metadata: run_metadata: 101 rows where technology = "10x" and tissue_curation

101 rows where technology = "10x" and tissue_curation_coarse = "Liver and Biliary System"

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.attributes	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
55196	55196	SRR10153191	SRX6878621	SRS5414403	SRP222786	PRJNA573063	Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC	GSE137784	Transcriptome Analysis	Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment.	parent bioproject:PRJNA573068	pubmed:31575545		NoHCC [Single cell]	GSM4087821	tissue:Liver\|transgenic line:Tgfabp10a flox beta catenin\|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC	NoHCC [Single cell]	10x Genomics’ Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp FASTQ files. Custom transgenic genomic reference was built with ‘cellranger mkref’ but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with ‘cellranger mkgtf’ for gene biotypes matching ‘protein coding’ ‘lincRNA’ and ‘antisense’ tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with ‘cellranger count’ pipeline with their respective transgenic genome build with parameter ‘ expect cells=3000’ In attempt to recover those perhaps lower quality GEM partitions the raw gene barcode matrices from ‘cellranger count’ located in ‘outs/raw gene bc matrices’ was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al. 2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al. 2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al. 2008. Cells with extremely low UMI counts extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells…	Liver	Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf	Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank’s Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with 3’ chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Se…	Fish were raised following IACUC approved protocols in insititutional zebrafish facility.	transgenic line:Tgfabp10a flox beta catenin\|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC	GSM4087821	GSM4087821: NoHCC [Single cell]; Danio rerio; RNA Seq	GSM4087821		1	Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with three prime chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three pri…	GEO Accession:GSM4087821	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP222786		15547X4_S11_L007_R2_001.fastq.gz 15547X4_S11_L007_R1_001.fastq.gz	fastq fastq	16861988178.0	133825303.0	GSM4087821 r1	0:26 1:100	A:4788108995;C:3905645218;G:3694064311;T:4468647482;N:5522172	26	100			4788108995	3905645218	3694064311	4468647482	5522172	SRX6878621	SRS5414403	SRA965504	GEO	Pathology, University of California, San Francisco	2	0.00236	0.93017	0.0008	0.04645	0.99626	0.89043	0.52233	0.64352	26	100	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-09-20	Multi-stage	Multi-stage	Liver	Liver and Biliary System
55197	55197	SRR10153190	SRX6878620	SRS5414402	SRP222786	PRJNA573063	Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC	GSE137784	Transcriptome Analysis	Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment.	parent bioproject:PRJNA573068	pubmed:31575545		HCCCreLox [Single cell]	GSM4087820	tissue:Liver\|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin\|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf	HCCCreLox [Single cell]	10x Genomics’ Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp FASTQ files. Custom transgenic genomic reference was built with ‘cellranger mkref’ but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with ‘cellranger mkgtf’ for gene biotypes matching ‘protein coding’ ‘lincRNA’ and ‘antisense’ tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with ‘cellranger count’ pipeline with their respective transgenic genome build with parameter ‘ expect cells=3000’ In attempt to recover those perhaps lower quality GEM partitions the raw gene barcode matrices from ‘cellranger count’ located in ‘outs/raw gene bc matrices’ was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al. 2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al. 2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al. 2008. Cells with extremely low UMI counts extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells…	Liver	Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf	Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank’s Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with 3’ chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Se…	Fish were raised following IACUC approved protocols in insititutional zebrafish facility.	transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin\|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf	GSM4087820	GSM4087820: HCCCreLox [Single cell]; Danio rerio; RNA Seq	GSM4087820		1	Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with three prime chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three pri…	GEO Accession:GSM4087820	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP222786		15547X2_S9_L006_R1_001.fastq.gz 15547X2_S9_L006_R2_001.fastq.gz	fastq fastq	16758654318.0	133005193.0	GSM4087820 r1	0:26 1:100	A:4758015356;C:3904784528;G:3787834220;T:4302283542;N:5736672	26	100			4758015356	3904784528	3787834220	4302283542	5736672	SRX6878620	SRS5414402	SRA965504	GEO	Pathology, University of California, San Francisco	2	0.00291	0.94432	0.00084	0.04281	0.99539	0.88203	0.48041	0.60684	26	100	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-09-20	Multi-stage	Multi-stage	Liver	Liver and Biliary System
55198	55198	SRR10153189	SRX6878619	SRS5414401	SRP222786	PRJNA573063	Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC	GSE137784	Transcriptome Analysis	Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding ß catenin. ß catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the ß catenin protein leading to nuclear and/or cytoplasmic localization of ß catenin and downstream activation of Wnt target genes. In patient HCC samples ß catenin nuclear and cytoplasmic localization are typically patchy even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in ß catenin activation are not well understood. To define mechanisms of ß catenin driven HCC initiation we generated a Cre lox system that enabled switching on activated ß catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated ß catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/ß catenin signaling heterogeneity later in hepatocarcinogenesis we performed RNA seq analysis of zebrafish ß catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that “Cancer” and “Liver Tumor” categories were significantly altered indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level 2.9% to 15.2% of hepatocytes from zebrafish ß catenin driven HCC expressed two or more of the Wnt target genes axin2 mtor glula myca and wif1 indicating focal activation of Wnt signaling in established tumors. Thus heterogeneous ß catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment.	parent bioproject:PRJNA573068	pubmed:31575545		HCCHepABC [Single cell]	GSM4087819	tissue:Liver\|transgenic line:Tgfabp10a pt beta catenin\|age:6 mpf at larval stg:N1\|diagnosis:HCC	HCCHepABC [Single cell]	10x Genomics’ Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp FASTQ files. Custom transgenic genomic reference was built with ‘cellranger mkref’ but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with ‘cellranger mkgtf’ for gene biotypes matching ‘protein coding’ ‘lincRNA’ and ‘antisense’ tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with ‘cellranger count’ pipeline with their respective transgenic genome build with parameter ‘ expect cells=3000’ In attempt to recover those perhaps lower quality GEM partitions the raw gene barcode matrices from ‘cellranger count’ located in ‘outs/raw gene bc matrices’ was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al. 2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al. 2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al. 2008. Cells with extremely low UMI counts extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells…	Liver	Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf	Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank’s Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with 3’ chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Se…	Fish were raised following IACUC approved protocols in insititutional zebrafish facility.	