metadata: run_metadata: 78 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "10x" and tissue

78 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", technology = "10x" and tissue_curation = "Liver"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.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.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
33210	33210	SRR29868290	SRX25365557	SRS22031297	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver PHx 11dpi	GSM8403320	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy\|geo loc name:missing\|collection date:missing	Liver PHx 11dpi	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy	GSM8403320	GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq	GSM8403320 r1	GSM8403320	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I1_001.fastq.gz	fastq fastq fastq fastq	14533781976.0	86510607.0	GSM8403320 r1												SRX25365557	SRS22031297	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92123		0.07848		0.87767		0.63307		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33211	33211	SRR29868291	SRX25365557	SRS22031297	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver PHx 11dpi	GSM8403320	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy\|geo loc name:missing\|collection date:missing	Liver PHx 11dpi	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy	GSM8403320	GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq	GSM8403320 r1	GSM8403320	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I1_001.fastq.gz	fastq fastq fastq fastq	14988315888.0	89216166.0	GSM8403320 r2	0:10 1:10 2:28 3:120	A:3248904317;C:2406836003;G:2506118019;T:2544017722;N:63859	10	10	28	120	3248904317	2406836003	2506118019	2544017722	63859	SRX25365557	SRS22031297	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92258		0.07901		0.87805		0.61529		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33212	33212	SRR29868292	SRX25365557	SRS22031297	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver PHx 11dpi	GSM8403320	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy\|geo loc name:missing\|collection date:missing	Liver PHx 11dpi	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy	GSM8403320	GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq	GSM8403320 r1	GSM8403320	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I1_001.fastq.gz	fastq fastq fastq fastq	15113782152.0	89962989.0	GSM8403320 r3	0:10 1:10 2:28 3:120	A:3272277396;C:2428985319;G:2529710055;T:2564489719;N:96191	10	10	28	120	3272277396	2428985319	2529710055	2564489719	96191	SRX25365557	SRS22031297	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92256		0.07848		0.87815		0.62057		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33213	33213	SRR29868293	SRX25365557	SRS22031297	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver PHx 11dpi	GSM8403320	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy\|geo loc name:missing\|collection date:missing	Liver PHx 11dpi	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy	GSM8403320	GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq	GSM8403320 r1	GSM8403320	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I1_001.fastq.gz	fastq fastq fastq fastq	14872072488.0	88524241.0	GSM8403320 r4	0:10 1:10 2:28 3:120	A:3227423261;C:2385566347;G:2480919292;T:2528894334;N:105686	10	10	28	120	3227423261	2385566347	2480919292	2528894334	105686	SRX25365557	SRS22031297	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92066		0.07821		0.87941		0.63528		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33214	33214	SRR29868294	SRX25365556	SRS22031296	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver PHx 4dpi	GSM8403319	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy\|geo loc name:missing\|collection date:missing	Liver PHx 4dpi	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy	GSM8403319	GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq	GSM8403319 r1	GSM8403319	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R2_001.fastq.gz	fastq fastq fastq fastq	17814930504.0	106041253.0	GSM8403319 r1	0:10 1:10 2:28 3:120	A:3778122253;C:2833144305;G:2888284601;T:3225338000;N:61201	10	10	28	120	3778122253	2833144305	2888284601	3225338000	61201	SRX25365556	SRS22031296	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92579		0.07861		0.82518		0.61746		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33215	33215	SRR29868295	SRX25365556	SRS22031296	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver PHx 4dpi	GSM8403319	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy\|geo loc name:missing\|collection date:missing	Liver PHx 4dpi	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy	GSM8403319	GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq	GSM8403319 r1	GSM8403319	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R2_001.fastq.gz	fastq fastq fastq fastq	18469195752.0	109935689.0	GSM8403319 r2	0:10 1:10 2:28 3:120	A:3912835271;C:2940938740;G:3000841815;T:3337590023;N:76831	10	10	28	120	3912835271	2940938740	3000841815	3337590023	76831	SRX25365556	SRS22031296	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92613		0.07975		0.82599		0.6186		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33216	33216	SRR29868296	SRX25365556	SRS22031296	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver PHx 4dpi	GSM8403319	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy\|geo loc name:missing\|collection date:missing	Liver PHx 4dpi	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy	GSM8403319	GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq	GSM8403319 r1	GSM8403319	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R2_001.fastq.gz	fastq fastq fastq fastq	18744044088.0	111571691.0	GSM8403319 r3	0:10 1:10 2:28 3:120	A:3967793098;C:2986585695;G:3048563710;T:3385544059;N:116358	10	10	28	120	3967793098	2986585695	3048563710	3385544059	116358	SRX25365556	SRS22031296	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.9274		0.07865		0.82605		0.61088		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33217	33217	SRR29868297	SRX25365556	SRS22031296	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver PHx 4dpi	GSM8403319	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy\|geo loc name:missing\|collection date:missing	Liver PHx 4dpi	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Hepatectomy	GSM8403319	GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq	GSM8403319 r1	GSM8403319	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R2_001.fastq.gz	fastq fastq fastq fastq	18250884624.0	108636218.0	GSM8403319 r4	0:10 1:10 2:28 3:120	A:3870590300;C:2903010183;G:2961077382;T:3301541312;N:126983	10	10	28	120	3870590300	2903010183	2961077382	3301541312	126983	SRX25365556	SRS22031296	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92712		0.07894		0.82509		0.60912		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33218	33218	SRR29868298	SRX25365555	SRS22031295	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 9dppa	GSM8403318	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 9dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403318	GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq	GSM8403318 r1	GSM8403318	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I1_001.fastq.gz	fastq fastq fastq fastq	17110767912.0	101849809.0	GSM8403318 r1	0:10 1:10 2:28 3:120	A:3788205667;C:2699657929;G:2699620981;T:3034435232;N:57271	10	10	28	120	3788205667	2699657929	2699620981	3034435232	57271	SRX25365555	SRS22031295	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.91437		0.05435		0.86983		0.62046		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33219	33219	SRR29868299	SRX25365555	SRS22031295	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 9dppa	GSM8403318	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 9dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403318	GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq	GSM8403318 r1	GSM8403318	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I1_001.fastq.gz	fastq fastq fastq fastq	17981827752.0	107034689.0	GSM8403318 r3	0:10 1:10 2:28 3:120	A:3977642248;C:2840653787;G:2844602651;T:3181150070;N:113924	10	10	28	120	3977642248	2840653787	2844602651	3181150070	113924	SRX25365555	SRS22031295	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.91394		0.05332		0.87		0.61803		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33220	33220	SRR29868300	SRX25365555	SRS22031295	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 9dppa	GSM8403318	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 9dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403318	GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq	GSM8403318 r1	GSM8403318	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I1_001.fastq.gz	fastq fastq fastq fastq	17550170232.0	104465299.0	GSM8403318 r4	0:10 1:10 2:28 3:120	A:3887199949;C:2768808747;G:2769733142;T:3109971563;N:122479	10	10	28	120	3887199949	2768808747	2769733142	3109971563	122479	SRX25365555	SRS22031295	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.91342		0.0541		0.87046		0.61388		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33221	33221	SRR29868306	SRX25365555	SRS22031295	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 9dppa	GSM8403318	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 9dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403318	GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq	GSM8403318 r1	GSM8403318	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I1_001.fastq.gz	fastq fastq fastq fastq	17719057944.0	105470583.0	GSM8403318 r2	0:10 1:10 2:28 3:120	A:3923720947;C:2796640453;G:2800418238;T:3135616927;N:73395	10	10	28	120	3923720947	2796640453	2800418238	3135616927	73395	SRX25365555	SRS22031295	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.91325		0.05422		0.86949		0.6266		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33222	33222	SRR29868301	SRX25365554	SRS22031294	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 1dppa	GSM8403317	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 1dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403317	GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq	GSM8403317 r1	GSM8403317	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R2_001.fastq.gz	fastq fastq fastq fastq	21323163288.0	126923591.0	GSM8403317 r1	0:10 1:10 2:28 3:120	A:4482829539;C:3366994739;G:3484245391;T:3896538980;N:222271	10	10	28	120	4482829539	3366994739	3484245391	3896538980	222271	SRX25365554	SRS22031294	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93349		0.07482		0.81925		0.57693		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33223	33223	SRR29868302	SRX25365554	SRS22031294	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 1dppa	GSM8403317	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 1dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403317	GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq	GSM8403317 r1	GSM8403317	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R1_001.fastq.gz	fastq fastq fastq fastq	7887231744.0	46947808.0	GSM8403317 r5	0:10 1:10 2:28 3:120	A:1641421944;C:1251181706;G:1291844073;T:1449242410;N:46827	10	10	28	120	1641421944	1251181706	1291844073	1449242410	46827	SRX25365554	SRS22031294	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93251		0.07497		0.81763		0.58245		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33224	33224	SRR29868303	SRX25365554	SRS22031294	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 1dppa	GSM8403317	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 1dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403317	GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq	GSM8403317 r1	GSM8403317	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R2_001.fastq.gz	fastq fastq fastq fastq	8028118896.0	47786422.0	GSM8403317 r6	0:10 1:10 2:28 3:120	A:1672066662;C:1273372069;G:1312792441;T:1476102756;N:36712	10	10	28	120	1672066662	1273372069	1312792441	1476102756	36712	SRX25365554	SRS22031294	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93266		0.07544		0.81675		0.57597		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33225	33225	SRR29868304	SRX25365554	SRS22031294	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 1dppa	GSM8403317	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 1dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403317	GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq	GSM8403317 r1	GSM8403317	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R2_001.fastq.gz	fastq fastq fastq fastq	8223531120.0	48949590.0	GSM8403317 r7	0:10 1:10 2:28 3:120	A:1713836781;C:1304685662;G:1345155931;T:1510228105;N:44321	10	10	28	120	1713836781	1304685662	1345155931	1510228105	44321	SRX25365554	SRS22031294	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93273		0.07513		0.81546		0.58099		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33226	33226	SRR29868305	SRX25365554	SRS22031294	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 1dppa	GSM8403317	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 1dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403317	GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq	GSM8403317 r1	GSM8403317	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I1_001.fastq.gz	fastq fastq fastq fastq	7715042160.0	45922870.0	GSM8403317 r8	0:10 1:10 2:28 3:120	A:1604997878;C:1222312105;G:1258545155;T:1424847802;N:41460	10	10	28	120	1604997878	1222312105	1258545155	1424847802	41460	SRX25365554	SRS22031294	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93359		0.07524		0.81479		0.57882		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33227	33227	SRR29868320	SRX25365554	SRS22031294	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 1dppa	GSM8403317	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 1dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403317	GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq	GSM8403317 r1	GSM8403317	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R2_001.fastq.gz	fastq fastq fastq fastq	21662633664.0	128944248.0	GSM8403317 r2	0:10 1:10 2:28 3:120	A:4553543446;C:3422125565;G:3539342477;T:3957989911;N:308361	10	10	28	120	4553543446	3422125565	3539342477	3957989911	308361	SRX25365554	SRS22031294	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93227		0.07246		0.81696		0.50066		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33228	33228	SRR29868321	SRX25365554	SRS22031294	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 1dppa	GSM8403317	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 1dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403317	GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq	GSM8403317 r1	GSM8403317	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I1_001.fastq.gz	fastq fastq fastq fastq	22267198800.0	132542850.0	GSM8403317 r3	0:10 1:10 2:28 3:120	A:4677084299;C:3522052285;G:3641789558;T:4063831592;N:384266	10	10	28	120	4677084299	3522052285	3641789558	4063831592	384266	SRX25365554	SRS22031294	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93308		0.07402		0.82035		0.58114		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33229	33229	SRR29868322	SRX25365554	SRS22031294	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 1dppa	GSM8403317	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 1dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403317	GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq	GSM8403317 r1	GSM8403317	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I1_001.fastq.gz	fastq fastq fastq fastq	21946980216.0	130636787.0	GSM8403317 r4	0:10 1:10 2:28 3:120	A:4613356051;C:3469396471;G:3586452720;T:4006684161;N:525037	10	10	28	120	4613356051	3469396471	3586452720	4006684161	525037	SRX25365554	SRS22031294	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.932		0.07454		0.8199		0.57856		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33230	33230	SRR29868307	SRX25365553	SRS22031298	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control2	GSM8403315	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control2	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403315	GSM8403315: Liver Control2; Danio rerio; RNA Seq	GSM8403315 r1	GSM8403315	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I1_001.fastq.gz	fastq fastq fastq fastq	9879931488.0	58809116.0	GSM8403315 r1	0:10 1:10 2:28 3:120	A:2083561937;C:1579881891;G:1601331938;T:1792234199;N:83955	10	10	28	120	2083561937	1579881891	1601331938	1792234199	83955	SRX25365553	SRS22031298	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.9245		0.07832		0.83207		0.59038		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33231	33231	SRR29868308	SRX25365553	SRS22031298	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control2	GSM8403315	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control2	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403315	GSM8403315: Liver Control2; Danio rerio; RNA Seq	GSM8403315 r1	GSM8403315	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I1_001.fastq.gz	fastq fastq fastq fastq	11728809288.0	69814341.0	