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 33210,SRR29868290,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I1_001.fastq.gz,fastq fastq fastq fastq,14533781976.0,86510607.0,GSM8403320 r1,,,,,,,,,,,,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92123,,0.07848,,0.87767,,0.63307,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33211,SRR29868291,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I1_001.fastq.gz,fastq fastq fastq fastq,14988315888.0,89216166.0,GSM8403320 r2,0:10 1:10 2:28 3:120,A:3248904317;C:2406836003;G:2506118019;T:2544017722;N:63859,10,10,28,120,3248904317,2406836003,2506118019,2544017722,63859,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92258,,0.07901,,0.87805,,0.61529,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33212,SRR29868292,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I1_001.fastq.gz,fastq fastq fastq fastq,15113782152.0,89962989.0,GSM8403320 r3,0:10 1:10 2:28 3:120,A:3272277396;C:2428985319;G:2529710055;T:2564489719;N:96191,10,10,28,120,3272277396,2428985319,2529710055,2564489719,96191,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92256,,0.07848,,0.87815,,0.62057,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33213,SRR29868293,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I1_001.fastq.gz,fastq fastq fastq fastq,14872072488.0,88524241.0,GSM8403320 r4,0:10 1:10 2:28 3:120,A:3227423261;C:2385566347;G:2480919292;T:2528894334;N:105686,10,10,28,120,3227423261,2385566347,2480919292,2528894334,105686,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92066,,0.07821,,0.87941,,0.63528,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33214,SRR29868294,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R2_001.fastq.gz,fastq fastq fastq fastq,17814930504.0,106041253.0,GSM8403319 r1,0:10 1:10 2:28 3:120,A:3778122253;C:2833144305;G:2888284601;T:3225338000;N:61201,10,10,28,120,3778122253,2833144305,2888284601,3225338000,61201,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92579,,0.07861,,0.82518,,0.61746,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33215,SRR29868295,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R2_001.fastq.gz,fastq fastq fastq fastq,18469195752.0,109935689.0,GSM8403319 r2,0:10 1:10 2:28 3:120,A:3912835271;C:2940938740;G:3000841815;T:3337590023;N:76831,10,10,28,120,3912835271,2940938740,3000841815,3337590023,76831,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92613,,0.07975,,0.82599,,0.6186,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33216,SRR29868296,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R2_001.fastq.gz,fastq fastq fastq fastq,18744044088.0,111571691.0,GSM8403319 r3,0:10 1:10 2:28 3:120,A:3967793098;C:2986585695;G:3048563710;T:3385544059;N:116358,10,10,28,120,3967793098,2986585695,3048563710,3385544059,116358,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9274,,0.07865,,0.82605,,0.61088,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33217,SRR29868297,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R2_001.fastq.gz,fastq fastq fastq fastq,18250884624.0,108636218.0,GSM8403319 r4,0:10 1:10 2:28 3:120,A:3870590300;C:2903010183;G:2961077382;T:3301541312;N:126983,10,10,28,120,3870590300,2903010183,2961077382,3301541312,126983,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92712,,0.07894,,0.82509,,0.60912,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33218,SRR29868298,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I1_001.fastq.gz,fastq fastq fastq fastq,17110767912.0,101849809.0,GSM8403318 r1,0:10 1:10 2:28 3:120,A:3788205667;C:2699657929;G:2699620981;T:3034435232;N:57271,10,10,28,120,3788205667,2699657929,2699620981,3034435232,57271,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91437,,0.05435,,0.86983,,0.62046,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33219,SRR29868299,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I1_001.fastq.gz,fastq fastq fastq fastq,17981827752.0,107034689.0,GSM8403318 r3,0:10 1:10 2:28 3:120,A:3977642248;C:2840653787;G:2844602651;T:3181150070;N:113924,10,10,28,120,3977642248,2840653787,2844602651,3181150070,113924,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91394,,0.05332,,0.87,,0.61803,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33220,SRR29868300,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I1_001.fastq.gz,fastq fastq fastq fastq,17550170232.0,104465299.0,GSM8403318 r4,0:10 1:10 2:28 3:120,A:3887199949;C:2768808747;G:2769733142;T:3109971563;N:122479,10,10,28,120,3887199949,2768808747,2769733142,3109971563,122479,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91342,,0.0541,,0.87046,,0.61388,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33221,SRR29868306,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I1_001.fastq.gz,fastq fastq fastq fastq,17719057944.0,105470583.0,GSM8403318 r2,0:10 1:10 2:28 3:120,A:3923720947;C:2796640453;G:2800418238;T:3135616927;N:73395,10,10,28,120,3923720947,2796640453,2800418238,3135616927,73395,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91325,,0.05422,,0.86949,,0.6266,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33222,SRR29868301,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R2_001.fastq.gz,fastq fastq fastq fastq,21323163288.0,126923591.0,GSM8403317 r1,0:10 1:10 2:28 