{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.platform = \"ILLUMINA\", technology = \"10x\" and tissue_curation = \"Liver\"", "rows": [[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.", null, "pubmed:40480975", null, "Liver PHx 11dpi", "GSM8403320", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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", null, null, null, null, null, null, null, null, null, null, null, "SRX25365557", "SRS22031297", "SRA1926595", "Regeneration and Stress Biology, IRIBHM, ULB", "Regeneration and Stress Biology, IRIBHM, ULB", 1, 0.92123, null, 0.07848, null, 0.87767, null, 0.63307, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 11dpi", "GSM8403320", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07901, null, 0.87805, null, 0.61529, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 11dpi", "GSM8403320", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07848, null, 0.87815, null, 0.62057, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 11dpi", "GSM8403320", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07821, null, 0.87941, null, 0.63528, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 4dpi", "GSM8403319", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07861, null, 0.82518, null, 0.61746, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 4dpi", "GSM8403319", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07975, null, 0.82599, null, 0.6186, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 4dpi", "GSM8403319", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07865, null, 0.82605, null, 0.61088, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 4dpi", "GSM8403319", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07894, null, 0.82509, null, 0.60912, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 9dppa", "GSM8403318", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.05435, null, 0.86983, null, 0.62046, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 9dppa", "GSM8403318", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.05332, null, 0.87, null, 0.61803, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 9dppa", "GSM8403318", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.0541, null, 0.87046, null, 0.61388, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 9dppa", "GSM8403318", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.05422, null, 0.86949, null, 0.6266, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07482, null, 0.81925, null, 0.57693, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07497, null, 0.81763, null, 0.58245, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07544, null, 0.81675, null, 0.57597, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07513, null, 0.81546, null, 0.58099, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07524, null, 0.81479, null, 0.57882, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07246, null, 0.81696, null, 0.50066, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07402, null, 0.82035, null, 0.58114, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07454, null, 0.8199, null, 0.57856, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07832, null, 0.83207, null, 0.59038, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.08084, null, 0.83181, null, 0.58855, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07874, null, 0.83321, null, 0.5933, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07899, null, 0.83246, null, 0.59733, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07869, null, 0.83274, null, 0.59327, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07865, null, 0.83435, null, 0.60287, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07706, null, 0.83311, null, 0.58482, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07908, null, 0.83368, null, 0.59597, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07462, null, 0.81168, null, 0.58593, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07425, null, 0.81251, null, 0.56065, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07425, null, 0.81085, null, 0.58414, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07514, null, 0.80862, null, 0.57745, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07612, null, 0.80862, null, 0.5708, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07597, null, 0.80937, null, 0.5877, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07665, null, 0.80876, null, 0.57512, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07653, null, 0.80803, null, 0.57631, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09448, null, 0.83725, null, 0.60089, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.0931, null, 0.83621, null, 0.60089, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09293, null, 0.83605, null, 0.59853, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09437, null, 0.83611, null, 0.58915, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09581, null, 0.83591, null, 0.59709, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09528, null, 0.8352, null, 0.60535, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09426, null, 0.83867, null, 0.53757, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include  introns\u201d 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", null, "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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s 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\u2019 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C 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 \u03bcm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M  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 \u00b5m 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/\u00b5l 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\u2014involving fragmentation  dA tailing  adapter ligation  and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09343, null, 0.83704, null, 0.59688, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2024-07-17", "Undetermined", "Larval", "Liver", "Liver and Biliary System"], [55196, "SRR10153191", "SRX6878621", "SRS5414403", "SRP222786", "PRJNA573063", "Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137784", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "NoHCC [Single cell]", "GSM4087821", null, "tissue:Liver|transgenic line:Tgfabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC", "NoHCC [Single cell]", "10x Genomics\u2019 Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp  FASTQ files. Custom transgenic genomic reference was built with \u2018cellranger mkref\u2019  but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with \u2018cellranger mkgtf\u2019 for gene biotypes matching \u2018protein coding\u2019  \u2018lincRNA\u2019 and \u2018antisense\u2019 tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with \u2018cellranger count\u2019 pipeline with their respective transgenic genome build with parameter \u2018  expect cells=3000\u2019 In attempt to recover those perhaps lower quality GEM partitions  the raw gene barcode matrices from \u2018cellranger count\u2019 located in \u2018outs/raw gene bc matrices\u2019 was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al.  2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells  while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al.  2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al.  2008. Cells with extremely low UMI counts  extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally  cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells suspected of being low quality were removed from downstream analysis. Genome build: GRCz11 Supplementary files format and content: MTX", "Liver", "Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank\u2019s Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with 3\u2019 chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC", "GSM4087821", "GSM4087821: NoHCC [Single cell]; Danio rerio; RNA Seq", "GSM4087821", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with three prime chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "GEO