GSM8403315 r5	0:10 1:10 2:28 3:120	A:2469898525;C:1869748167;G:1900689647;T:2137258339;N:126242	10	10	28	120	2469898525	1869748167	1900689647	2137258339	126242	SRX25365553	SRS22031298	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92438		0.08084		0.83181		0.58855		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33232	33232	SRR29868309	SRX25365553	SRS22031298	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control2	GSM8403315	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control2	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403315	GSM8403315: Liver Control2; Danio rerio; RNA Seq	GSM8403315 r1	GSM8403315	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I1_001.fastq.gz	fastq fastq fastq fastq	11877483744.0	70699308.0	GSM8403315 r6	0:10 1:10 2:28 3:120	A:2501780371;C:1893908685;G:1923797061;T:2164259893;N:170950	10	10	28	120	2501780371	1893908685	1923797061	2164259893	170950	SRX25365553	SRS22031298	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92477		0.07874		0.83321		0.5933		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33233	33233	SRR29868310	SRX25365553	SRS22031298	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control2	GSM8403315	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control2	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403315	GSM8403315: Liver Control2; Danio rerio; RNA Seq	GSM8403315 r1	GSM8403315	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I1_001.fastq.gz	fastq fastq fastq fastq	12148826256.0	72314442.0	GSM8403315 r7	0:10 1:10 2:28 3:120	A:2557348707;C:1939726759;G:1969388742;T:2211056576;N:212256	10	10	28	120	2557348707	1939726759	1969388742	2211056576	212256	SRX25365553	SRS22031298	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.9241		0.07899		0.83246		0.59733		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33234	33234	SRR29868311	SRX25365553	SRS22031298	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control2	GSM8403315	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control2	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403315	GSM8403315: Liver Control2; Danio rerio; RNA Seq	GSM8403315 r1	GSM8403315	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I1_001.fastq.gz	fastq fastq fastq fastq	12000520224.0	71431668.0	GSM8403315 r8	0:10 1:10 2:28 3:120	A:2527907019;C:1914860315;G:1943708096;T:2185034081;N:290649	10	10	28	120	2527907019	1914860315	1943708096	2185034081	290649	SRX25365553	SRS22031298	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92467		0.07869		0.83274		0.59327		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33235	33235	SRR29868331	SRX25365553	SRS22031298	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control2	GSM8403315	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control2	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403315	GSM8403315: Liver Control2; Danio rerio; RNA Seq	GSM8403315 r1	GSM8403315	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R2_001.fastq.gz	fastq fastq fastq fastq	10005892344.0	59558883.0	GSM8403315 r2	0:10 1:10 2:28 3:120	A:2111541927;C:1599222457;G:1620308600;T:1815908968;N:84008	10	10	28	120	2111541927	1599222457	1620308600	1815908968	84008	SRX25365553	SRS22031298	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.925		0.07865		0.83435		0.60287		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33236	33236	SRR29868332	SRX25365553	SRS22031298	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control2	GSM8403315	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control2	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403315	GSM8403315: Liver Control2; Danio rerio; RNA Seq	GSM8403315 r1	GSM8403315	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R2_001.fastq.gz	fastq fastq fastq fastq	10016183856.0	59620142.0	GSM8403315 r3	0:10 1:10 2:28 3:120	A:2111419802;C:1602592297;G:1623486867;T:1816842279;N:75795	10	10	28	120	2111419802	1602592297	1623486867	1816842279	75795	SRX25365553	SRS22031298	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.9252		0.07706		0.83311		0.58482		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33237	33237	SRR29868333	SRX25365553	SRS22031298	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control2	GSM8403315	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control2	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403315	GSM8403315: Liver Control2; Danio rerio; RNA Seq	GSM8403315 r1	GSM8403315	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I1_001.fastq.gz	fastq fastq fastq fastq	9972679080.0	59361185.0	GSM8403315 r4	0:10 1:10 2:28 3:120	A:2102584213;C:1595356295;G:1615800606;T:1809513301;N:87785	10	10	28	120	2102584213	1595356295	1615800606	1809513301	87785	SRX25365553	SRS22031298	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92471		0.07908		0.83368		0.59597		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33238	33238	SRR29868312	SRX25365552	SRS22031293	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 0dppa	GSM8403316	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 0dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403316	GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq	GSM8403316 r1	GSM8403316	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I1_001.fastq.gz	fastq fastq fastq fastq	21831966072.0	129952179.0	GSM8403316 r1	0:10 1:10 2:28 3:120	A:4479350098;C:3460914438;G:3623235900;T:4030530673;N:230371	10	10	28	120	4479350098	3460914438	3623235900	4030530673	230371	SRX25365552	SRS22031293	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93487		0.07462		0.81168		0.58593		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33239	33239	SRR29868313	SRX25365552	SRS22031293	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 0dppa	GSM8403316	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 0dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403316	GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq	GSM8403316 r1	GSM8403316	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R2_001.fastq.gz	fastq fastq fastq fastq	22210988016.0	132208262.0	GSM8403316 r2	0:10 1:10 2:28 3:120	A:4554555932;C:3523295618;G:3687384727;T:4099433293;N:321870	10	10	28	120	4554555932	3523295618	3687384727	4099433293	321870	SRX25365552	SRS22031293	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93515		0.07425		0.81251		0.56065		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33240	33240	SRR29868314	SRX25365552	SRS22031293	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 0dppa	GSM8403316	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 0dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403316	GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq	GSM8403316 r1	GSM8403316	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R2_001.fastq.gz	fastq fastq fastq fastq	22964241384.0	136691913.0	GSM8403316 r3	0:10 1:10 2:28 3:120	A:4705118723;C:3647298654;G:3815152922;T:4235059775;N:399486	10	10	28	120	4705118723	3647298654	3815152922	4235059775	399486	SRX25365552	SRS22031293	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93515		0.07425		0.81085		0.58414		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33241	33241	SRR29868315	SRX25365552	SRS22031293	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 0dppa	GSM8403316	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 0dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403316	GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq	GSM8403316 r1	GSM8403316	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R2_001.fastq.gz	fastq fastq fastq fastq	22572116784.0	134357838.0	GSM8403316 r4	0:10 1:10 2:28 3:120	A:4628982434;C:3582861623;G:3746732678;T:4163813221;N:550604	10	10	28	120	4628982434	3582861623	3746732678	4163813221	550604	SRX25365552	SRS22031293	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93487		0.07514		0.80862		0.57745		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33242	33242	SRR29868316	SRX25365552	SRS22031293	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 0dppa	GSM8403316	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 0dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403316	GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq	GSM8403316 r1	GSM8403316	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R2_001.fastq.gz	fastq fastq fastq fastq	9319118424.0	55470943.0	GSM8403316 r5	0:10 1:10 2:28 3:120	A:1895887547;C:1477863924;G:1543846946;T:1738857665;N:57078	10	10	28	120	1895887547	1477863924	1543846946	1738857665	57078	SRX25365552	SRS22031293	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93507		0.07612		