3:120,A:4482829539;C:3366994739;G:3484245391;T:3896538980;N:222271,10,10,28,120,4482829539,3366994739,3484245391,3896538980,222271,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93349,,0.07482,,0.81925,,0.57693,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33223,SRR29868302,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R1_001.fastq.gz,fastq fastq fastq fastq,7887231744.0,46947808.0,GSM8403317 r5,0:10 1:10 2:28 3:120,A:1641421944;C:1251181706;G:1291844073;T:1449242410;N:46827,10,10,28,120,1641421944,1251181706,1291844073,1449242410,46827,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93251,,0.07497,,0.81763,,0.58245,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33224,SRR29868303,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8028118896.0,47786422.0,GSM8403317 r6,0:10 1:10 2:28 3:120,A:1672066662;C:1273372069;G:1312792441;T:1476102756;N:36712,10,10,28,120,1672066662,1273372069,1312792441,1476102756,36712,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93266,,0.07544,,0.81675,,0.57597,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33225,SRR29868304,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8223531120.0,48949590.0,GSM8403317 r7,0:10 1:10 2:28 3:120,A:1713836781;C:1304685662;G:1345155931;T:1510228105;N:44321,10,10,28,120,1713836781,1304685662,1345155931,1510228105,44321,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93273,,0.07513,,0.81546,,0.58099,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33226,SRR29868305,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I1_001.fastq.gz,fastq fastq fastq fastq,7715042160.0,45922870.0,GSM8403317 r8,0:10 1:10 2:28 3:120,A:1604997878;C:1222312105;G:1258545155;T:1424847802;N:41460,10,10,28,120,1604997878,1222312105,1258545155,1424847802,41460,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93359,,0.07524,,0.81479,,0.57882,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33227,SRR29868320,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R2_001.fastq.gz,fastq fastq fastq fastq,21662633664.0,128944248.0,GSM8403317 r2,0:10 1:10 2:28 3:120,A:4553543446;C:3422125565;G:3539342477;T:3957989911;N:308361,10,10,28,120,4553543446,3422125565,3539342477,3957989911,308361,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93227,,0.07246,,0.81696,,0.50066,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33228,SRR29868321,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I1_001.fastq.gz,fastq fastq fastq fastq,22267198800.0,132542850.0,GSM8403317 r3,0:10 1:10 2:28 3:120,A:4677084299;C:3522052285;G:3641789558;T:4063831592;N:384266,10,10,28,120,4677084299,3522052285,3641789558,4063831592,384266,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93308,,0.07402,,0.82035,,0.58114,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33229,SRR29868322,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I1_001.fastq.gz,fastq fastq fastq fastq,21946980216.0,130636787.0,GSM8403317 r4,0:10 1:10 2:28 3:120,A:4613356051;C:3469396471;G:3586452720;T:4006684161;N:525037,10,10,28,120,4613356051,3469396471,3586452720,4006684161,525037,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.932,,0.07454,,0.8199,,0.57856,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33230,SRR29868307,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I1_001.fastq.gz,fastq fastq fastq fastq,9879931488.0,58809116.0,GSM8403315 r1,0:10 1:10 2:28 3:120,A:2083561937;C:1579881891;G:1601331938;T:1792234199;N:83955,10,10,28,120,2083561937,1579881891,1601331938,1792234199,83955,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9245,,0.07832,,0.83207,,0.59038,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33231,SRR29868308,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I1_001.fastq.gz,fastq fastq fastq fastq,11728809288.0,69814341.0,GSM8403315 r5,0:10 1:10 2:28 3:120,A:2469898525;C:1869748167;G:1900689647;T:2137258339;N:126242,10,10,28,120,2469898525,1869748167,1900689647,2137258339,126242,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92438,,0.08084,,0.83181,,0.58855,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33232,SRR29868309,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I1_001.fastq.gz,fastq fastq fastq fastq,11877483744.0,70699308.0,GSM8403315 r6,0:10 1:10 2:28 3:120,A:2501780371;C:1893908685;G:1923797061;T:2164259893;N:170950,10,10,28,120,2501780371,1893908685,1923797061,2164259893,170950,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92477,,0.07874,,0.83321,,0.5933,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33233,SRR29868310,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I1_001.fastq.gz,fastq fastq fastq fastq,12148826256.0,72314442.0,GSM8403315 r7,0:10 1:10 2:28 3:120,A:2557348707;C:1939726759;G:1969388742;T:2211056576;N:212256,10,10,28,120,2557348707,1939726759,1969388742,2211056576,212256,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9241,,0.07899,,0.83246,,0.59733,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33234,SRR29868311,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I1_001.fastq.gz,fastq fastq fastq fastq,12000520224.0,71431668.0,GSM8403315 r8,0:10 1:10 2:28 3:120,A:2527907019;C:1914860315;G:1943708096;T:2185034081;N:290649,10,10,28,120,2527907019,1914860315,1943708096,2185034081,290649,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92467,,0.07869,,0.83274,,0.59327,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33235,SRR29868331,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10005892344.0,59558883.0,GSM8403315 r2,0:10 1:10 2:28 