in zebrafish [scRNA seq],GSE283840,Transcriptome Analysis,Circadian clocks temporally orchestrate the behavioural and physiological rhythms. The core molecules establishing the circadian clock are clear; however  the critical signalling pathways that cause or favour the homeostasis are poorly understood. Here  we report that anti Müllerian hormone Amh mediated signalling plays an important role in sustaining circadian homeostasis in zebrafish. Remarkably  amh knockout dampens molecular clock oscillations and disrupts both behavioural and hormonal circadian rhythms  which were recapitulated in bmpr2a null mutants. Somatotropes and gonadotropes were identified as Amh positive pituitary cell populations. Single cell transcriptome analysis further revealed a lineage specific regulation of pituitary clock by Amh. Moreover  Amh induced effect on clock gene expression could be abolished by blocking Smad1/5/9 phosphorylation and bmpr2a knockout. Mechanistically  Amh binds to its receptors  Bmpr2a/Bmpr1bb  which in turn activate Smad1/5/9 by phosphorylation and promote circadian gene expression. Our findings reveal a key hormone signalling pathway for circadian homeostasis in zebrafish with implications for rhythmic organ functions and circadian health. Overall design: Molecular components of the circadian clock are known; however  the mechanisms by which long term circadian homeostasis and oscillation are achieved throughout complex systems and anatomical regions are poorly understood. We performed CUT&Tag and single cell RNA sequencing of wildtype  amh or bmpr2a knockout zebrafish pituitary to investigate the molecular mechanism by which Amh signaling sustains circadian homeostasis.,,pubmed:40348785,,pituitary gland  WT,GSM8672963,,source name:pituitary gland|tissue:pituitary gland|genotype:WT|geo loc name:missing|collection date:missing,pituitary gland  WT,Raw sequencing data were demultiplexed and aligned to the ENSEMBL GRCz11 zebrafish transcriptome to generate feature barcode matrices using CellRanger v5.0.1 with the default parameters. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,pituitary gland,,post dissection  zebrafish pituitaries from WT or amh /  females were washed with cold PBS or fresh Ringer’s solution for 5 10 min  followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies  400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer  centrifuged 2000 rpm  5 min  4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 according to the manufacturer’s instructions.,,tissue:pituitary gland|genotype:WT,GSM8672963,GSM8672963: pituitary gland  WT; Danio rerio; RNA Seq,GSM8672963 r1,GSM8672963,1,post dissection  zebrafish pituitaries from WT or amh /  females were washed with cold PBS or fresh Ringer's solution for 5 10 min  followed by mechanical and enzymatic dissociation in protease solution 0.25% trypsin Life Technologies  400 mg/ml collagenase D Sigma and 1 mM EDTA in PBS and incubated at 28.5 °C for 20 30 min or until full dissociation was observed. Dissociation was stopped by the addition of 6X stop solution 6 mM CaCl2 and 30% foetal bovine serum FBS in PBS. The samples were filtered with a 40 μm cell strainer  centrifuged 2000 rpm  5 min  4 °C and then resuspended in 1X PBS. Single cell cDNA libraries were synthesized using 10X Genomics Chromium Single Cell three prime Library & Gel Bead Kit v3.1 according to the manufacturer's instructions.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP550229,,,WT_R1.fq.gz WT_R2.fq.gz,fastq fastq,149500940700.0,498336469.0,GSM8672963 r1,0:150 1:150,A:49714239420;C:27445649314;G:26079818385;T:46259970208;N:1263373,150,150,,,49714239420,27445649314,26079818385,46259970208,1263373,SRX27010713,SRS23475006,SRA2029986,"Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences","Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-12-09,Undetermined,Undetermined,Pituitary Gland,Endocrine System
69988,SRR19217299,SRX15281308,SRS13012753,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB9278,GSM6153483,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing,AB9278,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month,GSM6153483,GSM6153483: AB9278; Danio rerio; RNA Seq,GSM6153483 r1,GSM6153483,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,loader:fastq load.py,AB9278_SB390_R1_01.fastq.gz AB9278_SB390_R2_01.fastq.gz,fastq fastq,1259447780.0,11770540.0,GSM6153483 r1,0:92 1:15,A:305608913;C:313550706;G:363197186;T:277079546;N:11429,92,15,,,305608913,313550706,363197186,277079546,11429,SRX15281308,SRS13012753,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.94767,0.0,0.32091,0.0,0.89796,1.0,0.7545,,92,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Adult,Adult,Pituitary Gland,Endocrine System
69989,SRR19217300,SRX15281307,SRS13012752,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB9277,GSM6153482,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing,AB9277,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month,GSM6153482,GSM6153482: AB9277; Danio rerio; RNA Seq,GSM6153482 r1,GSM6153482,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,loader:fastq load.py,AB9277_SB390_R1_01.fastq.gz AB9277_SB390_R2_01.fastq.gz,fastq fastq,1130776107.0,10568001.0,GSM6153482 r1,0:92 1:15,A:288600700;C:269726443;G:310844405;T:261594352;N:10207,92,15,,,288600700,269726443,310844405,261594352,10207,SRX15281307,SRS13012752,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.94379,0.0,0.28638,0.0,0.86415,1.0,0.63321,,92,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Adult,Adult,Pituitary Gland,Endocrine System
