{"database": "metadata", "table": "run_metadata", "rows": [[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"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["33248"], "units": {}, "query_ms": 9.903074002068024}