Accession:GSM4087821", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP222786", null, null, "15547X4_S11_L007_R2_001.fastq.gz 15547X4_S11_L007_R1_001.fastq.gz", "fastq fastq", 16861988178.0, 133825303.0, "GSM4087821 r1", "0:26 1:100", "A:4788108995;C:3905645218;G:3694064311;T:4468647482;N:5522172", 26, 100, null, null, 4788108995, 3905645218, 3694064311, 4468647482, 5522172, "SRX6878621", "SRS5414403", "SRA965504", "GEO", "Pathology, University of California, San Francisco", 2, 0.00236, 0.93017, 0.0008, 0.04645, 0.99626, 0.89043, 0.52233, 0.64352, 26, 100, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55197, "SRR10153190", "SRX6878620", "SRS5414402", "SRP222786", "PRJNA573063", "Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137784", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "HCCCreLox [Single cell]", "GSM4087820", null, "tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "HCCCreLox [Single cell]", "10x Genomics\u2019 Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp  FASTQ files. Custom transgenic genomic reference was built with \u2018cellranger mkref\u2019  but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with \u2018cellranger mkgtf\u2019 for gene biotypes matching \u2018protein coding\u2019  \u2018lincRNA\u2019 and \u2018antisense\u2019 tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with \u2018cellranger count\u2019 pipeline with their respective transgenic genome build with parameter \u2018  expect cells=3000\u2019 In attempt to recover those perhaps lower quality GEM partitions  the raw gene barcode matrices from \u2018cellranger count\u2019 located in \u2018outs/raw gene bc matrices\u2019 was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al.  2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells  while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al.  2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al.  2008. Cells with extremely low UMI counts  extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally  cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells suspected of being low quality were removed from downstream analysis. Genome build: GRCz11 Supplementary files format and content: MTX", "Liver", "Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank\u2019s Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with 3\u2019 chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "GSM4087820", "GSM4087820: HCCCreLox [Single cell]; Danio rerio; RNA Seq", "GSM4087820", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with three prime chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "GEO Accession:GSM4087820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP222786", null, null, "15547X2_S9_L006_R1_001.fastq.gz 15547X2_S9_L006_R2_001.fastq.gz", "fastq fastq", 16758654318.0, 133005193.0, "GSM4087820 r1", "0:26 1:100", "A:4758015356;C:3904784528;G:3787834220;T:4302283542;N:5736672", 26, 100, null, null, 4758015356, 3904784528, 3787834220, 4302283542, 5736672, "SRX6878620", "SRS5414402", "SRA965504", "GEO", "Pathology, University of California, San Francisco", 2, 0.00291, 0.94432, 0.00084, 0.04281, 0.99539, 0.88203, 0.48041, 0.60684, 26, 100, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55198, "SRR10153189", "SRX6878619", "SRS5414401", "SRP222786", "PRJNA573063", "Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137784", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "HCCHepABC [Single cell]", "GSM4087819", null, "tissue:Liver|transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:N1|diagnosis:HCC", "HCCHepABC [Single cell]", "10x Genomics\u2019 Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp  FASTQ files. Custom transgenic genomic reference was built with \u2018cellranger mkref\u2019  but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with \u2018cellranger mkgtf\u2019 for gene biotypes matching \u2018protein coding\u2019  \u2018lincRNA\u2019 and \u2018antisense\u2019 tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with \u2018cellranger count\u2019 pipeline with their respective transgenic genome build with parameter \u2018  expect cells=3000\u2019 In attempt to recover those perhaps lower quality GEM partitions  the raw gene barcode matrices from \u2018cellranger count\u2019 located in \u2018outs/raw gene bc matrices\u2019 was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al.  2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells  while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al.  2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al.  2008. Cells with extremely low UMI counts  extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally  cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells suspected of being low quality were removed from downstream analysis. Genome build: GRCz11 Supplementary files format and content: MTX", "Liver", "Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank\u2019s Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with 3\u2019 chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a pt beta catenin|age:6 mpf at larval stg:N1|diagnosis:HCC", "GSM4087819", "GSM4087819: HCCHepABC [Single cell]; Danio rerio; RNA Seq", "GSM4087819", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with three prime chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "GEO Accession:GSM4087819", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP222786", null, null, "15547X1_S8_L006_R1_001.fastq.gz 15547X1_S8_L006_R2_001.fastq.gz", "fastq fastq", 21400430184.0, 169844684.0, "GSM4087819 r1", "0:26 1:100", "A:6081828690;C:4958144407;G:4770562017;T:5582605586;N:7289484", 26, 100, null, null, 6081828690, 4958144407, 4770562017, 5582605586, 7289484, "SRX6878619", "SRS5414401", "SRA965504", "GEO", "Pathology, University of California, San Francisco", 2, 0.00253, 0.93502, 0.00092, 0.06641, 0.99624, 0.88164, 0.50505, 0.61652, 26, 100, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-20", "Adult", "Adult", "Liver", "Liver and Biliary System"], [59288, "SRR11806492", "SRX8357870", "SRS6673976", "SRP262133", "PRJNA633496", "Single cell sequencing reveals heterogeneity effects of arsenic or/and 2 2 dichloroacetamide on zebrafish liver", "GSE150751", "Transcriptome Analysis", "Arsenic and DBPs has been found to be one of the major risk in many regions of the world. However  current understanding of thier combined toxicities are unclear. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 13563 liver cells obtained from zebrafishes exposed to 100\u00b5g/L arsenic  300\u00b5g/L dichloroacetanilide DCAcAm and co exposure for 23 days. Five liver cell populations were identified. We found that the hepatocytes and macrophages were the main target of arsenic and DCAcAm exposure. And the hepatocytes of male and female showed a huge difference  when expsoure to arsenic and DCAcAm. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish liver exposure to arsenic and DCAcAm.", null, null, null, "As Dc", "GSM4558083", null, "source name:liver cells|tissue:liver single cell suspension|age:16 wpf|exposed pollutants:100ug/L arsenic and 300ug/L DCAcAm", "As Dc", "We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix", "liver cells", "Exposure solutions were prepared by adding 100\u03bcg/L arsenic  300\u03bcg/L DCAcAm or both of them to culture water. The exposure solution were was replaced every 2 days.  post 23 d exposure  zebrafish were collected and liver were rapidly extracted on ice.", "The isolated liver tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3\u2019 Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer\u2019s protocol. Libraries were sequenced on an Illumina Hiseq PE150.", null, "tissue:liver single cell suspension|age:16 wpf|exposed pollutants:100ug/L arsenic and 300ug/L DCAcAm", "GSM4558083", "GSM4558083: As Dc; Danio rerio; RNA Seq", "GSM4558083", null, "1", "The isolated liver tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.", "GEO Accession:GSM4558083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP262133", null, null, "As_Dc_1.fq.gz As_Dc_2.fq.gz", "fastq fastq", 115893045000.0, 386310150.0, "GSM4558083 r1", "0:150 1:150", "A:28430544743;C:22114323875;G:34731304363;T:30590487752;N:26384267", 150, 150, null, null, 28430544743, 22114323875, 34731304363, 30590487752, 26384267, "SRX8357870", "SRS6673976", "SRA1076689", "GEO", "Nanjing University", 2, 0.0, 0.91666, 0.0, 0.0203, 1.0, 0.91291, null, 0.46748, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-05-18", "Adult", "Adult", "Liver", "Liver and Biliary System"], [59289, "SRR11806491", "SRX8357869", "SRS6673975", "SRP262133", "PRJNA633496", "Single cell sequencing reveals heterogeneity effects of arsenic or/and 2 2 dichloroacetamide on zebrafish liver", "GSE150751", "Transcriptome Analysis", "Arsenic and DBPs has been found to be one of the major risk in many regions of the world. However  current understanding of thier combined toxicities are unclear. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 13563 liver cells obtained from zebrafishes exposed to 100\u00b5g/L arsenic  300\u00b5g/L dichloroacetanilide DCAcAm and co exposure for 23 days. Five liver cell populations were identified. We found that the hepatocytes and macrophages were the main target of arsenic and DCAcAm exposure. And the hepatocytes of male and female showed a huge difference  when expsoure to arsenic and DCAcAm. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish liver exposure to arsenic and DCAcAm.", null, null, null, "Dc300", "GSM4558082", null, "source name:liver cells|tissue:liver single cell suspension|age:16 wpf|exposed pollutants:300ug/L DCAcAm", "Dc300", "We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix", "liver cells", "Exposure solutions were prepared by adding 100\u03bcg/L arsenic  300\u03bcg/L DCAcAm or both of them to culture water. The exposure solution were was replaced every 2 days.  post 23 d exposure  zebrafish were collected and liver were rapidly extracted on ice.", "The isolated liver tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3\u2019 Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer\u2019s protocol. Libraries were sequenced on an Illumina Hiseq PE150.", null, "tissue:liver single cell suspension|age:16 wpf|exposed pollutants:300ug/L DCAcAm", "GSM4558082", "GSM4558082: Dc300; Danio rerio; RNA Seq", "GSM4558082", null, "1", "The isolated liver tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.", "GEO Accession:GSM4558082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP262133", null, null, "Dc300_1.fq.gz Dc300_2.fq.gz", "fastq fastq", 127027640400.0, 423425468.0, "GSM4558082 r1", "0:150 1:150", "A:30842125524;C:23778726057;G:39107636584;T:33274935260;N:24216975", 150, 150, null, null, 30842125524, 23778726057, 39107636584, 33274935260, 24216975, "SRX8357869", "SRS6673975", "SRA1076689", "GEO", "Nanjing University", 2, 0.0, 0.91236, 0.0, 0.02333, 1.0, 0.90879, null, 0.42849, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-05-18", "Adult", "Adult", "Liver", "Liver and Biliary System"], [59290, "SRR11806490", "SRX8357868", "SRS6673977", "SRP262133", "PRJNA633496", "Single cell sequencing reveals heterogeneity effects of arsenic or/and 2 2 dichloroacetamide on zebrafish liver", "GSE150751", "Transcriptome Analysis", "Arsenic and DBPs has been found to be one of the major risk in many regions of the world. However  current understanding of thier combined toxicities are unclear. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 13563 liver cells obtained from zebrafishes exposed to 100\u00b5g/L arsenic  300\u00b5g/L dichloroacetanilide DCAcAm and co exposure for 23 days. Five liver cell populations were identified. We found that the hepatocytes and macrophages were the main target of arsenic and DCAcAm exposure. And the hepatocytes of male and female showed a huge difference  when expsoure to arsenic and DCAcAm. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish liver exposure to arsenic and DCAcAm.", null, null, null, "As100", "GSM4558081", null, "source name:liver cells|tissue:liver single cell suspension|age:16 wpf|exposed pollutants:100ug/L arsenic", "As100", "We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix", "liver cells", "Exposure solutions were prepared by adding 100\u03bcg/L arsenic  300\u03bcg/L DCAcAm or both of them to culture water. The exposure solution were was replaced every 2 days.  post 23 d exposure  zebrafish were collected and liver were rapidly extracted on ice.", "The isolated liver tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3\u2019 Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer\u2019s protocol. Libraries were sequenced on an Illumina Hiseq PE150.", null, "tissue:liver single cell suspension|age:16 wpf|exposed pollutants:100ug/L arsenic", "GSM4558081", "GSM4558081: As100; Danio rerio; RNA Seq", "GSM4558081", null, "1", "The isolated liver tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.", "GEO Accession:GSM4558081", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP262133", null, null, "As100_2.fq.gz As100_1.fq.gz", "fastq fastq", 102837948900.0, 342793163.0, "GSM4558081 r1", "0:150 1:150", "A:24894384372;C:19593836618;G:31314101265;T:27014778377;N:20848268", 150, 150, null, null, 24894384372, 19593836618, 31314101265, 27014778377, 20848268, "SRX8357868", "SRS6673977", "SRA1076689", "GEO", "Nanjing University", 2, 0.0, 0.91738, 0.0, 0.02836, 1.0, 0.89536, null, 0.46528, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-05-18", "Adult", "Adult", "Liver", "Liver and Biliary System"], [59291, "SRR11806489", "SRX8357867", "SRS6673974", "SRP262133", "PRJNA633496", "Single cell sequencing reveals heterogeneity effects of arsenic or/and 2 2 dichloroacetamide on zebrafish liver", "GSE150751", "Transcriptome Analysis", "Arsenic and DBPs has been found to be one of the major risk in many regions of the world. However  current understanding of thier combined toxicities are unclear. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 13563 liver cells obtained from zebrafishes exposed to 100\u00b5g/L arsenic  300\u00b5g/L dichloroacetanilide DCAcAm and co exposure for 23 days. Five liver cell populations were identified. We found that the hepatocytes and macrophages were the main target of arsenic and DCAcAm exposure. And the hepatocytes of male and female showed a huge difference  when expsoure to arsenic and DCAcAm. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish liver exposure to arsenic and DCAcAm.", null, null, null, "CK", "GSM4558080", null, "source name:liver cells|tissue:liver single cell suspension|age:16 wpf|exposed pollutants:n1", "CK", "We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix", "liver cells", "Exposure solutions were prepared by adding 100\u03bcg/L arsenic  300\u03bcg/L DCAcAm or both of them to culture water. The exposure solution were was replaced every 2 days.  post 23 d exposure  zebrafish were collected and liver were rapidly extracted on ice.", "The isolated liver tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3\u2019 Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer\u2019s protocol. Libraries were sequenced on an Illumina Hiseq PE150.", null, "tissue:liver single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM4558080", "GSM4558080: CK; Danio rerio; RNA Seq", "GSM4558080", null, "1", "The isolated liver tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.", "GEO Accession:GSM4558080", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP262133", null, null, "CK_1.fq.gz CK_2.fq.gz", "fastq fastq", 133916231400.0, 446387438.0, "GSM4558080 r1", "0:150 1:150", "A:32477145943;C:25399997371;G:40326238358;T:35690408393;N:22441335", 150, 150, null, null, 32477145943, 25399997371, 40326238358, 35690408393, 22441335, "SRX8357867", "SRS6673974", "SRA1076689", "GEO", "Nanjing University", 2, 0.0, 0.91836, 0.0, 0.02382, 1.0, 0.90871, null, 0.46105, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2020-05-18", "Adult", "Adult", "Liver", "Liver and Biliary System"], [65633, "SRR15427704", "SRX11729087", "SRS9757823", "SRP332278", "PRJNA754150", "Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver", "GSE181987", "Other", "Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "MPI MT 3", "GSM5515736", null, "source