0.80862		0.5708		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33243	33243	SRR29868317	SRX25365552	SRS22031293	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 0dppa	GSM8403316	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 0dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403316	GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq	GSM8403316 r1	GSM8403316	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R2_001.fastq.gz	fastq fastq fastq fastq	9433874184.0	56154013.0	GSM8403316 r6	0:10 1:10 2:28 3:120	A:1919903956;C:1496318299;G:1560772790;T:1761443349;N:43166	10	10	28	120	1919903956	1496318299	1560772790	1761443349	43166	SRX25365552	SRS22031293	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93514		0.07597		0.80937		0.5877		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33244	33244	SRR29868318	SRX25365552	SRS22031293	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 0dppa	GSM8403316	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 0dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403316	GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq	GSM8403316 r1	GSM8403316	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I1_001.fastq.gz	fastq fastq fastq fastq	9674650944.0	57587208.0	GSM8403316 r7	0:10 1:10 2:28 3:120	A:1969538339;C:1535292977;G:1601577456;T:1804003343;N:52845	10	10	28	120	1969538339	1535292977	1601577456	1804003343	52845	SRX25365552	SRS22031293	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93521		0.07665		0.80876		0.57512		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33245	33245	SRR29868319	SRX25365552	SRS22031293	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver MTZ 0dppa	GSM8403316	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation\|geo loc name:missing\|collection date:missing	Liver MTZ 0dppa	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Partial Ablation	GSM8403316	GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq	GSM8403316 r1	GSM8403316	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R2_001.fastq.gz	fastq fastq fastq fastq	9063172776.0	53947457.0	GSM8403316 r8	0:10 1:10 2:28 3:120	A:1844279220;C:1435218712;G:1495137465;T:1699009389;N:50054	10	10	28	120	1844279220	1435218712	1495137465	1699009389	50054	SRX25365552	SRS22031293	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93431		0.07653		0.80803		0.57631		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33246	33246	SRR29868323	SRX25365551	SRS22031292	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control1	GSM8403314	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control1	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403314	GSM8403314: Liver Control1; Danio rerio; RNA Seq	GSM8403314 r1	GSM8403314	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I1_001.fastq.gz	fastq fastq fastq fastq	10244575656.0	60979617.0	GSM8403314 r1	0:10 1:10 2:28 3:120	A:2119295536;C:1665865582;G:1726802243;T:1805507036;N:83643	10	10	28	120	2119295536	1665865582	1726802243	1805507036	83643	SRX25365551	SRS22031292	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92821		0.09448		0.83725		0.60089		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33247	33247	SRR29868324	SRX25365551	SRS22031292	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control1	GSM8403314	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control1	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403314	GSM8403314: Liver Control1; Danio rerio; RNA Seq	GSM8403314 r1	GSM8403314	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I1_001.fastq.gz	fastq fastq fastq fastq	10380032880.0	61785910.0	GSM8403314 r2	0:10 1:10 2:28 3:120	A:2148125611;C:1687299842;G:1748516982;T:1830286430;N:80335	10	10	28	120	2148125611	1687299842	1748516982	1830286430	80335	SRX25365551	SRS22031292	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.93012		0.0931		0.83621		0.60089		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33248	33248	SRR29868325	SRX25365551	SRS22031292	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control1	GSM8403314	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control1	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403314	GSM8403314: Liver Control1; Danio rerio; RNA Seq	GSM8403314 r1	GSM8403314	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I1_001.fastq.gz	fastq fastq fastq fastq	10397790648.0	61891611.0	GSM8403314 r3	0:10 1:10 2:28 3:120	A:2150008358;C:1691781234;G:1752867785;T:1832258443;N:77500	10	10	28	120	2150008358	1691781234	1752867785	1832258443	77500	SRX25365551	SRS22031292	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.9284		0.09293		0.83605		0.59853		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33249	33249	SRR29868326	SRX25365551	SRS22031292	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control1	GSM8403314	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control1	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403314	GSM8403314: Liver Control1; Danio rerio; RNA Seq	GSM8403314 r1	GSM8403314	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I1_001.fastq.gz	fastq fastq fastq fastq	10333943592.0	61511569.0	GSM8403314 r4	0:10 1:10 2:28 3:120	A:2138003833;C:1680536471;G:1740834135;T:1821926938;N:86903	10	10	28	120	2138003833	1680536471	1740834135	1821926938	86903	SRX25365551	SRS22031292	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92828		0.09437		0.83611		0.58915		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33250	33250	SRR29868327	SRX25365551	SRS22031292	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control1	GSM8403314	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control1	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403314	GSM8403314: Liver Control1; Danio rerio; RNA Seq	GSM8403314 r1	GSM8403314	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I2_001.fastq.gz	fastq fastq fastq fastq	11552239440.0	68763330.0	GSM8403314 r5	0:10 1:10 2:28 3:120	A:2384461898;C:1875086137;G:1950680109;T:2041249149;N:122307	10	10	28	120	2384461898	1875086137	1950680109	2041249149	122307	SRX25365551	SRS22031292	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92842		0.09581		0.83591		0.59709		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33251	33251	SRR29868328	SRX25365551	SRS22031292	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control1	GSM8403314	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control1	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403314	GSM8403314: Liver Control1; Danio rerio; RNA Seq	GSM8403314 r1	GSM8403314	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I1_001.fastq.gz	fastq fastq fastq fastq	11713305912.0	69722059.0	GSM8403314 r6	0:10 1:10 2:28 3:120	A:2418305019;C:1901514145;G:1976625286;T:2070035096;N:167534	10	10	28	120	2418305019	1901514145	1976625286	2070035096	167534	SRX25365551	SRS22031292	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92987		0.09528		0.8352		0.60535		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33252	33252	SRR29868329	SRX25365551	SRS22031292	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control1	GSM8403314	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control1	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403314	GSM8403314: Liver Control1; Danio rerio; RNA Seq	GSM8403314 r1	GSM8403314	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I1_001.fastq.gz	fastq fastq fastq fastq	12060725208.0	71790031.0	GSM8403314 r7	0:10 1:10 2:28 3:120	A:2488941083;C:1959911465;G:2036435394;T:2129304281;N:211497	10	10	28	120	2488941083	1959911465	2036435394	2129304281	211497	SRX25365551	SRS22031292	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92896		0.09426		0.83867		0.53757		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
33253	33253	SRR29868330	SRX25365551	SRS22031292	SRP520597	PRJNA1136957	Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish	GSE272484	Transcriptome Analysis	Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.		pubmed:40480975		Liver Control1	GSM8403314	source name:Liver\|tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT\|geo loc name:missing\|collection date:missing	Liver Control1	A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file	Liver		Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …		tissue:Liver\|transgene:Tgfabp10a:CellCousin\|treatment:Control – No 4 OHT	GSM8403314	GSM8403314: Liver Control1; Danio rerio; RNA Seq	GSM8403314 r1	GSM8403314	1	Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550	SRP520597	loader:fastq load.py	ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R2_001.fastq.gz	fastq fastq fastq fastq	11892922944.0	70791208.0	GSM8403314 r8	0:10 1:10 2:28 3:120	A:2456445818;C:1931328609;G:2006328383;T:2100554789;N:287361	10	10	28	120	2456445818	1931328609	2006328383	2100554789	287361	SRX25365551	SRS22031292	SRA1926595	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB	1	0.92946		0.09343		0.83704		0.59688		120		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2024-07-17	Undetermined	Larval	Liver	Liver and Biliary System