3:120,A:2111541927;C:1599222457;G:1620308600;T:1815908968;N:84008,10,10,28,120,2111541927,1599222457,1620308600,1815908968,84008,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.925,,0.07865,,0.83435,,0.60287,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33236,SRR29868332,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10016183856.0,59620142.0,GSM8403315 r3,0:10 1:10 2:28 3:120,A:2111419802;C:1602592297;G:1623486867;T:1816842279;N:75795,10,10,28,120,2111419802,1602592297,1623486867,1816842279,75795,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9252,,0.07706,,0.83311,,0.58482,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33237,SRR29868333,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I1_001.fastq.gz,fastq fastq fastq fastq,9972679080.0,59361185.0,GSM8403315 r4,0:10 1:10 2:28 3:120,A:2102584213;C:1595356295;G:1615800606;T:1809513301;N:87785,10,10,28,120,2102584213,1595356295,1615800606,1809513301,87785,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92471,,0.07908,,0.83368,,0.59597,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33238,SRR29868312,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I1_001.fastq.gz,fastq fastq fastq fastq,21831966072.0,129952179.0,GSM8403316 r1,0:10 1:10 2:28 3:120,A:4479350098;C:3460914438;G:3623235900;T:4030530673;N:230371,10,10,28,120,4479350098,3460914438,3623235900,4030530673,230371,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93487,,0.07462,,0.81168,,0.58593,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33239,SRR29868313,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R2_001.fastq.gz,fastq fastq fastq fastq,22210988016.0,132208262.0,GSM8403316 r2,0:10 1:10 2:28 3:120,A:4554555932;C:3523295618;G:3687384727;T:4099433293;N:321870,10,10,28,120,4554555932,3523295618,3687384727,4099433293,321870,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93515,,0.07425,,0.81251,,0.56065,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33240,SRR29868314,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R2_001.fastq.gz,fastq fastq fastq fastq,22964241384.0,136691913.0,GSM8403316 r3,0:10 1:10 2:28 3:120,A:4705118723;C:3647298654;G:3815152922;T:4235059775;N:399486,10,10,28,120,4705118723,3647298654,3815152922,4235059775,399486,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93515,,0.07425,,0.81085,,0.58414,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33241,SRR29868315,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R2_001.fastq.gz,fastq fastq fastq fastq,22572116784.0,134357838.0,GSM8403316 r4,0:10 1:10 2:28 3:120,A:4628982434;C:3582861623;G:3746732678;T:4163813221;N:550604,10,10,28,120,4628982434,3582861623,3746732678,4163813221,550604,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93487,,0.07514,,0.80862,,0.57745,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33242,SRR29868316,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9319118424.0,55470943.0,GSM8403316 r5,0:10 1:10 2:28 3:120,A:1895887547;C:1477863924;G:1543846946;T:1738857665;N:57078,10,10,28,120,1895887547,1477863924,1543846946,1738857665,57078,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93507,,0.07612,,0.80862,,0.5708,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33243,SRR29868317,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9433874184.0,56154013.0,GSM8403316 r6,0:10 1:10 2:28 3:120,A:1919903956;C:1496318299;G:1560772790;T:1761443349;N:43166,10,10,28,120,1919903956,1496318299,1560772790,1761443349,43166,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93514,,0.07597,,0.80937,,0.5877,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33244,SRR29868318,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I1_001.fastq.gz,fastq fastq fastq fastq,9674650944.0,57587208.0,GSM8403316 r7,0:10 1:10 2:28 3:120,A:1969538339;C:1535292977;G:1601577456;T:1804003343;N:52845,10,10,28,120,1969538339,1535292977,1601577456,1804003343,52845,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93521,,0.07665,,0.80876,,0.57512,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33245,SRR29868319,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R2_001.fastq.gz,fastq fastq fastq fastq,9063172776.0,53947457.0,GSM8403316 r8,0:10 1:10 2:28 3:120,A:1844279220;C:1435218712;G:1495137465;T:1699009389;N:50054,10,10,28,120,1844279220,1435218712,1495137465,1699009389,50054,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93431,,0.07653,,0.80803,,0.57631,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33246,SRR29868323,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I1_001.fastq.gz,fastq fastq fastq fastq,10244575656.0,60979617.0,GSM8403314 r1,0:10 1:10 2:28 3:120,A:2119295536;C:1665865582;G:1726802243;T:1805507036;N:83643,10,10,28,120,2119295536,1665865582,1726802243,1805507036,83643,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92821,,0.09448,,0.83725,,0.60089,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33247,SRR29868324,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I1_001.fastq.gz,fastq fastq fastq fastq,10380032880.0,61785910.0,GSM8403314 r2,0:10 1:10 2:28 3:120,A:2148125611;C:1687299842;G:1748516982;T:1830286430;N:80335,10,10,28,120,2148125611,1687299842,1748516982,1830286430,80335,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93012,,0.0931,,0.83621,,0.60089,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33248,SRR29868325,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I1_001.fastq.gz,fastq fastq fastq fastq,10397790648.0,61891611.0,GSM8403314 r3,0:10 1:10 2:28 