transgenic line:Tgfabp10a pt beta catenin\|age:6 mpf at larval stg:N1\|diagnosis:HCC	GSM4087819	GSM4087819: HCCHepABC [Single cell]; Danio rerio; RNA Seq	GSM4087819		1	Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter and the filtrate was centrifuged at 1200 RPM 4C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin. The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific. The Chromium Single Cell Gene Expression Solution with three prime chemistry version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction. Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs the micro droplets. Within individual GEMs cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53°C for 45 min followed by 85°C for 5 min. Subsequent A tailing end repair adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three pri…	GEO Accession:GSM4087819	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP222786		15547X1_S8_L006_R1_001.fastq.gz 15547X1_S8_L006_R2_001.fastq.gz	fastq fastq	21400430184.0	169844684.0	GSM4087819 r1	0:26 1:100	A:6081828690;C:4958144407;G:4770562017;T:5582605586;N:7289484	26	100			6081828690	4958144407	4770562017	5582605586	7289484	SRX6878619	SRS5414401	SRA965504	GEO	Pathology, University of California, San Francisco	2	0.00253	0.93502	0.00092	0.06641	0.99624	0.88164	0.50505	0.61652	26	100	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2019-09-20	Adult	Adult	Liver	Liver and Biliary System
59288	59288	SRR11806492	SRX8357870	SRS6673976	SRP262133	PRJNA633496	Single cell sequencing reveals heterogeneity effects of arsenic or/and 2 2 dichloroacetamide on zebrafish liver	GSE150751	Transcriptome Analysis	Arsenic and DBPs has been found to be one of the major risk in many regions of the world. However current understanding of thier combined toxicities are unclear. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 13563 liver cells obtained from zebrafishes exposed to 100µg/L arsenic 300µg/L dichloroacetanilide DCAcAm and co exposure for 23 days. Five liver cell populations were identified. We found that the hepatocytes and macrophages were the main target of arsenic and DCAcAm exposure. And the hepatocytes of male and female showed a huge difference when expsoure to arsenic and DCAcAm. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish liver exposure to arsenic and DCAcAm.				As Dc	GSM4558083	source name:liver cells\|tissue:liver single cell suspension\|age:16 wpf\|exposed pollutants:100ug/L arsenic and 300ug/L DCAcAm	As Dc	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	liver cells	Exposure solutions were prepared by adding 100μg/L arsenic 300μg/L DCAcAm or both of them to culture water. The exposure solution were was replaced every 2 days. post 23 d exposure zebrafish were collected and liver were rapidly extracted on ice.	The isolated liver tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.		tissue:liver single cell suspension\|age:16 wpf\|exposed pollutants:100ug/L arsenic and 300ug/L DCAcAm	GSM4558083	GSM4558083: As Dc; Danio rerio; RNA Seq	GSM4558083		1	The isolated liver tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.	GEO Accession:GSM4558083	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP262133		As_Dc_1.fq.gz As_Dc_2.fq.gz	fastq fastq	115893045000.0	386310150.0	GSM4558083 r1	0:150 1:150	A:28430544743;C:22114323875;G:34731304363;T:30590487752;N:26384267	150	150			28430544743	22114323875	34731304363	30590487752	26384267	SRX8357870	SRS6673976	SRA1076689	GEO	Nanjing University	2	0.0	0.91666	0.0	0.0203	1.0	0.91291		0.46748	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-05-18	Adult	Adult	Liver	Liver and Biliary System