name:Adult zebrafish liver dissection|genotype:mpi+/  mss7|tissue:Liver", "MPI MT 3", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:mpi+/  mss7|tissue:Liver", "GSM5515736", "GSM5515736: MPI MT 3; Danio rerio; RNA Seq", "GSM5515736", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "GEO Accession:GSM5515736", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP332278", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JACH01 MT5 0 G S8 L001 I1 001.fastq.gz   read2PairFiles=JACH01 MT5 0 G S8 L001 R1 001.fastq.gz   read3PairFiles=JACH01 MT5 0 G S8 L001 R2 001.fastq.gz", "JACH01_MT5_0_G_S8_L001_I1_001.fastq.gz JACH01_MT5_0_G_S8_L001_R1_001.fastq.gz JACH01_MT5_0_G_S8_L001_R2_001.fastq.gz", "fastq fastq fastq", 12954775700.0, 129547757.0, "GSM5515736 r1", "0:8 1:30 2:62", "A:2373305749;C:1813473007;G:1779922398;T:2065049504;N:210276", 8, 30, 62, null, 2373305749, 1813473007, 1779922398, 2065049504, 210276, "SRX11729087", "SRS9757823", "SRA1277309", "GEO", "Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai", 1, 0.94564, null, 0.06912, null, 0.88712, null, 0.74857, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [65634, "SRR15427705", "SRX11729087", "SRS9757823", "SRP332278", "PRJNA754150", "Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver", "GSE181987", "Other", "Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "MPI MT 3", "GSM5515736", null, "source name:Adult zebrafish liver dissection|genotype:mpi+/  mss7|tissue:Liver", "MPI MT 3", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:mpi+/  mss7|tissue:Liver", "GSM5515736", "GSM5515736: MPI MT 3; Danio rerio; RNA Seq", "GSM5515736", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "GEO Accession:GSM5515736", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP332278", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JACH01 MT5 0 G S8 L002 I1 001.fastq.gz   read2PairFiles=JACH01 MT5 0 G S8 L002 R1 001.fastq.gz   read3PairFiles=JACH01 MT5 0 G S8 L002 R2 001.fastq.gz", "JACH01_MT5_0_G_S8_L002_I1_001.fastq.gz JACH01_MT5_0_G_S8_L002_R1_001.fastq.gz JACH01_MT5_0_G_S8_L002_R2_001.fastq.gz", "fastq fastq fastq", 12966987200.0, 129669872.0, "GSM5515736 r2", "0:8 1:30 2:62", "A:2375412279;C:1814593036;G:1781329886;T:2068062113;N:134750", 8, 30, 62, null, 2375412279, 1814593036, 1781329886, 2068062113, 134750, "SRX11729087", "SRS9757823", "SRA1277309", "GEO", "Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai", 1, 0.94477, null, 0.06799, null, 0.88929, null, 0.75006, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [65635, "SRR15427702", "SRX11729086", "SRS9757824", "SRP332278", "PRJNA754150", "Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver", "GSE181987", "Other", "Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "MPI MT 2", "GSM5515735", null, "source name:Adult zebrafish liver dissection|genotype:mpi+/  mss7|tissue:Liver", "MPI MT 2", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:mpi+/  mss7|tissue:Liver", "GSM5515735", "GSM5515735: MPI MT 2; Danio rerio; RNA Seq", "GSM5515735", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "GEO Accession:GSM5515735", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP332278", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JACH01 MT4 0 G S7 L001 I1 001.fastq.gz   read2PairFiles=JACH01 MT4 0 G S7 L001 R1 001.fastq.gz   read3PairFiles=JACH01 MT4 0 G S7 L001 R2 001.fastq.gz", "JACH01_MT4_0_G_S7_L001_I1_001.fastq.gz JACH01_MT4_0_G_S7_L001_R1_001.fastq.gz JACH01_MT4_0_G_S7_L001_R2_001.fastq.gz", "fastq fastq fastq", 13930172400.0, 139301724.0, "GSM5515735 r1", "0:8 1:30 2:62", "A:2520150103;C:1968356587;G:1962290731;T:2185685805;N:223662", 8, 30, 62, null, 2520150103, 1968356587, 1962290731, 2185685805, 223662, "SRX11729086", "SRS9757824", "SRA1277309", "GEO", "Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai", 1, 0.94376, null, 0.0702, null, 0.88233, null, 0.66983, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [65636, "SRR15427703", "SRX11729086", "SRS9757824", "SRP332278", "PRJNA754150", "Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver", "GSE181987", "Other", "Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "MPI MT 2", "GSM5515735", null, "source name:Adult zebrafish liver dissection|genotype:mpi+/  mss7|tissue:Liver", "MPI MT 2", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:mpi+/  mss7|tissue:Liver", "GSM5515735", "GSM5515735: MPI MT 2; Danio rerio; RNA Seq", "GSM5515735", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "GEO Accession:GSM5515735", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP332278", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JACH01 MT4 0 G S7 L002 I1 001.fastq.gz   read2PairFiles=JACH01 MT4 0 G S7 L002 R1 001.fastq.gz   read3PairFiles=JACH01 MT4 0 G S7 L002 R2 001.fastq.gz", "JACH01_MT4_0_G_S7_L002_I1_001.fastq.gz JACH01_MT4_0_G_S7_L002_R1_001.fastq.gz JACH01_MT4_0_G_S7_L002_R2_001.fastq.gz", "fastq fastq fastq", 13953736500.0, 139537365.0, "GSM5515735 r2", "0:8 1:30 2:62", "A:2524408821;C:1970748229;G:1965304712;T:2190710041;N:144827", 8, 30, 62, null, 2524408821, 1970748229, 1965304712, 2190710041, 144827, "SRX11729086", "SRS9757824", "SRA1277309", "GEO", "Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai", 1, 0.94393, null, 0.07007, null, 0.8827, null, 0.67588, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [65637, "SRR15427700", "SRX11729085", "SRS9757822", "SRP332278", "PRJNA754150", "Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver", "GSE181987", "Other", "Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "MPI MT 1", "GSM5515734", null, "source name:Adult zebrafish liver dissection|genotype:mpi+/  mss7|tissue:Liver", "MPI MT 1", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:mpi+/  mss7|tissue:Liver", "GSM5515734", "GSM5515734: MPI MT 1; Danio rerio; RNA Seq", "GSM5515734", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. 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The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "MPI MT 1", "GSM5515734", null, "source name:Adult zebrafish liver dissection|genotype:mpi+/  mss7|tissue:Liver", "MPI MT 1", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:mpi+/  mss7|tissue:Liver", "GSM5515734", "GSM5515734: MPI MT 1; Danio rerio; RNA Seq", "GSM5515734", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. 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The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "WT 3", "GSM5515733", null, "source name:Adult zebrafish liver dissection|genotype:WT|tissue:Liver", "WT 3", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:WT|tissue:Liver", "GSM5515733", "GSM5515733: WT 3; Danio rerio; RNA Seq", "GSM5515733", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. 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The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "WT 3", "GSM5515733", null, "source name:Adult zebrafish liver dissection|genotype:WT|tissue:Liver", "WT 3", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:WT|tissue:Liver", "GSM5515733", "GSM5515733: WT 3; Danio rerio; RNA Seq", "GSM5515733", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. 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The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "WT 2", "GSM5515732", null, "source name:Adult zebrafish liver dissection|genotype:WT|tissue:Liver", "WT 2", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:WT|tissue:Liver", "GSM5515732", "GSM5515732: WT 2; Danio rerio; RNA Seq", "GSM5515732", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. 