70706	70706	SRR21457012	SRX17460721	SRS15014532	SRP385641	PRJNA857143	Single cell transcriptomic data of zebrafish lbw mutant	PRJNA857143	Other	Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.					Liver in the WT S4 L004	isolate:wild type\|dev stage:6 dpf\|sex:female and male\|tissue:liver\|aliquot:aliquot 4\|BioSampleModel:Model organism or animal									scRNA Seq of zebrafish: 6 dpf wild type liver	Live S4 L004 aliquot 4	Live S4 L004 aliquot 4	using Chromium Single Cell three prime GEM v3.1 Reagent Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP385641		20200806_S4_Live_20200825NB_S4_L004_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L004_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L004_R2_001.fastq.gz	fastq fastq fastq	15359722785.0	82137555.0	20200806 S4 Live 20200825NB S4 L004 I1 001.fastq.gz	0:8 1:28 2:151	A:3860252969;C:2756020453;G:2781498176;T:3004915512;N:83695	8	28	151		3860252969	2756020453	2781498176	3004915512	83695	SRX17460721	SRS15014532	SRA1491985	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	1	0.90519		0.06757		0.88243		0.74961		151		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2022-09-11	Larval	Larval	Liver	Liver and Biliary System
70707	70707	SRR21457013	SRX17460720	SRS15014531	SRP385641	PRJNA857143	Single cell transcriptomic data of zebrafish lbw mutant	PRJNA857143	Other	Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.					Liver in the WT S4 L003	isolate:wild type\|dev stage:6 dpf\|sex:female and male\|tissue:liver\|aliquot:aliquot 3\|BioSampleModel:Model organism or animal									scRNA Seq of zebrafish: 6 dpf wild type liver	Live S4 L003 aliquot 3	Live S4 L003 aliquot 3	using Chromium Single Cell three prime GEM v3.1 Reagent Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP385641		20200806_S4_Live_20200825NB_S4_L003_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L003_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L003_R2_001.fastq.gz	fastq fastq fastq	15277905984.0	81700032.0	20200806 S4 Live 20200825NB S4 L003 I1 001.fastq.gz	0:8 1:28 2:151	A:3834498109;C:2745604041;G:2766967723;T:2989497144;N:137815	8	28	151		3834498109	2745604041	2766967723	2989497144	137815	SRX17460720	SRS15014531	SRA1491985	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	1	0.90792		0.06795		0.88089		0.75291		151		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2022-09-11	Larval	Larval	Liver	Liver and Biliary System
70710	70710	SRR21457016	SRX17460717	SRS15014528	SRP385641	PRJNA857143	Single cell transcriptomic data of zebrafish lbw mutant	PRJNA857143	Other	Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.					Liver in the WT S4 L002	isolate:wild type\|dev stage:6 dpf\|sex:female and male\|tissue:liver\|aliquot:aliquot 2\|BioSampleModel:Model organism or animal									scRNA Seq of zebrafish: 6 dpf wild type liver	Live S4 L002 aliquot 2	Live S4 L002 aliquot 2	using Chromium Single Cell three prime GEM v3.1 Reagent Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP385641		20200806_S4_Live_20200825NB_S4_L002_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L002_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L002_R2_001.fastq.gz	fastq fastq fastq	15033903335.0	80395205.0	20200806 S4 Live 20200825NB S4 L002 I1 001.fastq.gz	0:8 1:28 2:151	A:3774023536;C:2701104584;G:2719224706;T:2945204367;N:118762	8	28	151		3774023536	2701104584	2719224706	2945204367	118762	SRX17460717	SRS15014528	SRA1491985	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	1	0.90993		0.06896		0.88002		0.75003		151		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2022-09-11	Larval	Larval	Liver	Liver and Biliary System
70711	70711	SRR21457017	SRX17460716	SRS15014527	SRP385641	PRJNA857143	Single cell transcriptomic data of zebrafish lbw mutant	PRJNA857143	Other	Zebrafish lbw mutant exhibits hepatized anterior intestine. To characterize the functional liver cells in lbw intestine we dissected lbw intestine at 6 dpf and carried out scRNA seq to compare its cell population clusters with wild type liver and intestine.					Liver in the WT S4 L001	isolate:wild type\|dev stage:6 dpf\|sex:female and male\|tissue:liver\|aliquot:aliquot 1\|BioSampleModel:Model organism or animal									scRNA Seq of zebrafish: 6 dpf wild type liver	Live S4 L001 aliquot 1	Live S4 L001 aliquot 1	using Chromium Single Cell three prime GEM v3.1 Reagent Kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP385641		20200806_S4_Live_20200825NB_S4_L001_I1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L001_R1_001.fastq.gz 20200806_S4_Live_20200825NB_S4_L001_R2_001.fastq.gz	fastq fastq fastq	15047379303.0	80467269.0	20200806 S4 Live 20200825NB S4 L001 I1 001.fastq.gz	0:8 1:28 2:151	A:3778269770;C:2702450055;G:2724848747;T:2944890394;N:98653	8	28	151		3778269770	2702450055	2724848747	2944890394	98653	SRX17460716	SRS15014527	SRA1491985	Southwest University\|Institute of Developmental Biology and Regenerativ	Southwest University	1	0.90977		0.06799		0.87998		0.75241		151		B		usable mapping rate	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2022-09-11	Larval	Larval	Liver	Liver and Biliary System
74480	74480	SRR23824324	SRX19646191	SRS17014001	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver Ctrl replicate 2	GSM7092955	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver Ctrl replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092955	GSM7092955: liver Ctrl replicate 2; Danio rerio; RNA Seq	GSM7092955 r1	GSM7092955	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Liver-2_S7_L001_R1_001.fastq.gz Ctrl-Liver-2_S7_L001_R2_001.fastq.gz	fastq fastq	5104340986.0	43257127.0	GSM7092955 r1	0:28 1:90	A:1424416053;C:1192239684;G:1190425268;T:1297142390;N:117591	28	90			1424416053	1192239684	1190425268	1297142390	117591	SRX19646191	SRS17014001	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00469	0.94025	0.00107	0.05406	0.99533	0.87308	0.27077	0.46309	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74481	74481	SRR23824325	SRX19646191	SRS17014001	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver Ctrl replicate 2	GSM7092955	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver Ctrl replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092955	GSM7092955: liver Ctrl replicate 2; Danio rerio; RNA Seq	GSM7092955 r1	GSM7092955	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Liver-2_S7_L002_R1_001.fastq.gz Ctrl-Liver-2_S7_L002_R2_001.fastq.gz	fastq fastq	5141806812.0	43574634.0	GSM7092955 r2	0:28 1:90	A:1434538137;C:1200870495;G:1198733719;T:1307553313;N:111148	28	90			1434538137	1200870495	1198733719	1307553313	111148	SRX19646191	SRS17014001	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.0048	0.93996	0.00104	0.05254	0.99515	0.87499	0.26301	0.4732	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74482	74482	SRR23824326	SRX19646191	SRS17014001	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver Ctrl replicate 2	GSM7092955	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver Ctrl replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092955	GSM7092955: liver Ctrl replicate 2; Danio rerio; RNA Seq	GSM7092955 r1	GSM7092955	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Liver-2_S7_L003_R1_001.fastq.gz Ctrl-Liver-2_S7_L003_R2_001.fastq.gz	fastq fastq	5192564158.0	44004781.0	GSM7092955 r3	0:28 1:90	A:1448034478;C:1213477598;G:1211749223;T:1319197183;N:105676	28	90			1448034478	1213477598	1211749223	1319197183	105676	SRX19646191	SRS17014001	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00504	0.9401	0.00113	0.05317	0.99462	0.87361	0.27858	0.47856	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74483	74483	SRR23824327	SRX19646191	SRS17014001	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver Ctrl replicate 2	GSM7092955	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver Ctrl replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092955	GSM7092955: liver Ctrl replicate 2; Danio rerio; RNA Seq	GSM7092955 r1	GSM7092955	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Liver-2_S7_L004_R1_001.fastq.gz Ctrl-Liver-2_S7_L004_R2_001.fastq.gz	fastq fastq	5107398366.0	43283037.0	GSM7092955 r4	0:28 1:90	