RNAquarium Metadata Server
Institute Website Terms of Use Privacy Policy

run_metadata

28 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "dropseq" and tissue_curation_coarse = "Liver and Biliary System"

✎ View and edit SQL

This data as json, CSV (advanced)

tissue_curation_coarse 1

  • Liver and Biliary System · 28 ✖

tissue_curation 1

technology 1

  • dropseq · 28 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC SINGLE CELL · 28 ✖

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

Link 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
72137 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. Mock treated and uninjured animals were also sequenced.   pubmed:36625346   7 dpa replicate 31 scRNAseq GSM6727464   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 31 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   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.   tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa GSM6727464 GSM6727464: 7 dpa replicate 31 scRNAseq; Danio rerio; RNA Seq GSM6727464 r1 GSM6727464 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     20200107_LIB11R_IO7720_S6_R1_001.fastq.gz 20200107_LIB11R_IO7720_S6_R2_001.fastq.gz fastq fastq 4802290236.0 64895814.0 GSM6727464 r1 0:25 1:49 A:1351689314;C:1044099826;G:1084104790;T:1321739644;N:656662 25 49     1351689314 1044099826 1084104790 1321739644 656662 SRX18243019 SRS15738744     Division of Genetics, Brigham and Women's Hospital 2 0.01055 0.84852 0.00192 0.03717 0.99527 0.89234 0.86731 0.69661 25 49 T B sc-like readlen illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet dropseq   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72138 72138 SRR22266709 SRX18243018 SRS15738743 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.   pubmed:36625346   3 dpa replicate 3 scRNAseq GSM6727463   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 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   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.   tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:3 dpa GSM6727463 GSM6727463: 3 dpa replicate 3 scRNAseq; Danio rerio; RNA Seq GSM6727463 r1 GSM6727463 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     20200107_LIB11Q_IO7720_S5_R1_001.fastq.gz 20200107_LIB11Q_IO7720_S5_R2_001.fastq.gz fastq fastq 4327529324.0 58480126.0 GSM6727463 r1 0:25 1:49 A:1223359778;C:914892543;G:970000561;T:1218683252;N:593190 25 49     1223359778 914892543 970000561 1218683252 593190 SRX18243018 SRS15738743     Division of Genetics, Brigham and Women's Hospital 2 0.00899 0.83745 0.00188 0.04633 0.99431 0.84492 0.84148 0.68261 25 49 T B sc-like readlen illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet dropseq   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72139 72139 SRR22266710 SRX18243017 SRS15738742 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.   pubmed:36625346   2 dpa replicate 3 scRNAseq GSM6727462   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 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   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.   tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:2 dpa GSM6727462 GSM6727462: 2 dpa replicate 3 scRNAseq; Danio rerio; RNA Seq GSM6727462 r1 GSM6727462 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     20200107_LIB11P_IO7720_S4_R1_001.fastq.gz 20200107_LIB11P_IO7720_S4_R2_001.fastq.gz fastq fastq 5036062970.0 68054905.0 GSM6727462 r1 0:25 1:49 A:1410235407;C:1062242143;G:1134885588;T:1428020401;N:679431 25 49     1410235407 1062242143 1134885588 1428020401 679431 SRX18243017 SRS15738742     Division of Genetics, Brigham and Women's Hospital 2 0.00859 0.86477 0.00193 0.06588 0.99387 0.81124 0.81235 0.61962 25 49 T B sc-like readlen illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet dropseq   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72140 72140 SRR22266711 SRX18243016 SRS15738741 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.   pubmed:36625346   1 dpa replicate 3 scRNAseq GSM6727461   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 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   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.   tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:1 dpa GSM6727461 GSM6727461: 1 dpa replicate 3 scRNAseq; Danio rerio; RNA Seq GSM6727461 r1 GSM6727461 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     20200107_LIB11O_IO7720_S3_R1_001.fastq.gz 20200107_LIB11O_IO7720_S3_R2_001.fastq.gz fastq fastq 4734982870.0 63986255.0 GSM6727461 r1 0:25 1:49 A:1350059086;C:986396540;G:1055462585;T:1342412482;N:652177 25 49     1350059086 986396540 1055462585 1342412482 652177 SRX18243016 SRS15738741     Division of Genetics, Brigham and Women's Hospital 2 0.01072 0.82414 0.0025 0.06977 0.99159 0.83004 0.66346 0.59359 25 49 T B sc-like readlen illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet dropseq   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72141 72141 SRR22266712 SRX18243015 SRS15738740 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.   pubmed:36625346   0 dpa replicate 3 scRNAseq GSM6727460   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 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   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.   tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:0 dpa GSM6727460 GSM6727460: 0 dpa replicate 3 scRNAseq; Danio rerio; RNA Seq GSM6727460 r1 GSM6727460 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     20200107_LIB11N_IO7720_S2_R1_001.fastq.gz 20200107_LIB11N_IO7720_S2_R2_001.fastq.gz fastq fastq 4224737108.0 57091042.0 GSM6727460 r1 0:25 1:49 A:1171021854;C:919004861;G:955423740;T:1178700581;N:586072 25 49     1171021854 919004861 955423740 1178700581 586072 SRX18243015 SRS15738740     Division of Genetics, Brigham and Women's Hospital 2 0.00691 0.71165 0.00186 0.09225 0.99634 0.86354 0.77015 0.67507 25 49 T B sc-like readlen illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet dropseq   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72142 72142 SRR22266713 SRX18243014 SRS15738739 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.   pubmed:36625346   mock replicate 3 scRNAseq GSM6727459   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 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   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.   tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:mock GSM6727459 GSM6727459: mock replicate 3 scRNAseq; Danio rerio; RNA Seq GSM6727459 r1 GSM6727459 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     20200107_LIB11M_IO7720_S1_R1_001.fastq.gz 20200107_LIB11M_IO7720_S1_R2_001.fastq.gz fastq fastq 4136407822.0 55897403.0 GSM6727459 r1 0:25 1:49 A:1196087924;C:868741250;G:928417059;T:1142590047;N:571542 25 49     1196087924 868741250 928417059 1142590047 571542 SRX18243014 SRS15738739     Division of Genetics, Brigham and Women's Hospital 2 0.00992 0.78 0.00257 0.11335 0.99431 0.83747 0.75089 0.69588 25 49 T B sc-like readlen illumina nextseq unknown cdna_unspecified nextera sc single_cell_droplet dropseq   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72143 72143 SRR22266714 SRX18243013 SRS15738738 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.   pubmed:36625346   7 dpa replicate 2 scRNAseq GSM6727458   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 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   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.   