{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\", technology = \"10x\" and tissue_curation = \"Pancreas\"", "rows": [[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", null, "pubmed:37595046", null, "10X 22 029  10 dy post single ablation", "GSM7085299", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 029  10 dy post single ablation", "GSM7085299", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 028  10 dy post single ablation", "GSM7085298", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 028  10 dy post single ablation", "GSM7085298", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 023  2 dy post double ablation", "GSM7085297", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 023  2 dy post double ablation", "GSM7085297", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 022  2 dy post double ablation", "GSM7085296", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 022  2 dy post double ablation", "GSM7085296", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 021  2 dy post single ablation", "GSM7085295", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 021  2 dy post single ablation", "GSM7085295", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 020  2 dy post single ablation", "GSM7085294", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 020  2 dy post single ablation", "GSM7085294", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 019  no ablation", "GSM7085293", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 019  no ablation", "GSM7085293", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 018  no ablation", "GSM7085292", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 018  no ablation", "GSM7085292", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 017  5 dy post single ablation", "GSM7085291", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 017  5 dy post single ablation", "GSM7085291", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 016  5 dy post double ablation", "GSM7085290", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "pubmed:37595046", null, "10X 22 016  5 dy post double ablation", "GSM7085290", null, "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 \u2018count\u2019 command of the Cell Ranger software v5.0.1 10\u00d7 Genomics with the option \u2018  expect cells\u2019 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 \u03bcL 1\u00d7TrypLE\u2122 Thermofisher supplemented with 60 \u03bcL 100\u00d7 Pluronic\u2122 F68 Thermofisher at 37 \u00b0C on a shaker at 125 rpm for 45 \u2013 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 \u03bcL pre cooled solution containing 1% BSA  0.1% Pluronic F 68 and 0.1% DAPI  and used a Corning\u2122 Falcon\u2122 cell strainer Corning\u2122 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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u2019s instructions. Cells were partitioned into gel beads in emulsion in the controller for cell lysis and reverse transcription. The 10\u00d7 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\u2019s recommendations. Sequencing data was aligned to the zebrafish reference genome GRCz11 with addition of the mCherry sequence using Cell Ranger v5.0.1 10\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "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\u2032 Library and Gel Bead Kit v3 10\u00d7 Genomics and Chromium Single Cell 3\u2032 Chip G 10\u00d7 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\u00d7 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\u00d7 Genomics to generate a gene by cell count matrix with default parameters.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP428435", null, "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, null, null, 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", null, "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", null, "Pancreas Ctrl replicate 2", "GSM7092957", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas Ctrl replicate 2", "GSM7092957", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas Ctrl replicate 2", "GSM7092957", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas Ctrl replicate 2", "GSM7092957", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas Ctrl replicate 1", "GSM7092956", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas Ctrl replicate 1", "GSM7092956", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas Ctrl replicate 1", "GSM7092956", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas Ctrl replicate 1", "GSM7092956", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 7 dpi replicate 1", "GSM7092948", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 7 dpi replicate 1", "GSM7092948", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 7 dpi replicate 1", "GSM7092948", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 7 dpi replicate 1", "GSM7092948", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 7 dpi replicate 2", "GSM7092949", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 7 dpi replicate 2", "GSM7092949", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 7 dpi replicate 2", "GSM7092949", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 7 dpi replicate 2", "GSM7092949", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 1 dpi replicate 2", "GSM7092941", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 1 dpi replicate 2", "GSM7092941", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 1 dpi replicate 2", "GSM7092941", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 1 dpi replicate 2", "GSM7092941", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 1 dpi replicate 1", "GSM7092940", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 1 dpi replicate 1", "GSM7092940", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 1 dpi replicate 1", "GSM7092940", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "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", null, "Pancreas 1 dpi replicate 1", "GSM7092940", null, "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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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\u2019 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\u00b0C 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\u00b0C 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\u00b0C  the pellet was resuspended in 500 \uf06dl 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\u00b0C. 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\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "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, null, null, 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", null, "United States", "2023-03-12", "Undetermined", "Undetermined", "Pancreas", "Endocrine System"]], "truncated": false, "filtered_table_rows_count": 44, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC SINGLE CELL", "p1": "10x", "p2": "Pancreas"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas", "results": 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"/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas", "results": [{"value": "cDNA", "label": "cDNA", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 24, "toggle_url": 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"http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas&devstage_curation=Undetermined", "selected": false}, {"value": "Adult", "label": "Adult", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas&devstage_curation=Adult", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas", "results": [{"value": "Endocrine System", "label": "Endocrine System", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas&tissue_curation_coarse=Endocrine+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas", "results": [{"value": "Pancreas", "label": "Pancreas", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&technology=10x&tissue_curation=Pancreas", "results": [{"value": "10x", "label": "10x", "count": 44, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL&tissue_curation=Pancreas", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 91.74473999883048}