{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\", technology = \"dropseq\" and tissue_curation_coarse = \"Liver and Biliary System\"", "rows": [[72137, "SRR22266708", "SRX18243019", "SRS15738744", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. 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Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11L_IO7719-2_S6_R1_001.fastq.gz 20200117_LIB11L_IO7719-2_S6_R2_001.fastq.gz", "fastq fastq", 3331789616.0, 45024184.0, "GSM6727458 r1", "0:25 1:49", "A:946310105;C:719718901;G:749385111;T:915418300;N:957199", 25, 49, null, null, 946310105, 719718901, 749385111, 915418300, 957199, "SRX18243013", "SRS15738738", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01267, 0.86765, 0.00264, 0.03942, 0.99486, 0.90467, 0.88099, 0.69827, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72144, "SRR22266715", "SRX18243012", "SRS15738737", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "3 dpa replicate 2 scRNAseq", "GSM6727457", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "3 dpa replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "GSM6727457", "GSM6727457: 3 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727457 r1", "GSM6727457", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11K_IO7719-2_S5_R1_001.fastq.gz 20200117_LIB11K_IO7719-2_S5_R2_001.fastq.gz", "fastq fastq", 3365491954.0, 45479621.0, "GSM6727457 r1", "0:25 1:49", "A:971335843;C:704444584;G:748234229;T:940472048;N:1005250", 25, 49, null, null, 971335843, 704444584, 748234229, 940472048, 1005250, "SRX18243012", "SRS15738737", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01131, 0.8537, 0.00273, 0.04803, 0.99299, 0.85557, 0.84434, 0.68314, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72145, "SRR22266716", "SRX18243011", "SRS15738736", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "2 dpa replicate 2 scRNAseq", "GSM6727456", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "2 dpa replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "GSM6727456", "GSM6727456: 2 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727456 r1", "GSM6727456", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11J_IO7719-2_S4_R1_001.fastq.gz 20200117_LIB11J_IO7719-2_S4_R2_001.fastq.gz", "fastq fastq", 2957589524.0, 39967426.0, "GSM6727456 r1", "0:25 1:49", "A:854274479;C:615108438;G:659483480;T:827845660;N:877467", 25, 49, null, null, 854274479, 615108438, 659483480, 827845660, 877467, "SRX18243011", "SRS15738736", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01096, 0.85133, 0.00285, 0.07036, 0.99245, 0.82542, 0.82529, 0.61995, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72146, "SRR22266717", "SRX18243010", "SRS15738735", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "1 dpa replicate 2 scRNAseq", "GSM6727455", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "1 dpa replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "GSM6727455", "GSM6727455: 1 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727455 r1", "GSM6727455", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11I_IO7719-2_S3_R1_001.fastq.gz 20200117_LIB11I_IO7719-2_S3_R2_001.fastq.gz", "fastq fastq", 3092505880.0, 41790620.0, "GSM6727455 r1", "0:25 1:49", "A:895995983;C:641925155;G:682159952;T:871498883;N:925907", 25, 49, null, null, 895995983, 641925155, 682159952, 871498883, 925907, "SRX18243010", "SRS15738735", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01185, 0.82809, 0.00327, 0.07186, 0.99129, 0.84287, 0.7735, 0.60648, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72147, "SRR22266718", "SRX18243009", "SRS15738734", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "0 dpa replicate 2 scRNAseq", "GSM6727454", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "0 dpa replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "GSM6727454", "GSM6727454: 0 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727454 r1", "GSM6727454", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11H_IO7719-2_S2_R1_001.fastq.gz 20200117_LIB11H_IO7719-2_S2_R2_001.fastq.gz", "fastq fastq", 3244996940.0, 43851310.0, "GSM6727454 r1", "0:25 1:49", "A:946884027;C:670640701;G:719365748;T:907134285;N:972179", 25, 49, null, null, 946884027, 670640701, 719365748, 907134285, 972179, "SRX18243009", "SRS15738734", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01005, 0.81799, 0.00308, 0.10915, 0.99448, 0.86064, 0.79416, 