A:1425848029;C:1192174260;G:1189956127;T:1299322516;N:97434	28	90			1425848029	1192174260	1189956127	1299322516	97434	SRX19646191	SRS17014001	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00498	0.9401	0.00127	0.05293	0.99494	0.87572	0.27094	0.47517	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74484	74484	SRR23824328	SRX19646190	SRS17014000	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver Ctrl replicate 1	GSM7092954	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver Ctrl replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092954	GSM7092954: liver Ctrl replicate 1; Danio rerio; RNA Seq	GSM7092954 r1	GSM7092954	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Liver-1_S3_L001_R1_001.fastq.gz Ctrl-Liver-1_S3_L001_R2_001.fastq.gz	fastq fastq	4496614672.0	38106904.0	GSM7092954 r1	0:28 1:90	A:1236795920;C:1061685679;G:1067304176;T:1130725493;N:103404	28	90			1236795920	1061685679	1067304176	1130725493	103404	SRX19646190	SRS17014000	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00769	0.94857	0.00194	0.0642	0.9948	0.87919	0.26391	0.47988	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74485	74485	SRR23824329	SRX19646190	SRS17014000	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver Ctrl replicate 1	GSM7092954	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver Ctrl replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092954	GSM7092954: liver Ctrl replicate 1; Danio rerio; RNA Seq	GSM7092954 r1	GSM7092954	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Liver-1_S3_L002_R2_001.fastq.gz Ctrl-Liver-1_S3_L002_R1_001.fastq.gz	fastq fastq	4500848984.0	38142788.0	GSM7092954 r2	0:28 1:90	A:1237725640;C:1062772315;G:1068127847;T:1132125691;N:97491	28	90			1237725640	1062772315	1068127847	1132125691	97491	SRX19646190	SRS17014000	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00735	0.94796	0.00174	0.06344	0.99504	0.87706	0.23275	0.47453	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74486	74486	SRR23824330	SRX19646190	SRS17014000	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver Ctrl replicate 1	GSM7092954	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver Ctrl replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092954	GSM7092954: liver Ctrl replicate 1; Danio rerio; RNA Seq	GSM7092954 r1	GSM7092954	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Liver-1_S3_L003_R1_001.fastq.gz Ctrl-Liver-1_S3_L003_R2_001.fastq.gz	fastq fastq	4565971178.0	38694671.0	GSM7092954 r3	0:28 1:90	A:1255012168;C:1078579990;G:1084287166;T:1147999283;N:92571	28	90			1255012168	1078579990	1084287166	1147999283	92571	SRX19646190	SRS17014000	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00832	0.94796	0.00204	0.06357	0.99407	0.87775	0.26311	0.46735	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74487	74487	SRR23824331	SRX19646190	SRS17014000	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver Ctrl replicate 1	GSM7092954	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver Ctrl replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092954	GSM7092954: liver Ctrl replicate 1; Danio rerio; RNA Seq	GSM7092954 r1	GSM7092954	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	Ctrl-Liver-1_S3_L004_R1_001.fastq.gz Ctrl-Liver-1_S3_L004_R2_001.fastq.gz	fastq fastq	4487270016.0	38027712.0	GSM7092954 r4	0:28 1:90	A:1234826243;C:1058941866;G:1064097171;T:1129318562;N:86174	28	90			1234826243	1058941866	1064097171	1129318562	86174	SRX19646190	SRS17014000	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00802	0.94821	0.00201	0.06394	0.99472	0.87618	0.25364	0.46914	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74512	74512	SRR23824356	SRX19646183	SRS17013993	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 7 dpi replicate 2	GSM7092947	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 7 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092947	GSM7092947: liver 7 dpi replicate 2; Danio rerio; RNA Seq	GSM7092947 r1	GSM7092947	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Liver-2_S23_L001_R1_001.fastq.gz 7dpi-Liver-2_S23_L001_R2_001.fastq.gz	fastq fastq	2901696228.0	24590646.0	GSM7092947 r1	0:28 1:90	A:800794183;C:688235467;G:699322734;T:713278095;N:65749	28	90			800794183	688235467	699322734	713278095	65749	SRX19646183	SRS17013993	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01367	0.94349	0.00359	0.06447	0.99371	0.8983	0.35863	0.50961	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74513	74513	SRR23824357	SRX19646183	SRS17013993	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 7 dpi replicate 2	GSM7092947	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 7 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092947	GSM7092947: liver 7 dpi replicate 2; Danio rerio; RNA Seq	GSM7092947 r1	GSM7092947	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Liver-2_S23_L002_R1_001.fastq.gz 7dpi-Liver-2_S23_L002_R2_001.fastq.gz	fastq fastq	2911402436.0	24672902.0	GSM7092947 r2	0:28 1:90	A:803250356;C:690504502;G:701686700;T:715898105;N:62773	28	90			803250356	690504502	701686700	715898105	62773	SRX19646183	SRS17013993	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01353	0.94324	0.00375	0.06448	0.9934	0.89512	0.36797	0.50133	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74514	74514	SRR23824358	SRX19646183	SRS17013993	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 7 dpi replicate 2	GSM7092947	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 7 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092947	GSM7092947: liver 7 dpi replicate 2; Danio rerio; RNA Seq	GSM7092947 r1	GSM7092947	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Liver-2_S23_L003_R1_001.fastq.gz 7dpi-Liver-2_S23_L003_R2_001.fastq.gz	fastq fastq	2952479180.0	25021010.0	GSM7092947 r3	0:28 1:90	A:814071655;C:700696343;G:712162705;T:725488870;N:59607	28	90			814071655	700696343	712162705	725488870	59607	SRX19646183	SRS17013993	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01352	0.9422	0.00377	0.06446	0.99383	0.89858	0.3405	0.51469	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74515	74515	SRR23824359	SRX19646183	SRS17013993	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 7 dpi replicate 2	GSM7092947	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 7 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092947	GSM7092947: liver 7 dpi replicate 2; Danio rerio; RNA Seq	GSM7092947 r1	GSM7092947	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Liver-2_S23_L004_R1_001.fastq.gz 7dpi-Liver-2_S23_L004_R2_001.fastq.gz	fastq fastq	2888880956.0	24482042.0	GSM7092947 r4	0:28 1:90	A:797569254;C:684817990;G:695605635;T:710833096;N:54981	28	90			797569254	684817990	695605635	710833096	54981	SRX19646183	SRS17013993	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01297	0.94356	0.00358	0.0658	0.99366	0.89406	0.37493	0.50579	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74516	74516	SRR23824360	SRX19646182	SRS17013992	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 7 dpi replicate 1	GSM7092946	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 7 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092946	GSM7092946: liver 7 dpi replicate 1; Danio rerio; RNA Seq	GSM7092946 r1	GSM7092946	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Liver-1_S19_L001_R1_001.fastq.gz 7dpi-Liver-1_S19_L001_R2_001.fastq.gz	fastq fastq	3336256244.0	28273358.0	GSM7092946 r1	0:28 1:90	A:928141930;C:786200774;G:796573600;T:825264837;N:75103	28	90			928141930	786200774	796573600	825264837	75103	SRX19646182	SRS17013992	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01265	0.9442	0.00339	0.0656	0.9933	0.88477	0.39633	0.57337	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74517	74517	SRR23824361	SRX19646182	SRS17013992	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 7 dpi replicate 1	GSM7092946	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 7 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092946	GSM7092946: liver 7 dpi replicate 1; Danio rerio; RNA Seq	GSM7092946 r1	GSM7092946	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Liver-1_S19_L002_R1_001.fastq.gz 7dpi-Liver-1_S19_L002_R2_001.fastq.gz	fastq fastq	3339415222.0	28300129.0	GSM7092946 r2	0:28 1:90	A:928571814;C:786954831;G:797381996;T:826433990;N:72591	28	90			928571814	786954831	797381996	826433990	72591	SRX19646182	SRS17013992	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01263	0.94485	0.0034	0.06446	0.9935	0.88341	0.4136	0.56226	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74518	74518	SRR23824362	SRX19646182	SRS17013992	