3:120,A:2150008358;C:1691781234;G:1752867785;T:1832258443;N:77500,10,10,28,120,2150008358,1691781234,1752867785,1832258443,77500,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9284,,0.09293,,0.83605,,0.59853,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33249,SRR29868326,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I1_001.fastq.gz,fastq fastq fastq fastq,10333943592.0,61511569.0,GSM8403314 r4,0:10 1:10 2:28 3:120,A:2138003833;C:1680536471;G:1740834135;T:1821926938;N:86903,10,10,28,120,2138003833,1680536471,1740834135,1821926938,86903,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92828,,0.09437,,0.83611,,0.58915,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33250,SRR29868327,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I2_001.fastq.gz,fastq fastq fastq fastq,11552239440.0,68763330.0,GSM8403314 r5,0:10 1:10 2:28 3:120,A:2384461898;C:1875086137;G:1950680109;T:2041249149;N:122307,10,10,28,120,2384461898,1875086137,1950680109,2041249149,122307,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92842,,0.09581,,0.83591,,0.59709,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33251,SRR29868328,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I1_001.fastq.gz,fastq fastq fastq fastq,11713305912.0,69722059.0,GSM8403314 r6,0:10 1:10 2:28 3:120,A:2418305019;C:1901514145;G:1976625286;T:2070035096;N:167534,10,10,28,120,2418305019,1901514145,1976625286,2070035096,167534,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92987,,0.09528,,0.8352,,0.60535,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33252,SRR29868329,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I1_001.fastq.gz,fastq fastq fastq fastq,12060725208.0,71790031.0,GSM8403314 r7,0:10 1:10 2:28 3:120,A:2488941083;C:1959911465;G:2036435394;T:2129304281;N:211497,10,10,28,120,2488941083,1959911465,2036435394,2129304281,211497,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92896,,0.09426,,0.83867,,0.53757,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 33253,SRR29868330,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer’s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation dA tailing adapter ligation and indexing PCR—was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R2_001.fastq.gz,fastq fastq fastq fastq,11892922944.0,70791208.0,GSM8403314 r8,0:10 1:10 2:28 3:120,A:2456445818;C:1931328609;G:2006328383;T:2100554789;N:287361,10,10,28,120,2456445818,1931328609,2006328383,2100554789,287361,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92946,,0.09343,,0.83704,,0.59688,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System 70706,SRR21457012,SRX17460721,SRS15014532,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Liver in the WT S4 L004,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 4|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type liver,Live S4 L004 aliquot 4,Live S4 L004 aliquot 4,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S4_Live_20200825NB_S4_L004_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L004_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L004_R2_001.fastq.gz,fastq fastq fastq,15359722785.0,82137555.0,20200806 S4 Live 20200825NB S4 L004 I1 001.fastq.gz,0:8 1:28 2:151,A:3860252969;C:2756020453;G:2781498176;T:3004915512;N:83695,8,28,151,,3860252969,2756020453,2781498176,3004915512,83695,SRX17460721,SRS15014532,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.90519,,0.06757,,0.88243,,0.74961,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Liver,Liver and Biliary System 70707,SRR21457013,SRX17460720,SRS15014531,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Liver in the WT S4 L003,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 3|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type liver,Live S4 L003 aliquot 3,Live S4 L003 aliquot 3,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S4_Live_20200825NB_S4_L003_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L003_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L003_R2_001.fastq.gz,fastq fastq fastq,15277905984.0,81700032.0,20200806 S4 Live 20200825NB S4 L003 I1 001.fastq.gz,0:8 1:28 2:151,A:3834498109;C:2745604041;G:2766967723;T:2989497144;N:137815,8,28,151,,3834498109,2745604041,2766967723,2989497144,137815,SRX17460720,SRS15014531,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.90792,,0.06795,,0.88089,,0.75291,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Liver,Liver and Biliary System 70710,SRR21457016,SRX17460717,SRS15014528,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Liver in the WT S4 L002,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 2|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type liver,Live S4 L002 aliquot 2,Live S4 L002 aliquot 2,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S4_Live_20200825NB_S4_L002_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L002_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L002_R2_001.fastq.gz,fastq fastq fastq,15033903335.0,80395205.0,20200806 S4 Live 20200825NB S4 L002 I1 001.fastq.gz,0:8 1:28 2:151,A:3774023536;C:2701104584;G:2719224706;T:2945204367;N:118762,8,28,151,,3774023536,2701104584,2719224706,2945204367,118762,SRX17460717,SRS15014528,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.90993,,0.06896,,0.88002,,0.75003,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Liver,Liver and Biliary System 70711,SRR21457017,SRX17460716,SRS15014527,SRP385641,PRJNA857143,Single cell transcriptomic data of zebrafish lbw