0.67831, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72148, "SRR22266719", "SRX18243008", "SRS15738733", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "mock replicate 2 scRNAseq", "GSM6727453", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "mock replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "GSM6727453", "GSM6727453: mock replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727453 r1", "GSM6727453", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200117_LIB11G_IO7719-2_S1_R1_001.fastq.gz 20200117_LIB11G_IO7719-2_S1_R2_001.fastq.gz", "fastq fastq", 3356731834.0, 45361241.0, "GSM6727453 r1", "0:25 1:49", "A:980697276;C:699683694;G:745214776;T:930134870;N:1001218", 25, 49, null, null, 980697276, 699683694, 745214776, 930134870, 1001218, "SRX18243008", "SRS15738733", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.011, 0.79428, 0.00351, 0.11936, 0.99373, 0.85478, 0.75547, 0.68815, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72149, "SRR22266720", "SRX18243007", "SRS15738732", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "7 dpa replicate 1 scRNAseq", "GSM6727452", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa", "7 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa", "GSM6727452", "GSM6727452: 7 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727452 r1", "GSM6727452", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11F_IO7718_S6_R1_001.fastq.gz 20200107_LIB11F_IO7718_S6_R2_001.fastq.gz", "fastq fastq", 4840197106.0, 65408069.0, "GSM6727452 r1", "0:25 1:49", "A:1400160545;C:1045739437;G:1129539602;T:1263108590;N:1648932", 25, 49, null, null, 1400160545, 1045739437, 1129539602, 1263108590, 1648932, "SRX18243007", "SRS15738732", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00433, 0.87197, 0.00121, 0.03946, 0.99849, 0.89603, 0.90123, 0.67206, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72150, "SRR22266721", "SRX18243006", "SRS15738731", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "3 dpa replicate 1 scRNAseq", "GSM6727451", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "3 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa", "GSM6727451", "GSM6727451: 3 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727451 r1", "GSM6727451", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11E_IO7718_S5_R1_001.fastq.gz 20200107_LIB11E_IO7718_S5_R2_001.fastq.gz", "fastq fastq", 3874899962.0, 52363513.0, "GSM6727451 r1", "0:25 1:49", "A:1146498594;C:801586968;G:878214009;T:1047253303;N:1347088", 25, 49, null, null, 1146498594, 801586968, 878214009, 1047253303, 1347088, "SRX18243006", "SRS15738731", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00431, 0.83478, 0.00141, 0.0513, 0.99803, 0.84839, 0.89787, 0.68748, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72151, "SRR22266722", "SRX18243005", "SRS15738730", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "2 dpa replicate 1 scRNAseq", "GSM6727450", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "2 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa", "GSM6727450", "GSM6727450: 2 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727450 r1", "GSM6727450", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11D_IO7718_S4_R1_001.fastq.gz 20200107_LIB11D_IO7718_S4_R2_001.fastq.gz", "fastq fastq", 4290500982.0, 57979743.0, "GSM6727450 r1", "0:25 1:49", "A:1253875889;C:893179946;G:979642333;T:1162325902;N:1476912", 25, 49, null, null, 1253875889, 893179946, 979642333, 1162325902, 1476912, "SRX18243005", "SRS15738730", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00318, 0.85906, 0.00119, 0.07192, 0.99791, 0.81201, 0.87066, 0.6047, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72152, "SRR22266723", "SRX18243004", "SRS15738729", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "1 dpa replicate 1 scRNAseq", "GSM6727449", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "1 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa", "GSM6727449", "GSM6727449: 1 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727449 r1", "GSM6727449", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11C_IO7718_S3_R1_001.fastq.gz 20200107_LIB11C_IO7718_S3_R2_001.fastq.gz", "fastq fastq", 4132383258.0, 55843017.0, "GSM6727449 r1", "0:25 1:49", "A:1190680505;C:866874473;G:962110856;T:1111280875;N:1436549", 25, 49, null, null, 1190680505, 866874473, 962110856, 1111280875, 