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 7 dpi replicate 1	GSM7092946	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 7 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092946	GSM7092946: liver 7 dpi replicate 1; Danio rerio; RNA Seq	GSM7092946 r1	GSM7092946	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Liver-1_S19_L003_R1_001.fastq.gz 7dpi-Liver-1_S19_L003_R2_001.fastq.gz	fastq fastq	3389089446.0	28721097.0	GSM7092946 r3	0:28 1:90	A:942057789;C:799054157;G:809649273;T:838259397;N:68830	28	90			942057789	799054157	809649273	838259397	68830	SRX19646182	SRS17013992	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01251	0.94572	0.00331	0.06443	0.99279	0.88469	0.38873	0.57466	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74519	74519	SRR23824363	SRX19646182	SRS17013992	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 7 dpi replicate 1	GSM7092946	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 7 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092946	GSM7092946: liver 7 dpi replicate 1; Danio rerio; RNA Seq	GSM7092946 r1	GSM7092946	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	7dpi-Liver-1_S19_L004_R1_001.fastq.gz 7dpi-Liver-1_S19_L004_R2_001.fastq.gz	fastq fastq	3326239460.0	28188470.0	GSM7092946 r4	0:28 1:90	A:925663531;C:783373500;G:793504177;T:823634415;N:63837	28	90			925663531	783373500	793504177	823634415	63837	SRX19646182	SRS17013992	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.01246	0.94489	0.00337	0.06529	0.9933	0.88556	0.39241	0.55747	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74540	74540	SRR23824378	SRX19646176	SRS17013986	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 1 dpi replicate 2	GSM7092939	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 1 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092939	GSM7092939: liver 1 dpi replicate 2; Danio rerio; RNA Seq	GSM7092939 r1	GSM7092939	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Liver-2_S15_L001_R1_001.fastq.gz 1dpi-Liver-2_S15_L001_R2_001.fastq.gz	fastq fastq	3974430452.0	33681614.0	GSM7092939 r1	0:28 1:90	A:1095528573;C:930228144;G:956778552;T:991804101;N:91082	28	90			1095528573	930228144	956778552	991804101	91082	SRX19646176	SRS17013986	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.0077	0.93007	0.00172	0.08628	0.99308	0.86448	0.28435	0.51435	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74541	74541	SRR23824379	SRX19646176	SRS17013986	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 1 dpi replicate 2	GSM7092939	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 1 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092939	GSM7092939: liver 1 dpi replicate 2; Danio rerio; RNA Seq	GSM7092939 r1	GSM7092939	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Liver-2_S15_L002_R1_001.fastq.gz 1dpi-Liver-2_S15_L002_R2_001.fastq.gz	fastq fastq	4016739824.0	34040168.0	GSM7092939 r2	0:28 1:90	A:1107054312;C:940103463;G:966907262;T:1002588445;N:86342	28	90			1107054312	940103463	966907262	1002588445	86342	SRX19646176	SRS17013986	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00824	0.92962	0.00199	0.08535	0.99318	0.86444	0.2722	0.50248	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74542	74542	SRR23824402	SRX19646176	SRS17013986	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 1 dpi replicate 2	GSM7092939	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 1 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092939	GSM7092939: liver 1 dpi replicate 2; Danio rerio; RNA Seq	GSM7092939 r1	GSM7092939	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Liver-2_S15_L003_R1_001.fastq.gz 1dpi-Liver-2_S15_L003_R2_001.fastq.gz	fastq fastq	4043460452.0	34266614.0	GSM7092939 r3	0:28 1:90	A:1113324543;C:946991884;G:974101052;T:1008961554;N:81419	28	90			1113324543	946991884	974101052	1008961554	81419	SRX19646176	SRS17013986	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00748	0.93039	0.00169	0.08606	0.99289	0.86716	0.29448	0.51523	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74543	74543	SRR23824403	SRX19646176	SRS17013986	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 1 dpi replicate 2	GSM7092939	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 1 dpi replicate 2	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092939	GSM7092939: liver 1 dpi replicate 2; Danio rerio; RNA Seq	GSM7092939 r1	GSM7092939	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Liver-2_S15_L004_R1_001.fastq.gz 1dpi-Liver-2_S15_L004_R2_001.fastq.gz	fastq fastq	3977097134.0	33704213.0	GSM7092939 r4	0:28 1:90	A:1096872592;C:930325395;G:956420114;T:993402280;N:76753	28	90			1096872592	930325395	956420114	993402280	76753	SRX19646176	SRS17013986	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00756	0.93049	0.00182	0.08655	0.99354	0.86488	0.29659	0.50942	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74552	74552	SRR23824392	SRX19646173	SRS17013982	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 1 dpi replicate 1	GSM7092938	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 1 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092938	GSM7092938: liver 1 dpi replicate 1; Danio rerio; RNA Seq	GSM7092938 r1	GSM7092938	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Liver-1_S11_L001_R1_001.fastq.gz 1dpi-Liver-1_S11_L001_R2_001.fastq.gz	fastq fastq	4161718400.0	35268800.0	GSM7092938 r1	0:28 1:90	A:1156237978;C:969526154;G:993733251;T:1042125334;N:95683	28	90			1156237978	969526154	993733251	1042125334	95683	SRX19646173	SRS17013982	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00742	0.93962	0.00193	0.08534	0.99405	0.86931	0.28289	0.47838	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74553	74553	SRR23824393	SRX19646173	SRS17013982	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 1 dpi replicate 1	GSM7092938	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 1 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092938	GSM7092938: liver 1 dpi replicate 1; Danio rerio; RNA Seq	GSM7092938 r1	GSM7092938	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Liver-1_S11_L002_R1_001.fastq.gz 1dpi-Liver-1_S11_L002_R2_001.fastq.gz	fastq fastq	4194311652.0	35545014.0	GSM7092938 r2	0:28 1:90	A:1164793350;C:977205946;G:1001366769;T:1050855725;N:89862	28	90			1164793350	977205946	1001366769	1050855725	89862	SRX19646173	SRS17013982	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.0076	0.9407	0.0018	0.08601	0.99389	0.86831	0.256	0.50037	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74554	74554	SRR23824400	SRX19646173	SRS17013982	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 1 dpi replicate 1	GSM7092938	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 1 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092938	GSM7092938: liver 1 dpi replicate 1; Danio rerio; RNA Seq	GSM7092938 r1	GSM7092938	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Liver-1_S11_L003_R1_001.fastq.gz 1dpi-Liver-1_S11_L003_R2_001.fastq.gz	fastq fastq	4236970186.0	35906527.0	GSM7092938 r3	0:28 1:90	A:1175860194;C:987702516;G:1012476545;T:1060846608;N:84323	28	90			1175860194	987702516	1012476545	1060846608	84323	SRX19646173	SRS17013982	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00758	0.94031	0.00187	0.08613	0.99381	0.86819	0.28494	0.50439	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74555	74555	SRR23824401	SRX19646173	SRS17013982	SRP426909	PRJNA943553	Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish [zebrafish]	GSE227190	Transcriptome Analysis	Mice respond to myocardial infarction MI by generating a fibrotic scar in the heart. This is accompanied by systemic inflammation post the MI resolves. In contrast zebrafish can fully regenerate their heart post heart injury. To further investigate the divergent species' responses to cardiac injury single cell transcriptomic analyses were performed on the heart blood liver kidney and pancreatic islets. Overall design: Upon heart cryoinjury cells from multiple organs heart liver pancreas and whole kidney marrow were isolated for scRNA seq at 1 and 7 xxx post injury together with the uninjured controls.	parent bioproject:PRJNA943547	pubmed:39627536		liver 1 dpi replicate 1	GSM7092938	source name:Liver\|tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	liver 1 dpi replicate 1	Demultiplexing alignment filtering and UMI counting was performed with Cell Ranger v6.0.0 using the cellranger count command. Sample integration batch correction expression value normalization clustering cell type annotation and so on were done scater and scran. For more details and the cell type annotation information see https://github.com/abcwcm/CZI MI mouseZebrafish Assembly: GRCz11 Supplementary files format and content: CellRanger produced filtered feature barcode matrix in H5 format.	