59289	59289	SRR11806491	SRX8357869	SRS6673975	SRP262133	PRJNA633496	Single cell sequencing reveals heterogeneity effects of arsenic or/and 2 2 dichloroacetamide on zebrafish liver	GSE150751	Transcriptome Analysis	Arsenic and DBPs has been found to be one of the major risk in many regions of the world. However current understanding of thier combined toxicities are unclear. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 13563 liver cells obtained from zebrafishes exposed to 100µg/L arsenic 300µg/L dichloroacetanilide DCAcAm and co exposure for 23 days. Five liver cell populations were identified. We found that the hepatocytes and macrophages were the main target of arsenic and DCAcAm exposure. And the hepatocytes of male and female showed a huge difference when expsoure to arsenic and DCAcAm. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish liver exposure to arsenic and DCAcAm.				Dc300	GSM4558082	source name:liver cells\|tissue:liver single cell suspension\|age:16 wpf\|exposed pollutants:300ug/L DCAcAm	Dc300	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	liver cells	Exposure solutions were prepared by adding 100μg/L arsenic 300μg/L DCAcAm or both of them to culture water. The exposure solution were was replaced every 2 days. post 23 d exposure zebrafish were collected and liver were rapidly extracted on ice.	The isolated liver tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.		tissue:liver single cell suspension\|age:16 wpf\|exposed pollutants:300ug/L DCAcAm	GSM4558082	GSM4558082: Dc300; Danio rerio; RNA Seq	GSM4558082		1	The isolated liver tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.	GEO Accession:GSM4558082	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP262133		Dc300_1.fq.gz Dc300_2.fq.gz	fastq fastq	127027640400.0	423425468.0	GSM4558082 r1	0:150 1:150	A:30842125524;C:23778726057;G:39107636584;T:33274935260;N:24216975	150	150			30842125524	23778726057	39107636584	33274935260	24216975	SRX8357869	SRS6673975	SRA1076689	GEO	Nanjing University	2	0.0	0.91236	0.0	0.02333	1.0	0.90879		0.42849	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-05-18	Adult	Adult	Liver	Liver and Biliary System
59290	59290	SRR11806490	SRX8357868	SRS6673977	SRP262133	PRJNA633496	Single cell sequencing reveals heterogeneity effects of arsenic or/and 2 2 dichloroacetamide on zebrafish liver	GSE150751	Transcriptome Analysis	Arsenic and DBPs has been found to be one of the major risk in many regions of the world. However current understanding of thier combined toxicities are unclear. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 13563 liver cells obtained from zebrafishes exposed to 100µg/L arsenic 300µg/L dichloroacetanilide DCAcAm and co exposure for 23 days. Five liver cell populations were identified. We found that the hepatocytes and macrophages were the main target of arsenic and DCAcAm exposure. And the hepatocytes of male and female showed a huge difference when expsoure to arsenic and DCAcAm. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish liver exposure to arsenic and DCAcAm.				As100	GSM4558081	source name:liver cells\|tissue:liver single cell suspension\|age:16 wpf\|exposed pollutants:100ug/L arsenic	As100	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	liver cells	Exposure solutions were prepared by adding 100μg/L arsenic 300μg/L DCAcAm or both of them to culture water. The exposure solution were was replaced every 2 days. post 23 d exposure zebrafish were collected and liver were rapidly extracted on ice.	The isolated liver tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.		tissue:liver single cell suspension\|age:16 wpf\|exposed pollutants:100ug/L arsenic	GSM4558081	GSM4558081: As100; Danio rerio; RNA Seq	GSM4558081		1	The isolated liver tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.	GEO Accession:GSM4558081	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP262133		As100_2.fq.gz As100_1.fq.gz	fastq fastq	102837948900.0	342793163.0	GSM4558081 r1	0:150 1:150	A:24894384372;C:19593836618;G:31314101265;T:27014778377;N:20848268	150	150			24894384372	19593836618	31314101265	27014778377	20848268	SRX8357868	SRS6673977	SRA1076689	GEO	Nanjing University	2	0.0	0.91738	0.0	0.02836	1.0	0.89536		0.46528	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-05-18	Adult	Adult	Liver	Liver and Biliary System