1436549, "SRX18243004", "SRS15738729", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00379, 0.84562, 0.00142, 0.07321, 0.99793, 0.82974, 0.87967, 0.60001, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72153, "SRR22266724", "SRX18243003", "SRS15738728", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "0 dpa replicate 1 scRNAseq", "GSM6727448", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "0 dpa replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa", "GSM6727448", "GSM6727448: 0 dpa replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727448 r1", "GSM6727448", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11B_IO7718_S2_R1_001.fastq.gz 20200107_LIB11B_IO7718_S2_R2_001.fastq.gz", "fastq fastq", 3517854180.0, 47538570.0, "GSM6727448 r1", "0:25 1:49", "A:1048135042;C:723233290;G:804794008;T:940454450;N:1237390", 25, 49, null, null, 1048135042, 723233290, 804794008, 940454450, 1237390, "SRX18243003", "SRS15738728", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00348, 0.83158, 0.00149, 0.11394, 0.99817, 0.84737, 0.77258, 0.68387, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72154, "SRR22266725", "SRX18243002", "SRS15738727", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "mock replicate 1 scRNAseq", "GSM6727447", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "mock replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock", "GSM6727447", "GSM6727447: mock replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727447 r1", "GSM6727447", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20200107_LIB11A_IO7718_S1_R1_001.fastq.gz 20200107_LIB11A_IO7718_S1_R2_001.fastq.gz", "fastq fastq", 3054768766.0, 41280659.0, "GSM6727447 r1", "0:25 1:49", "A:927118702;C:625458757;G:696040428;T:805077948;N:1072931", 25, 49, null, null, 927118702, 625458757, 696040428, 805077948, 1072931, "SRX18243002", "SRS15738727", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.00329, 0.78939, 0.00143, 0.12148, 0.99819, 0.84214, 0.82711, 0.67658, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72155, "SRR22266726", "SRX18243001", "SRS15738726", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured GFP+ cells replicate 1 scRNAseq", "GSM6727446", null, "source name:liver|tissue:liver|cell type:GFP+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "uninjured GFP+ cells replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:GFP+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "GSM6727446", "GSM6727446: uninjured GFP+ cells replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727446 r1", "GSM6727446", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20191106_LIB10D_IO7549_S4_R1_001.fastq.gz 20191106_LIB10D_IO7549_S4_R2_001.fastq.gz", "fastq fastq", 8587107112.0, 116041988.0, "GSM6727446 r1", "0:25 1:49", "A:2580895720;C:1753463233;G:1921984995;T:2327869497;N:2893667", 25, 49, null, null, 2580895720, 1753463233, 1921984995, 2327869497, 2893667, "SRX18243001", "SRS15738726", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.02318, 0.81602, 0.00376, 0.07042, 0.99464, 0.925, 0.94019, 0.87362, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72156, "SRR22266727", "SRX18243000", "SRS15738725", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured mCherry+ cells replicate 3 scRNAseq", "GSM6727445", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "uninjured mCherry+ cells replicate 3 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "GSM6727445", "GSM6727445: uninjured mCherry+ cells replicate 3 scRNAseq; Danio rerio; RNA Seq", "GSM6727445 r1", "GSM6727445", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20191106_LIB10C_IO7549_S3_R1_001.fastq.gz 20191106_LIB10C_IO7549_S3_R2_001.fastq.gz", "fastq fastq", 8043400252.0, 108694598.0, "GSM6727445 r1", "0:25 1:49", "A:2306379322;C:1670142146;G:1834433742;T:2229698464;N:2746578", 25, 49, null, null, 2306379322, 1670142146, 1834433742, 2229698464, 2746578, "SRX18243000", "SRS15738725", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.02105, 0.77629, 0.00529, 0.12681, 0.98827, 0.84358, 0.77585, 0.67675, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72157, "SRR22266728", "SRX18242999", "SRS15738724", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured mCherry+ cells replicate 2 scRNAseq", "GSM6727444", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "uninjured mCherry+ cells replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "GSM6727444", "GSM6727444: uninjured mCherry+ cells replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727444 r1", "GSM6727444", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20191106_LIB10B_IO7549_S2_R1_001.fastq.gz 20191106_LIB10B_IO7549_S2_R2_001.fastq.gz", "fastq fastq", 7485031772.0, 101149078.0, "GSM6727444 r1", "0:25 1:49", "A:2109751380;C:1556629400;G:1728261758;T:2087832467;N:2556767", 25, 49, null, null, 2109751380, 1556629400, 1728261758, 2087832467, 2556767, "SRX18242999", "SRS15738724", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.02151, 0.80489, 0.00493, 0.13325, 0.9893, 0.84776, 0.77861, 0.68035, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72158, "SRR22266729", "SRX18242998", "SRS15738723", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured mCherry+ cells replicate 1 scRNAseq", "GSM6727443", null, "source name:liver|tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "uninjured mCherry+ cells replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:Uninjured", "GSM6727443", "GSM6727443: uninjured mCherry+ cells replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727443 r1", "GSM6727443", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20191106_LIB10A_IO7549_S1_R1_001.fastq.gz 20191106_LIB10A_IO7549_S1_R2_001.fastq.gz", "fastq fastq", 9329321266.0, 126071909.0, "GSM6727443 r1", "0:25 1:49", "A:2676820500;C:1936185283;G:2114138905;T:2598981203;N:3195375", 25, 49, null, null, 2676820500, 1936185283, 2114138905, 2598981203, 3195375, "SRX18242998", "SRS15738723", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01987, 0.75428, 0.00528, 0.13497, 0.98963, 0.84887, 0.73157, 0.68004, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72159, "SRR22266730", "SRX18242997", "SRS15738722", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 6 scRNAseq", "GSM6727442", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 6 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727442", "GSM6727442: uninjured replicate 6 scRNAseq; Danio rerio; RNA Seq", "GSM6727442 r1", "GSM6727442", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180316_LIB3D_IO5377-2_S3_R1_001.fastq.gz 20180316_LIB3D_IO5377-2_S3_R2_001.fastq.gz", "fastq fastq", 8019262192.0, 108368408.0, "GSM6727442 r1", "0:25 1:49", "A:2321354742;C:1785680783;G:1617017094;T:2294899508;N:310065", 25, 49, null, null, 2321354742, 1785680783, 1617017094, 2294899508, 310065, "SRX18242997", "SRS15738722", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01825, 0.43176, 0.00603, 0.0356, 0.99054, 0.93872, 0.39005, 0.39912, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72160, "SRR22266731", "SRX18242996", "SRS15738721", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 5 scRNAseq", "GSM6727441", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 5 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727441", "GSM6727441: uninjured replicate 5 scRNAseq; Danio rerio; RNA Seq", "GSM6727441 r1", "GSM6727441", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180316_LIB3C_IO5377-2_S2_R1_001.fastq.gz 20180316_LIB3C_IO5377-2_S2_R2_001.fastq.gz", "fastq fastq", 9922950894.0, 134093931.0, "GSM6727441 r1", "0:25 1:49", "A:2400612356;C:2523653639;G:2164027118;T:2834273253;N:384528", 25, 49, null, null, 2400612356, 2523653639, 2164027118, 2834273253, 384528, "SRX18242996", "SRS15738721", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01765, 0.24689, 0.00828, 0.03521, 0.9891, 0.93519, 0.74426, 0.65974, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72161, "SRR22266732", "SRX18242995", "SRS15738720", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 4 scRNAseq", "GSM6727440", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 4 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727440", "GSM6727440: uninjured replicate 4 scRNAseq; Danio rerio; RNA Seq", "GSM6727440 r1", "GSM6727440", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180316_LIB3A_IO5377-2_S1_R1_001.fastq.gz 20180316_LIB3A_IO5377-2_S1_R2_001.fastq.gz", "fastq fastq", 7562034174.0, 102189651.0, "GSM6727440 r1", "0:25 1:49", "A:2082168365;C:1773377474;G:1641155438;T:2065037229;N:295668", 25, 49, null, null, 2082168365, 1773377474, 1641155438, 2065037229, 295668, "SRX18242995", "SRS15738720", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01855, 0.34293, 0.00452, 0.03498, 0.9876, 0.94, 0.33164, 0.69274, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72162, "SRR22266733", "SRX18242994", "SRS15738719", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 