mutant,PRJNA857143,Other,Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.,,,,,Liver in the WT S4 L001,,isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 1|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of zebrafish: 6 dpf wild type liver,Live S4 L001 aliquot 1,Live S4 L001 aliquot 1,using Chromium Single Cell three prime GEM v3.1 Reagent Kit,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385641,,,20200806_S4_Live_20200825NB_S4_L001_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L001_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L001_R2_001.fastq.gz,fastq fastq fastq,15047379303.0,80467269.0,20200806 S4 Live 20200825NB S4 L001 I1 001.fastq.gz,0:8 1:28 2:151,A:3778269770;C:2702450055;G:2724848747;T:2944890394;N:98653,8,28,151,,3778269770,2702450055,2724848747,2944890394,98653,SRX17460716,SRS15014527,SRA1491985,Southwest University|Institute of Developmental Biology and Regenerativ,Southwest University,1,0.90977,,0.06799,,0.87998,,0.75241,,151,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2022-09-11,Larval,Larval,Liver,Liver and Biliary System 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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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 74480,SRR23824324,SRX19646191,SRS17014001,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver Ctrl replicate 2,GSM7092955,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver Ctrl replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092955,GSM7092955: liver Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092955 r1,GSM7092955,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Liver-2_S7_L001_R1_001.fastq.gz Ctrl-Liver-2_S7_L001_R2_001.fastq.gz,fastq fastq,5104340986.0,43257127.0,GSM7092955 r1,0:28 1:90,A:1424416053;C:1192239684;G:1190425268;T:1297142390;N:117591,28,90,,,1424416053,1192239684,1190425268,1297142390,117591,SRX19646191,SRS17014001,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00469,0.94025,0.00107,0.05406,0.99533,0.87308,0.27077,0.46309,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74481,SRR23824325,SRX19646191,SRS17014001,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver Ctrl replicate 2,GSM7092955,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver Ctrl replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092955,GSM7092955: liver Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092955 r1,GSM7092955,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Liver-2_S7_L002_R1_001.fastq.gz Ctrl-Liver-2_S7_L002_R2_001.fastq.gz,fastq fastq,5141806812.0,43574634.0,GSM7092955 r2,0:28 1:90,A:1434538137;C:1200870495;G:1198733719;T:1307553313;N:111148,28,90,,,1434538137,1200870495,1198733719,1307553313,111148,SRX19646191,SRS17014001,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0048,0.93996,0.00104,0.05254,0.99515,0.87499,0.26301,0.4732,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74482,SRR23824326,SRX19646191,SRS17014001,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver Ctrl replicate 2,GSM7092955,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver Ctrl replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092955,GSM7092955: liver Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092955 r1,GSM7092955,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Liver-2_S7_L003_R1_001.fastq.gz Ctrl-Liver-2_S7_L003_R2_001.fastq.gz,fastq fastq,5192564158.0,44004781.0,GSM7092955 r3,0:28 1:90,A:1448034478;C:1213477598;G:1211749223;T:1319197183;N:105676,28,90,,,1448034478,1213477598,1211749223,1319197183,105676,SRX19646191,SRS17014001,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00504,0.9401,0.00113,0.05317,0.99462,0.87361,0.27858,0.47856,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74483,SRR23824327,SRX19646191,SRS17014001,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver Ctrl replicate 2,GSM7092955,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver Ctrl replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092955,GSM7092955: liver Ctrl replicate 2; Danio rerio; RNA Seq,GSM7092955 r1,GSM7092955,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Liver-2_S7_L004_R1_001.fastq.gz Ctrl-Liver-2_S7_L004_R2_001.fastq.gz,fastq fastq,5107398366.0,43283037.0,GSM7092955 r4,0:28 1:90,A:1425848029;C:1192174260;G:1189956127;T:1299322516;N:97434,28,90,,,1425848029,1192174260,1189956127,1299322516,97434,SRX19646191,SRS17014001,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00498,0.9401,0.00127,0.05293,0.99494,0.87572,0.27094,0.47517,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74484,SRR23824328,SRX19646190,SRS17014000,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver Ctrl replicate 1,GSM7092954,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver Ctrl replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092954,GSM7092954: liver Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092954 r1,GSM7092954,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Liver-1_S3_L001_R1_001.fastq.gz Ctrl-Liver-1_S3_L001_R2_001.fastq.gz,fastq fastq,4496614672.0,38106904.0,GSM7092954 r1,0:28 1:90,A:1236795920;C:1061685679;G:1067304176;T:1130725493;N:103404,28,90,,,1236795920,1061685679,1067304176,1130725493,103404,SRX19646190,SRS17014000,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00769,0.94857,0.00194,0.0642,0.9948,0.87919,0.26391,0.47988,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74485,SRR23824329,SRX19646190,SRS17014000,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver Ctrl replicate 1,GSM7092954,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver Ctrl replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092954,GSM7092954: liver Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092954 r1,GSM7092954,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Liver-1_S3_L002_R2_001.fastq.gz Ctrl-Liver-1_S3_L002_R1_001.fastq.gz,fastq fastq,4500848984.0,38142788.0,GSM7092954 r2,0:28 1:90,A:1237725640;C:1062772315;G:1068127847;T:1132125691;N:97491,28,90,,,1237725640,1062772315,1068127847,1132125691,97491,SRX19646190,SRS17014000,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00735,0.94796,0.00174,0.06344,0.99504,0.87706,0.23275,0.47453,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74486,SRR23824330,SRX19646190,SRS17014000,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver Ctrl replicate 1,GSM7092954,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver Ctrl replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092954,GSM7092954: liver Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092954 r1,GSM7092954,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Liver-1_S3_L003_R1_001.fastq.gz Ctrl-Liver-1_S3_L003_R2_001.fastq.gz,fastq fastq,4565971178.0,38694671.0,GSM7092954 r3,0:28 1:90,A:1255012168;C:1078579990;G:1084287166;T:1147999283;N:92571,28,90,,,1255012168,1078579990,1084287166,1147999283,92571,SRX19646190,SRS17014000,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00832,0.94796,0.00204,0.06357,0.99407,0.87775,0.26311,0.46735,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74487,SRR23824331,SRX19646190,SRS17014000,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver Ctrl replicate 1,GSM7092954,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver Ctrl replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092954,GSM7092954: liver Ctrl replicate 1; Danio rerio; RNA Seq,GSM7092954 r1,GSM7092954,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,Ctrl-Liver-1_S3_L004_R1_001.fastq.gz Ctrl-Liver-1_S3_L004_R2_001.fastq.gz,fastq fastq,4487270016.0,38027712.0,GSM7092954 r4,0:28 1:90,A:1234826243;C:1058941866;G:1064097171;T:1129318562;N:86174,28,90,,,1234826243,1058941866,1064097171,1129318562,86174,SRX19646190,SRS17014000,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00802,0.94821,0.00201,0.06394,0.99472,0.87618,0.25364,0.46914,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74512,SRR23824356,SRX19646183,SRS17013993,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 7 dpi replicate 2,GSM7092947,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 7 dpi replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092947,GSM7092947: liver 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092947 r1,GSM7092947,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Liver-2_S23_L001_R1_001.fastq.gz 7dpi-Liver-2_S23_L001_R2_001.fastq.gz,fastq fastq,2901696228.0,24590646.0,GSM7092947 r1,0:28 1:90,A:800794183;C:688235467;G:699322734;T:713278095;N:65749,28,90,,,800794183,688235467,699322734,713278095,65749,SRX19646183,SRS17013993,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01367,0.94349,0.00359,0.06447,0.99371,0.8983,0.35863,0.50961,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74513,SRR23824357,SRX19646183,SRS17013993,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 7 dpi replicate 2,GSM7092947,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 7 dpi replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092947,GSM7092947: liver 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092947 r1,GSM7092947,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Liver-2_S23_L002_R1_001.fastq.gz 7dpi-Liver-2_S23_L002_R2_001.fastq.gz,fastq fastq,2911402436.0,24672902.0,GSM7092947 r2,0:28 1:90,A:803250356;C:690504502;G:701686700;T:715898105;N:62773,28,90,,,803250356,690504502,701686700,715898105,62773,SRX19646183,SRS17013993,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01353,0.94324,0.00375,0.06448,0.9934,0.89512,0.36797,0.50133,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74514,SRR23824358,SRX19646183,SRS17013993,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 7 dpi replicate 2,GSM7092947,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 7 dpi replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092947,GSM7092947: liver 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092947 r1,GSM7092947,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Liver-2_S23_L003_R1_001.fastq.gz 7dpi-Liver-2_S23_L003_R2_001.fastq.gz,fastq fastq,2952479180.0,25021010.0,GSM7092947 r3,0:28 1:90,A:814071655;C:700696343;G:712162705;T:725488870;N:59607,28,90,,,814071655,700696343,712162705,725488870,59607,SRX19646183,SRS17013993,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01352,0.9422,0.00377,0.06446,0.99383,0.89858,0.3405,0.51469,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74515,SRR23824359,SRX19646183,SRS17013993,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 7 dpi replicate 2,GSM7092947,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 7 dpi replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092947,GSM7092947: liver 7 dpi replicate 2; Danio rerio; RNA Seq,GSM7092947 r1,GSM7092947,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Liver-2_S23_L004_R1_001.fastq.gz 7dpi-Liver-2_S23_L004_R2_001.fastq.gz,fastq fastq,2888880956.0,24482042.0,GSM7092947 r4,0:28 