69990,SRR19217301,SRX15281306,SRS13012751,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB9280,GSM6153481,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing,AB9280,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month,GSM6153481,GSM6153481: AB9280; Danio rerio; RNA Seq,GSM6153481 r1,GSM6153481,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,loader:fastq load.py,AB9280_SB390_R1_01.fastq.gz AB9280_SB390_R2_01.fastq.gz,fastq fastq,1172966528.0,10962304.0,GSM6153481 r1,0:92 1:15,A:311089180;C:274626206;G:310304031;T:276936052;N:11059,92,15,,,311089180,274626206,310304031,276936052,11059,SRX15281306,SRS13012751,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.92936,0.0,0.23628,0.0,0.86147,1.0,0.74656,,92,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Adult,Adult,Pituitary Gland,Endocrine System
69991,SRR19217302,SRX15281305,SRS13012750,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB9279,GSM6153480,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing,AB9279,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month,GSM6153480,GSM6153480: AB9279; Danio rerio; RNA Seq,GSM6153480 r1,GSM6153480,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,loader:fastq load.py,AB9279_SB390_R1_01.fastq.gz AB9279_SB390_R2_01.fastq.gz,fastq fastq,1383147163.0,12926609.0,GSM6153480 r1,0:92 1:15,A:364575971;C:320901229;G:367626618;T:330030659;N:12686,92,15,,,364575971,320901229,367626618,330030659,12686,SRX15281305,SRS13012750,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.92462,0.0,0.26743,0.0,0.8493,1.0,0.74133,,92,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Adult,Adult,Pituitary Gland,Endocrine System
69992,SRR19217303,SRX15281304,SRS13012749,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB7418,GSM6153479,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing,AB7418,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf,GSM6153479,GSM6153479: AB7418; Danio rerio; RNA Seq,GSM6153479 r1,GSM6153479,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,,AB7418_SB350_S35_R1_001.fastq.gz AB7418_SB350_S35_R2_001.fastq.gz,fastq fastq,2468773944.0,29390166.0,GSM6153479 r1,0:69 1:15,A:764359919;C:520031317;G:592699381;T:591594655;N:88672,69,15,,,764359919,520031317,592699381,591594655,88672,SRX15281304,SRS13012749,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.85786,0.0,0.15143,0.0,0.84885,1.0,0.67021,,69,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Juvenile,Juvenile,Pituitary Gland,Endocrine System
69993,SRR19217304,SRX15281303,SRS13012748,SRP375342,PRJNA838481,Neural plate progenitors give rise to both anterior and posterior pituitary cells,GSE203075,Transcriptome Analysis,The pituitary is the master neuroendocrine tissue  which regulates body homeostasis. It consists of the adenohypophysis AH  which harbors hormones producing cells and the neurohypophysis NH  which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al.  2020. However  the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al.  2014  we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries  which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf  5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.,,pubmed:37683631,,AB7417,GSM6153478,,source name:Neurohypophysis enriched cells|strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing,AB7417,"bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header  delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data  allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al.  2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=""LogNormalize""  scale.factor= 10000 and ScaleData vars.to.regress = c""nCount RNA""  ""percent.mito"". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = ""pca""  resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster",Neurohypophysis enriched cells,5ul of 4.6mM β Ala Lys Nε AMCA Biotrend #BP0352 was injected into 37 dpf juvenile  or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours  the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,37 dpf  5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.,strain:AB  Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf,GSM6153478,GSM6153478: AB7417; Danio rerio; RNA Seq,GSM6153478 r1,GSM6153478,1,5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS  which was later changed to 250μl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750μl of TrypLE Express and 16μl DNaseI for 6 minutes at room temperature and stopped with 50μl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C  therepost resuspended in 500μl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine  penicillin 50 U/mL + streptomycin 0.05 mg/mL  FBS 1%  BSA 0.04% and passed through a 40μm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al.  2014. In short  mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate  then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated  reverse transcribed  and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina  USA at a median sequencing depth around 40 000 reads per cell.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP375342,,,AB7417_SB350_S24_R1_001.fastq.gz AB7417_SB350_S24_R2_001.fastq.gz,fastq fastq,2586526488.0,30791982.0,GSM6153478 r1,0:69 1:15,A:833353097;C:525447349;G:601496569;T:626135990;N:93483,69,15,,,833353097,525447349,601496569,626135990,93483,SRX15281303,SRS13012748,SRA1420605,"Molecular Cell Biology, Weizmann Institute of Science","Molecular Cell Biology, Weizmann Institute of Science",2,0.84125,0.0,0.10717,0.0,0.84768,1.0,0.63154,,69,15,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,marsseq,,Israel,2022-05-16,Juvenile,Juvenile,Pituitary Gland,Endocrine System
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