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The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "WT 2", "GSM5515732", null, "source name:Adult zebrafish liver dissection|genotype:WT|tissue:Liver", "WT 2", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:WT|tissue:Liver", "GSM5515732", "GSM5515732: WT 2; Danio rerio; RNA Seq", "GSM5515732", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "GEO Accession:GSM5515732", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP332278", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JACH01 WT4 0 G S4 L002 I1 001.fastq.gz   read2PairFiles=JACH01 WT4 0 G S4 L002 R1 001.fastq.gz   read3PairFiles=JACH01 WT4 0 G S4 L002 R2 001.fastq.gz", "JACH01_WT4_0_G_S4_L002_I1_001.fastq.gz JACH01_WT4_0_G_S4_L002_R1_001.fastq.gz JACH01_WT4_0_G_S4_L002_R2_001.fastq.gz", "fastq fastq fastq", 14869012700.0, 148690127.0, "GSM5515732 r2", "0:8 1:30 2:62", "A:2762560965;C:2138448212;G:2021327816;T:2296295190;N:155691", 8, 30, 62, null, 2762560965, 2138448212, 2021327816, 2296295190, 155691, "SRX11729083", "SRS9757821", "SRA1277309", "GEO", "Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai", 1, 0.94954, null, 0.05588, null, 0.89438, null, 0.75111, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [65643, "SRR15427694", "SRX11729082", "SRS9757819", "SRP332278", "PRJNA754150", "Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver", "GSE181987", "Other", "Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "WT 1", "GSM5515731", null, "source name:Adult zebrafish liver dissection|genotype:WT|tissue:Liver", "WT 1", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:WT|tissue:Liver", "GSM5515731", "GSM5515731: WT 1; Danio rerio; RNA Seq", "GSM5515731", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "GEO Accession:GSM5515731", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP332278", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JACH01 WT2 0 G S3 L001 I1 001.fastq.gz   read2PairFiles=JACH01 WT2 0 G S3 L001 R1 001.fastq.gz   read3PairFiles=JACH01 WT2 0 G S3 L001 R2 001.fastq.gz", "JACH01_WT2_0_G_S3_L001_I1_001.fastq.gz JACH01_WT2_0_G_S3_L001_R1_001.fastq.gz JACH01_WT2_0_G_S3_L001_R2_001.fastq.gz", "fastq fastq fastq", 14974124300.0, 149741243.0, "GSM5515731 r1", "0:8 1:30 2:62", "A:2755810823;C:2157907927;G:2041659391;T:2328338949;N:239976", 8, 30, 62, null, 2755810823, 2157907927, 2041659391, 2328338949, 239976, "SRX11729082", "SRS9757819", "SRA1277309", "GEO", "Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai", 1, 0.9462, null, 0.05451, null, 0.89832, null, 0.7809, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [65644, "SRR15427695", "SRX11729082", "SRS9757819", "SRP332278", "PRJNA754150", "Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver", "GSE181987", "Other", "Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs  the driver cell in liver fibrosis  specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel  conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis  we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early  progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver  highlights the high degree of similarity to the human liver  and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/  mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset   GSM5515731 GSM5515736 zf WT MPIMT liver   GSM5515731 GSM5515736 zf liver atlas   GSM5515731 GSM5515733 joint fish human   GSM5515731 GSM5515733 as well as data from GSE115469 samples GSM317872 317876. and the description of each file is provided in the readme.txt.", null, "pubmed:35315595", null, "WT 1", "GSM5515731", null, "source name:Adult zebrafish liver dissection|genotype:WT|tissue:Liver", "WT 1", "FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d output UMI matrices of CellRanger Genome build: danRer11", "Adult zebrafish liver dissection", null, "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "Adult fish were maintained on a 14:10 light/dark cycle at 28\u00b0C.", "genotype:WT|tissue:Liver", "GSM5515731", "GSM5515731: WT 1; Danio rerio; RNA Seq", "GSM5515731", null, "1", "Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium", "GEO Accession:GSM5515731", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP332278", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JACH01 WT2 0 G S3 L002 I1 001.fastq.gz   read2PairFiles=JACH01 WT2 0 G S3 L002 R1 001.fastq.gz   read3PairFiles=JACH01 WT2 0 G S3 L002 R2 001.fastq.gz", "JACH01_WT2_0_G_S3_L002_I1_001.fastq.gz JACH01_WT2_0_G_S3_L002_R1_001.fastq.gz JACH01_WT2_0_G_S3_L002_R2_001.fastq.gz", "fastq fastq fastq", 14981913300.0, 149819133.0, "GSM5515731 r2", "0:8 1:30 2:62", "A:2757221756;C:2158264290;G:2042268570;T:2330874969;N:156661", 8, 30, 62, null, 2757221756, 2158264290, 2042268570, 2330874969, 156661, "SRX11729082", "SRS9757819", "SRA1277309", "GEO", "Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai", 1, 0.94701, null, 0.05368, null, 0.89591, null, 0.57205, null, 62, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-08-12", "Adult", "Adult", "Liver", "Liver and Biliary System"], [67832, "SRR17375072", "SRX13549231", "SRS11443005", "SRP352824", "PRJNA793009", "Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells", "GSE192740", "Other", "Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver", "parent bioproject:PRJNA793005", "pubmed:35021063;pubmed:36304458", null, "Zebrafish 002 Whole Liver Cells Zebrafish", "GSM5764413", null, "tissue:Liver|shortfilename:CS131|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1241", "Zebrafish 002 Whole Liver Cells Zebrafish", "Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene \u2013 and if present \u2013 antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object", "Liver", null, "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.", null, "shortfilename:CS131|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1241", "GSM5764413", "GSM5764413: Zebrafish 002 Whole Liver Cells Zebrafish; Danio rerio; RNA Seq", "GSM5764413", null, "1", "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.", "GEO Accession:GSM5764413", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352824", null, null, "CS131_R1.fastq.gz CS131_R2.fastq.gz", "fastq fastq", 27410113115.0, 230337085.0, "GSM5764413 r1", "0:28 1:91", "A:7502899227;C:6375936516;G:6281396027;T:7241238684;N:8642661", 28, 91, null, null, 7502899227, 6375936516, 6281396027, 7241238684, 8642661, "SRX13549231", "SRS11443005", "SRA1349905", "GEO", "VIB Inflammation Research Center, VIB-University of Ghent", 2, 0.00522, 0.93004, 0.00164, 0.0692, 0.99476, 0.85098, 0.48648, 0.60903, 28, 91, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2021-12-29", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [67833, "SRR17375071", "SRX13549230", "SRS11443004", "SRP352824", "PRJNA793009", "Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells", "GSE192740", "Other", "Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver", "parent bioproject:PRJNA793005", "pubmed:35021063;pubmed:36304458", null, "Zebrafish 001 Whole Liver Cells Zebrafish", "GSM5764412", null, "tissue:Liver|shortfilename:CS130|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:2256", "Zebrafish 001 Whole Liver Cells Zebrafish", "Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene \u2013 and if present \u2013 antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object", "Liver", null, "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.", null, "shortfilename:CS130|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:2256", "GSM5764412", "GSM5764412: Zebrafish 001 Whole Liver Cells Zebrafish; Danio rerio; RNA Seq", "GSM5764412", null, "1", "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.", "GEO Accession:GSM5764412", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352824", null, null, "CS130_R1.fastq.gz CS130_R2.fastq.gz", "fastq fastq", 29028764681.0, 243939199.0, "GSM5764412 r1", "0:28 1:91", "A:7990080958;C:6832189305;G:6802247428;T:7395232074;N:9014916", 28, 91, null, null, 7990080958, 6832189305, 6802247428, 7395232074, 9014916, "SRX13549230", "SRS11443004", "SRA1349905", "GEO", "VIB Inflammation Research Center, VIB-University of Ghent", 2, 0.00621, 0.93648, 0.00152, 0.07051, 0.99466, 0.85036, 0.33907, 0.45636, 28, 91, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2021-12-29", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [67834, "SRR17375070", "SRX13549229", "SRS11443003", "SRP352824", "PRJNA793009", "Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells", "GSE192740", "Other", "Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver", "parent bioproject:PRJNA793005", "pubmed:35021063;pubmed:36304458", null, "Zebrafish 002 Liver mpeg1.1+ cells Zebrafish", "GSM5764411", null, "tissue:Liver|shortfilename:CS129|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:4126", "Zebrafish 002 Liver mpeg1.1+ cells Zebrafish", "Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene \u2013 and if present \u2013 antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object", "Liver", null, "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.", null, "shortfilename:CS129|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:4126", "GSM5764411", "GSM5764411: Zebrafish 002 Liver mpeg1.1+ cells Zebrafish; Danio rerio; RNA Seq", "GSM5764411", null, "1", "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.", "GEO Accession:GSM5764411", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352824", null, null, "CS129_R1.fastq.gz CS129_R2.fastq.gz", "fastq fastq", 37123150869.0, 311959251.0, "GSM5764411 r1", "0:28 1:91", "A:10576275333;C:7976755033;G:8122940005;T:10435522767;N:11657731", 28, 91, null, null, 10576275333, 7976755033, 8122940005, 10435522767, 11657731, "SRX13549229", "SRS11443003", "SRA1349905", "GEO", "VIB Inflammation Research Center, VIB-University of Ghent", 2, 0.00585, 0.89093, 0.00199, 0.20548, 0.99269, 0.82597, 0.42801, 0.61509, 28, 91, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2021-12-29", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [67835, "SRR17375069", "SRX13549228", "SRS11443002", "SRP352824", "PRJNA793009", "Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells", "GSE192740", "Other", "Analysis of CITE seq data   Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45  cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar  from healthy and steatotic human livers  from hamster liver  pig liver  chicken liver  monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers  NAFLD mouse livers  healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45  cells derived from mice fed a standard diet SD or western diet WD; fat  cholesterol and sugar. Liver CD45+ and CD45  cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver  mouse StSt capsule  mouse NAFLD liver   human non steatotic liver  human steatotic liver", "parent bioproject:PRJNA793005", "pubmed:35021063;pubmed:36304458", null, "Zebrafish 001 Liver mpeg1.1+ cells Zebrafish", "GSM5764410", null, "tissue:Liver|shortfilename:CS128|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1229", "Zebrafish 001 Liver mpeg1.1+ cells Zebrafish", "Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse  hg19 Human  GRCz10 Zebrafish  MesAur1.0.100 Hamster  GRCg6a.96 Chicken  Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene \u2013 and if present \u2013 antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object", "Liver", null, "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.", null, "shortfilename:CS128|strain:Tgmpeg1:EGFPgl22|platform:10x Genomics \u2013 v3|digestion method:Ex Vivo|number of added abs:0|number of cells:1229", "GSM5764410", "GSM5764410: Zebrafish 001 Liver mpeg1.1+ cells Zebrafish; Danio rerio; RNA Seq", "GSM5764410", null, "1", "All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.", "GEO Accession:GSM5764410", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352824", null, null, "CS128_R1.fastq.gz CS128_R2.fastq.gz", "fastq fastq", 38316694094.0, 321989026.0, "GSM5764410 r1", "0:28 1:91", "A:10814226120;C:8293271134;G:8575797871;T:10621330197;N:12068772", 28, 91, null, null, 10814226120, 8293271134, 8575797871, 10621330197, 12068772, "SRX13549228", "SRS11443002", "SRA1349905", "GEO", "VIB Inflammation Research Center, VIB-University of Ghent", 2, 0.00626, 0.88237, 0.00215, 0.18876, 0.99249, 0.83049, 0.41451, 0.59559, 28, 91, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Belgium", "2021-12-29", "Undetermined", "Undetermined", "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.", null, null, null, null, "Liver in the WT S4 L004", null, "isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP385641", null, null, "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, null, 3860252969, 2756020453, 2781498176, 3004915512, 83695, "SRX17460721", "SRS15014532", "SRA1491985", "Southwest University|Institute of Developmental Biology and Regenerativ", "Southwest University", 1, 0.90519, null, 0.06757, null, 0.88243, null, 0.74961, null, 151, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, null, "Liver in the WT S4 L003", null, "isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP385641", null, null, "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, null, 3834498109, 2745604041, 2766967723, 2989497144, 137815, "SRX17460720", "SRS15014531", "SRA1491985", "Southwest University|Institute of Developmental Biology and Regenerativ", "Southwest University", 1, 0.90792, null, 0.06795, null, 0.88089, null, 0.75291, null, 151, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, null, "Liver in the WT S4 L002", null, "isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP385641", null, null, "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, null, 3774023536, 2701104584, 2719224706, 2945204367, 118762, "SRX17460717", "SRS15014528", "SRA1491985", "Southwest University|Institute of Developmental Biology and Regenerativ", "Southwest University", 1, 0.90993, null, 0.06896, null, 0.88002, null, 0.75003, null, 151, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, null, "Liver in the WT S4 L001", null, "isolate:wild type|dev stage:6 dpf|sex:female and male|tissue:liver|aliquot:aliquot 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "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", null, null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP385641", null, null, "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, null, 3778269770, 2702450055, 2724848747, 2944890394, 98653, "SRX17460716", "SRS15014527", "SRA1491985", "Southwest University|Institute of Developmental Biology and Regenerativ", "Southwest University", 1, 0.90977, null, 0.06799, null, 0.87998, null, 0.75241, null, 151, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2022-09-11", "Larval", "Larval", "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", null, "liver Ctrl replicate 2", "GSM7092955", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "Ctrl-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, null, null, 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", null, "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", null, "liver Ctrl replicate 2", "GSM7092955", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "Ctrl-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, null, null, 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", null, "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", null, "liver Ctrl replicate 2", "GSM7092955", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "Ctrl-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, null, null, 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", null, "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", null, "liver Ctrl replicate 2", "GSM7092955", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "Ctrl-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, null, null, 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", null, "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", null, "liver Ctrl replicate 1", "GSM7092954", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "Ctrl-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, null, null, 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", null, "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", null, "liver Ctrl replicate 1", "GSM7092954", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "Ctrl-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, null, null, 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", null, "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", null, "liver Ctrl replicate 1", "GSM7092954", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "Ctrl-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, null, null, 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", null, "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", null, "liver