3 scRNAseq", "GSM6727439", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 3 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727439", "GSM6727439: uninjured replicate 3 scRNAseq; Danio rerio; RNA Seq", "GSM6727439 r1", "GSM6727439", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180110_LIB2C_IO5170_S3_R1_001.fastq.gz 20180110_LIB2C_IO5170_S3_R2_001.fastq.gz", "fastq fastq", 6157056188.0, 83203462.0, "GSM6727439 r1", "0:25 1:49", "A:1886755825;C:1290134096;G:1216099330;T:1757471956;N:6594981", 25, 49, null, null, 1886755825, 1290134096, 1216099330, 1757471956, 6594981, "SRX18242994", "SRS15738719", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.0143, 0.53292, 0.0083, 0.06283, 0.99492, 0.94065, 0.83431, 0.72216, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72163, "SRR22266734", "SRX18242993", "SRS15738718", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 2 scRNAseq", "GSM6727438", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 2 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727438", "GSM6727438: uninjured replicate 2 scRNAseq; Danio rerio; RNA Seq", "GSM6727438 r1", "GSM6727438", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180110_LIB2B_IO5170_S2_R1_001.fastq.gz 20180110_LIB2B_IO5170_S2_R2_001.fastq.gz", "fastq fastq", 4085425374.0, 55208451.0, "GSM6727438 r1", "0:25 1:49", "A:1148951414;C:943475846;G:839192575;T:1149676508;N:4129031", 25, 49, null, null, 1148951414, 943475846, 839192575, 1149676508, 4129031, "SRX18242993", "SRS15738718", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.01678, 0.38499, 0.00747, 0.03999, 0.99299, 0.95298, 0.82687, 0.74374, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [72164, "SRR22266735", "SRX18242992", "SRS15738717", "SRP407581", "PRJNA900999", "Biliary epithelial cells are facultative liver stem cells during liver regeneration in adult zebrafish", "GSE217839", "Transcriptome Analysis", "Single cell sequencing was performed on the adult zebrafish liver on both uninjured animals and animals regenerating from hepatocyte ablation. Overall design: Samples were sequenced at 0 1 2 3 and 7 days post ablation. Mock treated and uninjured animals were also sequenced.", null, "pubmed:36625346", null, "uninjured replicate 1 scRNAseq", "GSM6727437", null, "source name:liver|tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "uninjured replicate 1 scRNAseq", "Fastq files were processed as described using the 2.4.0 version of the Drop seq tools mapping the reads to GRCz11 with the default parameters. For the DigitalExpression command we set NUM CORE BARCODES=5000. We used STAR version 2.5.3 and fastqc version 0.11.2. Assembly: GRCz11 Supplementary files format and content: *.txt.gz Supplementary files format and content: Digital Gene Expression Matrix", "liver", null, "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "tissue:liver|cell type:all cells|genotype:TU|treatment:Uninjured", "GSM6727437", "GSM6727437: uninjured replicate 1 scRNAseq; Danio rerio; RNA Seq", "GSM6727437 r1", "GSM6727437", "1", "Adult zebrafish livers were enyzmatically dissociated and live nucleated cells were enriched using FACS. The resultant single cell suspension was subjected to the Drop seq protocol. Beads were subjected to reverse transcription with Maxima H Minus Reverse Transcripase. cDNA was amplified with KAPA HiFi HotStart ReadyMix. Amplified cDNA was made into libraries using the Nextera XT DNA Library Preparation Kit with the goal of capturing 1000 cells per library. Libraries were sequenced on an Illumina NextSeq 500 using the Single End 75bp kit with the following parameters: Read 1: 20 bp Read 2: 50 bp Read 1 Index: 8 bp Custom Read 1 primer GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP407581", null, null, "20180110_LIB2A_IO5170_S1_R1_001.fastq.gz 20180110_LIB2A_IO5170_S1_R2_001.fastq.gz", "fastq fastq", 5454978746.0, 73715929.0, "GSM6727437 r1", "0:25 1:49", "A:1662394748;C:1166773893;G:1080027941;T:1540187839;N:5594325", 25, 49, null, null, 1662394748, 1166773893, 1080027941, 1540187839, 5594325, "SRX18242992", "SRS15738717", null, null, "Division of Genetics, Brigham and Women's Hospital", 2, 0.02089, 0.45353, 0.01367, 0.0687, 0.99168, 0.93139, 0.76523, 0.68002, 25, 49, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_droplet", "dropseq", null, "United States", "2022-11-12", "Adult", 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