59291	59291	SRR11806489	SRX8357867	SRS6673974	SRP262133	PRJNA633496	Single cell sequencing reveals heterogeneity effects of arsenic or/and 2 2 dichloroacetamide on zebrafish liver	GSE150751	Transcriptome Analysis	Arsenic and DBPs has been found to be one of the major risk in many regions of the world. However current understanding of thier combined toxicities are unclear. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 13563 liver cells obtained from zebrafishes exposed to 100µg/L arsenic 300µg/L dichloroacetanilide DCAcAm and co exposure for 23 days. Five liver cell populations were identified. We found that the hepatocytes and macrophages were the main target of arsenic and DCAcAm exposure. And the hepatocytes of male and female showed a huge difference when expsoure to arsenic and DCAcAm. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish liver exposure to arsenic and DCAcAm.				CK	GSM4558080	source name:liver cells\|tissue:liver single cell suspension\|age:16 wpf\|exposed pollutants:n1	CK	We use FastQC to perform basic statistics on the quality of the raw reads. Then those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window cutting when the average quality per base drops below 10 SLIDINGWINDOW: 4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a. alignment with the adapter sequence the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30 removed non overlapping portions ILLUMINACLIP: adapter.fa: 2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic intronic and intergenic and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon intronic if it is non exonic and intersects an intron and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts looking for compatibility. A read that is compatible with the exons of an annotated transcript and aligned to the same strand is considered mapped to the transcriptome. If the read is compatible with a single gene annotation it is considered uniquely confidently mapped to the transcrip…	liver cells	Exposure solutions were prepared by adding 100μg/L arsenic 300μg/L DCAcAm or both of them to culture water. The exposure solution were was replaced every 2 days. post 23 d exposure zebrafish were collected and liver were rapidly extracted on ice.	The isolated liver tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.		tissue:liver single cell suspension\|age:16 wpf\|exposed pollutants:n1	GSM4558080	GSM4558080: CK; Danio rerio; RNA Seq	GSM4558080		1	The isolated liver tissue was digested into cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.	GEO Accession:GSM4558080	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP262133		CK_1.fq.gz CK_2.fq.gz	fastq fastq	133916231400.0	446387438.0	GSM4558080 r1	0:150 1:150	A:32477145943;C:25399997371;G:40326238358;T:35690408393;N:22441335	150	150			32477145943	25399997371	40326238358	35690408393	22441335	SRX8357867	SRS6673974	SRA1076689	GEO	Nanjing University	2	0.0	0.91836	0.0	0.02382	1.0	0.90871		0.46105	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2020-05-18	Adult	Adult	Liver	Liver and Biliary System
65633	65633	SRR15427704	SRX11729087	SRS9757823	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		MPI MT 3	GSM5515736	source name:Adult zebrafish liver dissection\|genotype:mpi+/ mss7\|tissue:Liver	MPI MT 3	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:mpi+/ mss7\|tissue:Liver	GSM5515736	GSM5515736: MPI MT 3; Danio rerio; RNA Seq	GSM5515736		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515736	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 MT5 0 G S8 L001 I1 001.fastq.gz read2PairFiles=JACH01 MT5 0 G S8 L001 R1 001.fastq.gz read3PairFiles=JACH01 MT5 0 G S8 L001 R2 001.fastq.gz	JACH01_MT5_0_G_S8_L001_I1_001.fastq.gz JACH01_MT5_0_G_S8_L001_R1_001.fastq.gz JACH01_MT5_0_G_S8_L001_R2_001.fastq.gz	fastq fastq fastq	12954775700.0	129547757.0	GSM5515736 r1	0:8 1:30 2:62	A:2373305749;C:1813473007;G:1779922398;T:2065049504;N:210276	8	30	62		2373305749	1813473007	1779922398	2065049504	210276	SRX11729087	SRS9757823	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.94564		0.06912		0.88712		0.74857		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65634	