tissue:liver|cell type:mCherry+ cells|genotype:TgTp1:CreERT2 Tg 3.5ubb:LOXP EGFP LOXP mCherry Tgfabp10a:CFP NTR|treatment:7 dpa GSM6727458 GSM6727458: 7 dpa replicate 2 scRNAseq; Danio rerio; RNA Seq GSM6727458 r1 GSM6727458 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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     946310105 719718901 749385111 915418300 957199 SRX18243013 SRS15738738     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72144 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.   pubmed:36625346   3 dpa replicate 2 scRNAseq GSM6727457   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     971335843 704444584 748234229 940472048 1005250 SRX18243012 SRS15738737     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72145 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.   pubmed:36625346   2 dpa replicate 2 scRNAseq GSM6727456   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     854274479 615108438 659483480 827845660 877467 SRX18243011 SRS15738736     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72146 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.   pubmed:36625346   1 dpa replicate 2 scRNAseq GSM6727455   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     895995983 641925155 682159952 871498883 925907 SRX18243010 SRS15738735     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72147 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.   pubmed:36625346   0 dpa replicate 2 scRNAseq GSM6727454   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     946884027 670640701 719365748 907134285 972179 SRX18243009 SRS15738734     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72148 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.   pubmed:36625346   mock replicate 2 scRNAseq GSM6727453   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     980697276 699683694 745214776 930134870 1001218 SRX18243008 SRS15738733     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72149 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.   pubmed:36625346   7 dpa replicate 1 scRNAseq GSM6727452   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     1400160545 1045739437 1129539602 1263108590 1648932 SRX18243007 SRS15738732     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72150 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.   pubmed:36625346   3 dpa replicate 1 scRNAseq GSM6727451   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     1146498594 801586968 878214009 1047253303 1347088 SRX18243006 SRS15738731     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72151 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.   pubmed:36625346   2 dpa replicate 1 scRNAseq GSM6727450   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     1253875889 893179946 979642333 1162325902 1476912 SRX18243005 SRS15738730     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72152 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.   pubmed:36625346   1 dpa replicate 1 scRNAseq GSM6727449   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     1190680505 866874473 962110856 1111280875 1436549 SRX18243004 SRS15738729     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72153 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.   pubmed:36625346   0 dpa replicate 1 scRNAseq GSM6727448   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     1048135042 723233290 804794008 940454450 1237390 SRX18243003 SRS15738728     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72154 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.   pubmed:36625346   mock replicate 1 scRNAseq GSM6727447   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     927118702 625458757 696040428 805077948 1072931 SRX18243002 SRS15738727     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72155 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.   pubmed:36625346   uninjured GFP+ cells replicate 1 scRNAseq GSM6727446   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     2580895720 1753463233 1921984995 2327869497 2893667 SRX18243001 SRS15738726     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72156 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.   pubmed:36625346   uninjured mCherry+ cells replicate 3 scRNAseq GSM6727445   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     2306379322 1670142146 1834433742 2229698464 2746578 SRX18243000 SRS15738725     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72157 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.   pubmed:36625346   uninjured mCherry+ cells replicate 2 scRNAseq GSM6727444   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     2109751380 1556629400 1728261758 2087832467 2556767 SRX18242999 SRS15738724     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72158 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.   pubmed:36625346   uninjured mCherry+ cells replicate 1 scRNAseq GSM6727443   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     2676820500 1936185283 2114138905 2598981203 3195375 SRX18242998 SRS15738723     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72159 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.   pubmed:36625346   uninjured replicate 6 scRNAseq GSM6727442   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     2321354742 1785680783 1617017094 2294899508 310065 SRX18242997 SRS15738722     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72160 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.   pubmed:36625346   uninjured replicate 5 scRNAseq GSM6727441   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     2400612356 2523653639 2164027118 2834273253 384528 SRX18242996 SRS15738721     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72161 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.   pubmed:36625346   uninjured replicate 4 scRNAseq GSM6727440   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     2082168365 1773377474 1641155438 2065037229 295668 SRX18242995 SRS15738720     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72162 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.   pubmed:36625346   uninjured replicate 3 scRNAseq GSM6727439   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     1886755825 1290134096 1216099330 1757471956 6594981 SRX18242994 SRS15738719     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72163 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.   pubmed:36625346   uninjured replicate 2 scRNAseq GSM6727438   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     1148951414 943475846 839192575 1149676508 4129031 SRX18242993 SRS15738718     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System
72164 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.   pubmed:36625346   uninjured replicate 1 scRNAseq GSM6727437   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   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.   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.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP407581     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     1662394748 1166773893 1080027941 1540187839 5594325 SRX18242992 SRS15738717     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   United States 2022-11-12 Adult Adult Liver Liver and Biliary System

Advanced export

JSON shape: default, array, newline-delimited

CSV options: 

CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;