1:90,A:797569254;C:684817990;G:695605635;T:710833096;N:54981,28,90,,,797569254,684817990,695605635,710833096,54981,SRX19646183,SRS17013993,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01297,0.94356,0.00358,0.0658,0.99366,0.89406,0.37493,0.50579,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74516,SRR23824360,SRX19646182,SRS17013992,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 7 dpi replicate 1,GSM7092946,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 7 dpi replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092946,GSM7092946: liver 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092946 r1,GSM7092946,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Liver-1_S19_L001_R1_001.fastq.gz 7dpi-Liver-1_S19_L001_R2_001.fastq.gz,fastq fastq,3336256244.0,28273358.0,GSM7092946 r1,0:28 1:90,A:928141930;C:786200774;G:796573600;T:825264837;N:75103,28,90,,,928141930,786200774,796573600,825264837,75103,SRX19646182,SRS17013992,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01265,0.9442,0.00339,0.0656,0.9933,0.88477,0.39633,0.57337,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74517,SRR23824361,SRX19646182,SRS17013992,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 7 dpi replicate 1,GSM7092946,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 7 dpi replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092946,GSM7092946: liver 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092946 r1,GSM7092946,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Liver-1_S19_L002_R1_001.fastq.gz 7dpi-Liver-1_S19_L002_R2_001.fastq.gz,fastq fastq,3339415222.0,28300129.0,GSM7092946 r2,0:28 1:90,A:928571814;C:786954831;G:797381996;T:826433990;N:72591,28,90,,,928571814,786954831,797381996,826433990,72591,SRX19646182,SRS17013992,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01263,0.94485,0.0034,0.06446,0.9935,0.88341,0.4136,0.56226,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74518,SRR23824362,SRX19646182,SRS17013992,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 7 dpi replicate 1,GSM7092946,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 7 dpi replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092946,GSM7092946: liver 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092946 r1,GSM7092946,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Liver-1_S19_L003_R1_001.fastq.gz 7dpi-Liver-1_S19_L003_R2_001.fastq.gz,fastq fastq,3389089446.0,28721097.0,GSM7092946 r3,0:28 1:90,A:942057789;C:799054157;G:809649273;T:838259397;N:68830,28,90,,,942057789,799054157,809649273,838259397,68830,SRX19646182,SRS17013992,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01251,0.94572,0.00331,0.06443,0.99279,0.88469,0.38873,0.57466,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74519,SRR23824363,SRX19646182,SRS17013992,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 7 dpi replicate 1,GSM7092946,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 7 dpi replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092946,GSM7092946: liver 7 dpi replicate 1; Danio rerio; RNA Seq,GSM7092946 r1,GSM7092946,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,7dpi-Liver-1_S19_L004_R1_001.fastq.gz 7dpi-Liver-1_S19_L004_R2_001.fastq.gz,fastq fastq,3326239460.0,28188470.0,GSM7092946 r4,0:28 1:90,A:925663531;C:783373500;G:793504177;T:823634415;N:63837,28,90,,,925663531,783373500,793504177,823634415,63837,SRX19646182,SRS17013992,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.01246,0.94489,0.00337,0.06529,0.9933,0.88556,0.39241,0.55747,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74540,SRR23824378,SRX19646176,SRS17013986,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 1 dpi replicate 2,GSM7092939,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 1 dpi replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092939,GSM7092939: liver 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092939 r1,GSM7092939,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Liver-2_S15_L001_R1_001.fastq.gz 1dpi-Liver-2_S15_L001_R2_001.fastq.gz,fastq fastq,3974430452.0,33681614.0,GSM7092939 r1,0:28 1:90,A:1095528573;C:930228144;G:956778552;T:991804101;N:91082,28,90,,,1095528573,930228144,956778552,991804101,91082,SRX19646176,SRS17013986,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0077,0.93007,0.00172,0.08628,0.99308,0.86448,0.28435,0.51435,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74541,SRR23824379,SRX19646176,SRS17013986,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 1 dpi replicate 2,GSM7092939,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 1 dpi replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092939,GSM7092939: liver 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092939 r1,GSM7092939,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Liver-2_S15_L002_R1_001.fastq.gz 1dpi-Liver-2_S15_L002_R2_001.fastq.gz,fastq fastq,4016739824.0,34040168.0,GSM7092939 r2,0:28 1:90,A:1107054312;C:940103463;G:966907262;T:1002588445;N:86342,28,90,,,1107054312,940103463,966907262,1002588445,86342,SRX19646176,SRS17013986,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00824,0.92962,0.00199,0.08535,0.99318,0.86444,0.2722,0.50248,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74542,SRR23824402,SRX19646176,SRS17013986,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 1 dpi replicate 2,GSM7092939,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 1 dpi replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092939,GSM7092939: liver 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092939 r1,GSM7092939,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Liver-2_S15_L003_R1_001.fastq.gz 1dpi-Liver-2_S15_L003_R2_001.fastq.gz,fastq fastq,4043460452.0,34266614.0,GSM7092939 r3,0:28 1:90,A:1113324543;C:946991884;G:974101052;T:1008961554;N:81419,28,90,,,1113324543,946991884,974101052,1008961554,81419,SRX19646176,SRS17013986,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00748,0.93039,0.00169,0.08606,0.99289,0.86716,0.29448,0.51523,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74543,SRR23824403,SRX19646176,SRS17013986,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 1 dpi replicate 2,GSM7092939,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 1 dpi replicate 2,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092939,GSM7092939: liver 1 dpi replicate 2; Danio rerio; RNA Seq,GSM7092939 r1,GSM7092939,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Liver-2_S15_L004_R1_001.fastq.gz 1dpi-Liver-2_S15_L004_R2_001.fastq.gz,fastq fastq,3977097134.0,33704213.0,GSM7092939 r4,0:28 1:90,A:1096872592;C:930325395;G:956420114;T:993402280;N:76753,28,90,,,1096872592,930325395,956420114,993402280,76753,SRX19646176,SRS17013986,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00756,0.93049,0.00182,0.08655,0.99354,0.86488,0.29659,0.50942,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74552,SRR23824392,SRX19646173,SRS17013982,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 1 dpi replicate 1,GSM7092938,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 1 dpi replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092938,GSM7092938: liver 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092938 r1,GSM7092938,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Liver-1_S11_L001_R1_001.fastq.gz 1dpi-Liver-1_S11_L001_R2_001.fastq.gz,fastq fastq,4161718400.0,35268800.0,GSM7092938 r1,0:28 1:90,A:1156237978;C:969526154;G:993733251;T:1042125334;N:95683,28,90,,,1156237978,969526154,993733251,1042125334,95683,SRX19646173,SRS17013982,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00742,0.93962,0.00193,0.08534,0.99405,0.86931,0.28289,0.47838,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74553,SRR23824393,SRX19646173,SRS17013982,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 1 dpi replicate 1,GSM7092938,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 1 dpi replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092938,GSM7092938: liver 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092938 r1,GSM7092938,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Liver-1_S11_L002_R1_001.fastq.gz 1dpi-Liver-1_S11_L002_R2_001.fastq.gz,fastq fastq,4194311652.0,35545014.0,GSM7092938 r2,0:28 1:90,A:1164793350;C:977205946;G:1001366769;T:1050855725;N:89862,28,90,,,1164793350,977205946,1001366769,1050855725,89862,SRX19646173,SRS17013982,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.0076,0.9407,0.0018,0.08601,0.99389,0.86831,0.256,0.50037,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74554,SRR23824400,SRX19646173,SRS17013982,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 1 dpi replicate 1,GSM7092938,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 1 dpi replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092938,GSM7092938: liver 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092938 r1,GSM7092938,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Liver-1_S11_L003_R1_001.fastq.gz 1dpi-Liver-1_S11_L003_R2_001.fastq.gz,fastq fastq,4236970186.0,35906527.0,GSM7092938 r3,0:28 1:90,A:1175860194;C:987702516;G:1012476545;T:1060846608;N:84323,28,90,,,1175860194,987702516,1012476545,1060846608,84323,SRX19646173,SRS17013982,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00758,0.94031,0.00187,0.08613,0.99381,0.86819,0.28494,0.50439,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System 74555,SRR23824401,SRX19646173,SRS17013982,SRP426909,PRJNA943553,Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish],GSE227190,Transcriptome Analysis,Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.,parent bioproject:PRJNA943547,pubmed:39627536,,liver 1 dpi replicate 1,GSM7092938,,source name:Liver|tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,liver 1 dpi replicate 1,Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.,Liver,Heart cryoinjury or untreated,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,Standard zebrafish husbandry protocol.,tissue:Liver|cell type:whole organ|genotype:wild type|treatment:Heart cryoinjury,GSM7092938,GSM7092938: liver 1 dpi replicate 1; Danio rerio; RNA Seq,GSM7092938 r1,GSM7092938,1,Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM Library & Gel Bead Kit v3 and Chromium Single Cell B Chip Kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP426909,,loader:fastq load.py,1dpi-Liver-1_S11_L004_R1_001.fastq.gz 1dpi-Liver-1_S11_L004_R2_001.fastq.gz,fastq fastq,4158915900.0,35245050.0,GSM7092938 r4,0:28 1:90,A:1156072890;C:968215633;G:991941070;T:1042607465;N:78842,28,90,,,1156072890,968215633,991941070,1042607465,78842,SRX19646173,SRS17013982,SRA1603354,"Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine","Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine",2,0.00789,0.9395,0.00206,0.08611,0.99352,0.86963,0.28343,0.50985,28,90,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2023-03-12,Undetermined,Undetermined,Liver,Liver and Biliary System