65634	SRR15427705	SRX11729087	SRS9757823	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		MPI MT 3	GSM5515736	source name:Adult zebrafish liver dissection\|genotype:mpi+/ mss7\|tissue:Liver	MPI MT 3	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:mpi+/ mss7\|tissue:Liver	GSM5515736	GSM5515736: MPI MT 3; Danio rerio; RNA Seq	GSM5515736		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515736	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 MT5 0 G S8 L002 I1 001.fastq.gz read2PairFiles=JACH01 MT5 0 G S8 L002 R1 001.fastq.gz read3PairFiles=JACH01 MT5 0 G S8 L002 R2 001.fastq.gz	JACH01_MT5_0_G_S8_L002_I1_001.fastq.gz JACH01_MT5_0_G_S8_L002_R1_001.fastq.gz JACH01_MT5_0_G_S8_L002_R2_001.fastq.gz	fastq fastq fastq	12966987200.0	129669872.0	GSM5515736 r2	0:8 1:30 2:62	A:2375412279;C:1814593036;G:1781329886;T:2068062113;N:134750	8	30	62		2375412279	1814593036	1781329886	2068062113	134750	SRX11729087	SRS9757823	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.94477		0.06799		0.88929		0.75006		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65635	65635	SRR15427702	SRX11729086	SRS9757824	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		MPI MT 2	GSM5515735	source name:Adult zebrafish liver dissection\|genotype:mpi+/ mss7\|tissue:Liver	MPI MT 2	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:mpi+/ mss7\|tissue:Liver	GSM5515735	GSM5515735: MPI MT 2; Danio rerio; RNA Seq	GSM5515735		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515735	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 MT4 0 G S7 L001 I1 001.fastq.gz read2PairFiles=JACH01 MT4 0 G S7 L001 R1 001.fastq.gz read3PairFiles=JACH01 MT4 0 G S7 L001 R2 001.fastq.gz	JACH01_MT4_0_G_S7_L001_I1_001.fastq.gz JACH01_MT4_0_G_S7_L001_R1_001.fastq.gz JACH01_MT4_0_G_S7_L001_R2_001.fastq.gz	fastq fastq fastq	13930172400.0	139301724.0	GSM5515735 r1	0:8 1:30 2:62	A:2520150103;C:1968356587;G:1962290731;T:2185685805;N:223662	8	30	62		2520150103	1968356587	1962290731	2185685805	223662	SRX11729086	SRS9757824	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.94376		0.0702		0.88233		0.66983		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65636	65636	SRR15427703	SRX11729086	SRS9757824	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		MPI MT 2	GSM5515735	source name:Adult zebrafish liver dissection\|genotype:mpi+/ mss7\|tissue:Liver	MPI MT 2	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:mpi+/ mss7\|tissue:Liver	GSM5515735	GSM5515735: MPI MT 2; Danio rerio; RNA Seq	GSM5515735		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515735	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 MT4 0 G S7 L002 I1 001.fastq.gz read2PairFiles=JACH01 MT4 0 G S7 L002 R1 001.fastq.gz read3PairFiles=JACH01 MT4 0 G S7 L002 R2 001.fastq.gz	JACH01_MT4_0_G_S7_L002_I1_001.fastq.gz JACH01_MT4_0_G_S7_L002_R1_001.fastq.gz JACH01_MT4_0_G_S7_L002_R2_001.fastq.gz	fastq fastq fastq	13953736500.0	139537365.0	GSM5515735 r2	0:8 1:30 2:62	A:2524408821;C:1970748229;G:1965304712;T:2190710041;N:144827	8	30	62		2524408821	1970748229	1965304712	2190710041	144827	SRX11729086	SRS9757824	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.94393		0.07007		0.8827		0.67588		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65637	65637	SRR15427700	SRX11729085	SRS9757822	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		MPI MT 1	GSM5515734	source name:Adult zebrafish liver dissection\|genotype:mpi+/ mss7\|tissue:Liver	MPI MT 1	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:mpi+/ mss7\|tissue:Liver	GSM5515734	GSM5515734: MPI MT 1; Danio rerio; RNA Seq	GSM5515734		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515734	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 MT1 0 G S6 L001 I1 001.fastq.gz read2PairFiles=JACH01 MT1 0 G S6 L001 R1 001.fastq.gz read3PairFiles=JACH01 MT1 0 G S6 L001 R2 001.fastq.gz	JACH01_MT1_0_G_S6_L001_I1_001.fastq.gz JACH01_MT1_0_G_S6_L001_R1_001.fastq.gz JACH01_MT1_0_G_S6_L001_R2_001.fastq.gz	fastq fastq fastq	4637200.0	46372.0	GSM5515734 r1	0:8 1:30 2:62	A:1286183;C:585985;G:400665;T:602163;N:68	8	30	62		