Ctrl replicate 1", "GSM7092954", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "Ctrl-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, null, null, 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", null, "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", null, "liver 7 dpi replicate 2", "GSM7092947", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "7dpi-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, null, null, 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", null, "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", null, "liver 7 dpi replicate 2", "GSM7092947", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "7dpi-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, null, null, 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", null, "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", null, "liver 7 dpi replicate 2", "GSM7092947", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "7dpi-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, null, null, 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", null, "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", null, "liver 7 dpi replicate 2", "GSM7092947", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "7dpi-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, null, null, 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", null, "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", null, "liver 7 dpi replicate 1", "GSM7092946", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "7dpi-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, null, null, 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", null, "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", null, "liver 7 dpi replicate 1", "GSM7092946", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "7dpi-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, null, null, 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", null, "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", null, "liver 7 dpi replicate 1", "GSM7092946", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "7dpi-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, null, null, 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", null, "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", null, "liver 7 dpi replicate 1", "GSM7092946", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "7dpi-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, null, null, 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", null, "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", null, "liver 1 dpi replicate 2", "GSM7092939", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "1dpi-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, null, null, 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", null, "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", null, "liver 1 dpi replicate 2", "GSM7092939", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "1dpi-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, null, null, 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", null, "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", null, "liver 1 dpi replicate 2", "GSM7092939", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "1dpi-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, null, null, 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", null, "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", null, "liver 1 dpi replicate 2", "GSM7092939", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "1dpi-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, null, null, 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", null, "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", null, "liver 1 dpi replicate 1", "GSM7092938", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "1dpi-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, null, null, 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", null, "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", null, "liver 1 dpi replicate 1", "GSM7092938", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "1dpi-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, null, null, 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", null, "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", null, "liver 1 dpi replicate 1", "GSM7092938", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "1dpi-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, null, null, 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", null, "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", null, "liver 1 dpi replicate 1", "GSM7092938", null, "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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", "Standard zebrafish husbandry protocol.", "tissue: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\u00b0C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum  and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4\u00b0C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4\u00b0C  the pellet was resuspended in 500 \uf06dl and filtered through a 35 mm strainer.  Whole kidney marrow cells were isolated as described previously. Briefly  kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4\u00b0C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products  and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4\u00b0C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min  pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min  the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stained with trypan blue and counted using a hemocytometer. Standard library construction protocol using 10x Genomics Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3  and Chromium Single Cell B Chip Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP426909", null, "loader:fastq load.py", "1dpi-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, null, null, 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", null, "United States", "2023-03-12", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"], [74852, "SRR24049041", "SRX19850771", "SRS17208526", "SRP430632", "PRJNA951670", "Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs", "GSE228806", "Transcriptome Analysis", "Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity  tissue regeneration  and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish  we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish  a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures  respectively  as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties.  Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish", null, "pubmed:37453064", null, "liver", "GSM7139012", null, "source name:liver|tissue:liver|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing", "liver", "Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files", "liver", null, "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "tissue:liver|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT", "GSM7139012", "GSM7139012: liver; Danio rerio; RNA Seq", "GSM7139012 r1", "GSM7139012", "1", "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430632", null, null, "liver_S1_L001_R1_001.fastq.gz liver_S1_L001_R2_001.fastq.gz", "fastq fastq", 78604332900.0, 262014443.0, "GSM7139012 r1", "0:150 1:150", "A:28430764523;C:14592565311;G:14134523628;T:21443665055;N:2814383", 150, 150, null, null, 28430764523, 14592565311, 14134523628, 21443665055, 2814383, "SRX19850771", "SRS17208526", "SRA1615101", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.0, 0.88681, 0.0, 0.20278, 1.0, 0.8268, null, 0.59667, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-03", "Adult", "Adult", "Liver", "Liver and Biliary System"], [74853, "SRR24049042", "SRX19850771", "SRS17208526", "SRP430632", "PRJNA951670", "Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs", "GSE228806", "Transcriptome Analysis", "Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity  tissue regeneration  and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish  we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish  a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures  respectively  as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties.  Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish", null, "pubmed:37453064", null, "liver", "GSM7139012", null, "source name:liver|tissue:liver|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing", "liver", "Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files", "liver", null, "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "tissue:liver|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT", "GSM7139012", "GSM7139012: liver; Danio rerio; RNA Seq", "GSM7139012 r1", "GSM7139012", "1", "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430632", null, null, "liver_S1_L002_R1_001.fastq.gz liver_S1_L002_R2_001.fastq.gz", "fastq fastq", 52853094600.0, 176176982.0, "GSM7139012 r2", "0:150 1:150", "A:19118908369;C:9845119252;G:9524330259;T:14362840318;N:1896402", 150, 150, null, null, 19118908369, 9845119252, 9524330259, 14362840318, 1896402, "SRX19850771", "SRS17208526", "SRA1615101", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.0, 0.88841, 0.0, 0.20218, 1.0, 0.82584, null, 0.62565, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-03", "Adult", "Adult", "Liver", "Liver and Biliary System"], [74854, "SRR24049043", "SRX19850771", "SRS17208526", "SRP430632", "PRJNA951670", "Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs", "GSE228806", "Transcriptome Analysis", "Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity  tissue regeneration  and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish  we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish  a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures  respectively  as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties.  Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish", null, "pubmed:37453064", null, "liver", "GSM7139012", null, "source name:liver|tissue:liver|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing", "liver", "Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files", "liver", null, "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "tissue:liver|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT", "GSM7139012", "GSM7139012: liver; Danio rerio; RNA Seq", "GSM7139012 r1", "GSM7139012", "1", "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430632", null, null, "liver_S1_L003_R1_001.fastq.gz liver_S1_L003_R2_001.fastq.gz", "fastq fastq", 46431569400.0, 154771898.0, "GSM7139012 r3", "0:150 1:150", "A:16787687066;C:8624697066;G:8355409083;T:12662108960;N:1667225", 150, 150, null, null, 16787687066, 8624697066, 8355409083, 12662108960, 1667225, "SRX19850771", "SRS17208526", "SRA1615101", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.0, 0.88677, 0.0, 0.20355, 1.0, 0.82501, null, 0.61082, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-03", "Adult", "Adult", "Liver", "Liver and Biliary System"], [74855, "SRR24049044", "SRX19850771", "SRS17208526", "SRP430632", "PRJNA951670", "Single cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity across six zebrafish organs", "GSE228806", "Transcriptome Analysis", "Tissue resident macrophages TRMs and dendritic cells DCs are highly diverse and play essential roles in immunity  tissue regeneration  and homeostasis maintenance. To systematically assess the heterogeneity of TRM and DC in adult zebrafish  we performed droplet based scRNA seq on mpeg1.1+ cells sorted from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish  a widely used myeloid cell reporter line. We identified two macrophage subpopulations with pro inflammatory and pro remodeling signatures  respectively  as well as one conventional dendritic cell population with prominent antigen presentation capacity and plasmacytoid dendritic cells featuring anti viral properties.  Our study provides a comprehensive landscape of TRMs and DCs in zebrafish and offers valuable tools for future in depth investigations of these cell types. Overall design: scRNA seq 10X genomics three prime V3.1 of FACS sorted mpeg1.1+ cells isolated from six different organs epidermis  gill  intestine  liver  heart  and brain of 6 mpf Tgmpeg1.1:DsRedx fish", null, "pubmed:37453064", null, "liver", "GSM7139012", null, "source name:liver|tissue:liver|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT|geo loc name:missing|collection date:missing", "liver", "Raw reads were aligned to zebrafish reference genome genome reference: GRCz11; annotation reference: GRCz11.103 combined with the sequences for DsRedx using the Cell Ranger pipelines v6.0. Downstream analysis of unique molecular identifiers UMI count matrix was conducted in R using the Seurat pipeline v4.0.5. Assembly: danRer11 Supplementary files format and content: Tab separated values files and matrix files", "liver", null, "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "tissue:liver|age:6 mpf|cell type:mpeg1.1+ cells|strain:Tgmpeg1.1:DsRedx|genotype:WT", "GSM7139012", "GSM7139012: liver; Danio rerio; RNA Seq", "GSM7139012 r1", "GSM7139012", "1", "For each organ  six sex balanced zebrafish were pooled together for the cell sorting and a total of 30000 DAPI mpeg1.1 DsRedx+ cells were sorted into 5 \u03bcl collection buffer 4.5 \u03bcl 1% BSA/PBS + 0.5 \u03bcl RNaseOUT using BD Influx high speed Cell Sorter BD Biosciences. scRNA seq was carried out with a 10X Chromium single cell platform 10X Genomics. In brief  post the cell sorting  single cell suspensions were prepared according to the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide and loaded onto the 10x Chromium Single Cell Controller to generate single cell Gel Beads in emulsion GEMs. Libraries were prepared using Chromium Single Cell three prime GEM  Library & Gel Bead Kit v3.1 according to the manufacturer's instructions. Library quality was assessed using an Agilent Fragment Analyzer System  followed by sequencing on Illumina Novaseq 6000 system Illumina for a targeting average depth of around 100 000 read pairs per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP430632", null, null, "liver_S1_L004_R1_001.fastq.gz liver_S1_L004_R2_001.fastq.gz", "fastq fastq", 55439857500.0, 184799525.0, "GSM7139012 r4", "0:150 1:150", "A:20062196194;C:10303732038;G:9970882987;T:15101055492;N:1990789", 150, 150, null, null, 20062196194, 10303732038, 9970882987, 15101055492, 1990789, "SRX19850771", "SRS17208526", "SRA1615101", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", "Room 6319, Division of Life Science, Hong Kong University of Science and Technology", 2, 0.0, 0.88645, 0.0, 0.2012, 1.0, 0.82546, null, 0.62152, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-04-03", "Adult", "Adult", "Liver", "Liver and Biliary System"], [75608, "SRR24742192", "SRX20519420", "SRS17829368", "SRP439656", "PRJNA975724", "Key factors in the process of biliary epithelial cells to bipotential progenitor cells dedifferentiation", "PRJNA975724", "Other", "Uncover the regulatory mechanisms underlying biliary cell dedifferentiation.", null, null, "The fish were treated with mtz at 5 dpf  and then the livers were collected post 24 hours treatment  namly regeneration 0 hour.", "scRNA seq of zebrafish R0h livers", "Livers of lfabp:Dendra2 NTR fish at mtz  R0h", null, "strain:ABGO|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:mtz  R0h|sex:pooled male and female|tissue:liver|birth location:China|collection date:2021 04 29|geo loc name:China: Chongqing|BioSampleModel:Model organism or animal", null, null, null, 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"SRX20519420", "SRS17829368", "SRA1643264", "Institute of Developmental Biology and Regenerative Medicine|Southwest University", "Institute of Developmental Biology and Regenerative Medicine AccuraMed Company", 2, 0.0, 0.92113, 0.0, 0.15798, 1.0, 0.81215, null, 0.58532, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-05-25", "Zygote", "Embryo", "Liver", "Liver and Biliary System"]], "truncated": false, "filtered_table_rows_count": 101, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", 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