Liver	Heart cryoinjury or untreated	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	Standard zebrafish husbandry protocol.	tissue:Liver\|cell type:whole organ\|genotype:wild type\|treatment:Heart cryoinjury	GSM7092938	GSM7092938: liver 1 dpi replicate 1; Danio rerio; RNA Seq	GSM7092938 r1	GSM7092938	1	Heart ventricles were placed in the ice cold PBS buffer with 1% BSA. post several washes removing blood cells ventricles were gently cut into small pieces. Tissues were incubated in digestion buffer 0.5 ml HBSS plus 0.26 U/ml Liberase DH [Roche] and 1% sheep serum for 45 minutes at 37°C while agitating at 750 rpm on an Eppendorf ThermoMixer. Supernatants were collected every 15 min and neutralized with 10% sheep serum and cells were completely disaggregated by gently pipetting up and down. The dissociated cells were centrifuged at 200 g for 5 min at 4°C and re suspended in HBSS with 0.05% BSA. The cell suspension 2 ml was then gently added on top of 2 ml HBSS buffer with 7.5% BSA. post spinning down at 200 g for 5 min at 4°C the pellet was resuspended in 500 l and filtered through a 35 mm strainer. Whole kidney marrow cells were isolated as described previously. Briefly kidneys were collected on ice and homogenized immediately in PBS plus 0.05% BSA by using a 10ml syringe with 18 1/2 G. The dissociated cells were washed twice in PBS plus 0.05% BSA and spun down at 300 g for 5 min at 4°C. Pellets were re suspended in PBS plus 0.05% BSA and filtered through a 35 mm strainer. Livers were collected on ice and incubated in digestion buffer 0.5 ml HBSS plus 0.13 U/ml Liberase DH [Roche] and 1% sheep serum at room temperature. The cell lyses was gently stirred with a Spinbar magnetic stirring bar Bel Art Products and the supernatant were collected every 5 minutes. The cell lysate was filtered through a 70 mm strainer and centrifuged at 150 g for 3 min at 4°C. Pellet was resuspended in PBS plus 0.05% BSA and then gently added on top of HBSS buffer with 7.5% BSA. post spinning down at 300 g for 5 min pellets were washed one more time with PBS plus 0.05% BSA. post centrifuging at 300 g for 5 min the resuspended cell lyses was filtered through a 35 mm strainer. Pancreatic cells were isolated using the same protocol as liver cells except for the initial spinning down at 300 g for 5 min. All suspended cells were stai…	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP426909	loader:fastq load.py	1dpi-Liver-1_S11_L004_R1_001.fastq.gz 1dpi-Liver-1_S11_L004_R2_001.fastq.gz	fastq fastq	4158915900.0	35245050.0	GSM7092938 r4	0:28 1:90	A:1156072890;C:968215633;G:991941070;T:1042607465;N:78842	28	90			1156072890	968215633	991941070	1042607465	78842	SRX19646173	SRS17013982	SRA1603354	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	Applied Bioinformatics Core, Applied Bioinformatics Core, Weill Cornell Medicine	2	0.00789	0.9395	0.00206	0.08611	0.99352	0.86963	0.28343	0.50985	28	90	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-03-12	Undetermined	Undetermined	Liver	Liver and Biliary System
74852	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		pubmed:37453064		liver	GSM7139012	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		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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.		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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP430632		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			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		0.59667	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-03	Adult	Adult	Liver	Liver and Biliary System
74853	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		pubmed:37453064		liver	GSM7139012	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		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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.		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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP430632		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			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		0.62565	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-03	Adult	Adult	Liver	Liver and Biliary System
74854	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		pubmed:37453064		liver	GSM7139012	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		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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.		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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP430632		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			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		0.61082	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-03	Adult	Adult	Liver	Liver and Biliary System
74855	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		pubmed:37453064		liver	GSM7139012	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		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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.		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 μl collection buffer 4.5 μl 1% BSA/PBS + 0.5 μl 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.	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP430632		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			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		0.62152	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2023-04-03	Adult	Adult	Liver	Liver and Biliary System
75608	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.			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	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									scRNA seq of zebrafish R0h livers	20210429 S3 R0	20210429 S3 R0	Using Chromium Single cell three prime GEM v3.1 Reagent kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439656		R21049148-20210429-S3-R0-1_combined_R1.fastq.gz R21049148-20210429-S3-R0-1_combined_R2.fastq.gz R21049148-20210429-S3-R0-2_combined_R1.fastq.gz R21049148-20210429-S3-R0-2_combined_R2.fastq.gz R21049148-20210429-S3-R0-3_combined_R1.fastq.gz R21049148-20210429-S3-R0-3_combined_R2.fastq.gz R21049148-20210429-S3-R0-4_combined_R1.fastq.gz R21049148-20210429-S3-R0-4_combined_R2.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	108860887800.0	362869626.0	R21049148 20210429 S3 R0 1 combined R1.fastq.gz	0:150 1:150	A:46078842047;C:20145501988;G:19787836142;T:22846772612;N:1935011	150	150			46078842047	20145501988	19787836142	22846772612	1935011	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		0.58532	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2023-05-25	Zygote	Embryo	Liver	Liver and Biliary System
75609	75609	SRR24742193	SRX20519419	SRS17829369	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.			The livers of fish were collected at 6 dpf	scRNA seq of zebrafish 6 dpf livers	Livers of lfabp:Dendra2 NTR fish at 6 dpf	strain:ABGO\|isolate:not applicable\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:6 dpf\|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									scRNA seq of zebrafish 6 dpf livers	20210429 S2 D6	20210429 S2 D6	Using Chromium Single cell three prime GEM v3.1 Reagent kit		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP439656		R21049147-20210429-S2-D6-1_combined_R1.fastq.gz R21049147-20210429-S2-D6-1_combined_R2.fastq.gz R21049147-20210429-S2-D6-2_combined_R1.fastq.gz R21049147-20210429-S2-D6-2_combined_R2.fastq.gz R21049147-20210429-S2-D6-3_combined_R1.fastq.gz R21049147-20210429-S2-D6-3_combined_R2.fastq.gz R21049147-20210429-S2-D6-4_combined_R1.fastq.gz R21049147-20210429-S2-D6-4_combined_R2.fastq.gz	fastq fastq fastq fastq fastq fastq fastq fastq	122319275400.0	407730918.0	R21049147 20210429 S2 D6 1 combined R1.fastq.gz	0:150 1:150	A:36198844657;C:27630980168;G:25561495158;T:32927451902;N:503515	150	150			36198844657	27630980168	25561495158	32927451902	503515	SRX20519419	SRS17829369	SRA1643264	Institute of Developmental Biology and Regenerative Medicine\|Southwest University	Institute of Developmental Biology and Regenerative Medicine AccuraMed Company	2	0.00072	0.9132	0.00023	0.11357	0.99995	0.88909	0.5	0.69408	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	sc	single_cell_droplet	10x	China	2023-05-25	Larval	Larval	Liver	Liver and Biliary System

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