1286183	585985	400665	602163	68	SRX11729085	SRS9757822	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.60068		0.04081		0.9819		0.72989		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65638	65638	SRR15427701	SRX11729085	SRS9757822	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		MPI MT 1	GSM5515734	source name:Adult zebrafish liver dissection\|genotype:mpi+/ mss7\|tissue:Liver	MPI MT 1	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:mpi+/ mss7\|tissue:Liver	GSM5515734	GSM5515734: MPI MT 1; Danio rerio; RNA Seq	GSM5515734		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515734	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 MT1 0 G S6 L002 I1 001.fastq.gz read2PairFiles=JACH01 MT1 0 G S6 L002 R1 001.fastq.gz read3PairFiles=JACH01 MT1 0 G S6 L002 R2 001.fastq.gz	JACH01_MT1_0_G_S6_L002_I1_001.fastq.gz JACH01_MT1_0_G_S6_L002_R1_001.fastq.gz JACH01_MT1_0_G_S6_L002_R2_001.fastq.gz	fastq fastq fastq	4610800.0	46108.0	GSM5515734 r2	0:8 1:30 2:62	A:1276135;C:582988;G:399491;T:600069;N:13	8	30	62		1276135	582988	399491	600069	13	SRX11729085	SRS9757822	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.5938		0.03604		0.98194		0.56926		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65639	65639	SRR15427698	SRX11729084	SRS9757820	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		WT 3	GSM5515733	source name:Adult zebrafish liver dissection\|genotype:WT\|tissue:Liver	WT 3	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:WT\|tissue:Liver	GSM5515733	GSM5515733: WT 3; Danio rerio; RNA Seq	GSM5515733		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515733	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 WT5 0 G S5 L001 I1 001.fastq.gz read2PairFiles=JACH01 WT5 0 G S5 L001 R1 001.fastq.gz read3PairFiles=JACH01 WT5 0 G S5 L001 R2 001.fastq.gz	JACH01_WT5_0_G_S5_L001_I1_001.fastq.gz JACH01_WT5_0_G_S5_L001_R1_001.fastq.gz JACH01_WT5_0_G_S5_L001_R2_001.fastq.gz	fastq fastq fastq	13673595000.0	136735950.0	GSM5515733 r1	0:8 1:30 2:62	A:2495771346;C:1908538453;G:1867817596;T:2205282624;N:218881	8	30	62		2495771346	1908538453	1867817596	2205282624	218881	SRX11729084	SRS9757820	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.94243		0.06253		0.87925		0.62425		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65640	65640	SRR15427699	SRX11729084	SRS9757820	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		WT 3	GSM5515733	source name:Adult zebrafish liver dissection\|genotype:WT\|tissue:Liver	WT 3	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:WT\|tissue:Liver	GSM5515733	GSM5515733: WT 3; Danio rerio; RNA Seq	GSM5515733		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515733	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 WT5 0 G S5 L002 I1 001.fastq.gz read2PairFiles=JACH01 WT5 0 G S5 L002 R1 001.fastq.gz read3PairFiles=JACH01 WT5 0 G S5 L002 R2 001.fastq.gz	JACH01_WT5_0_G_S5_L002_I1_001.fastq.gz JACH01_WT5_0_G_S5_L002_R1_001.fastq.gz JACH01_WT5_0_G_S5_L002_R2_001.fastq.gz	fastq fastq fastq	13692132800.0	136921328.0	GSM5515733 r2	0:8 1:30 2:62	A:2499252536;C:1910269997;G:1869946744;T:2209509870;N:143189	8	30	62		2499252536	1910269997	1869946744	2209509870	143189	SRX11729084	SRS9757820	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.94302		0.06357		0.88024		0.61719		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65641	65641	SRR15427696	SRX11729083	SRS9757821	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		WT 2	GSM5515732	source name:Adult zebrafish liver dissection\|genotype:WT\|tissue:Liver	WT 2	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:WT\|tissue:Liver	GSM5515732	GSM5515732: WT 2; Danio rerio; RNA Seq	GSM5515732		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515732	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 WT4 0 G S4 L001 I1 001.fastq.gz read2PairFiles=JACH01 WT4 0 G S4 L001 R1 001.fastq.gz read3PairFiles=JACH01 WT4 0 G S4 L001 R2 001.fastq.gz	JACH01_WT4_0_G_S4_L001_I1_001.fastq.gz JACH01_WT4_0_G_S4_L001_R1_001.fastq.gz JACH01_WT4_0_G_S4_L001_R2_001.fastq.gz	fastq fastq fastq	14852482500.0	148524825.0	GSM5515732 r1	0:8 1:30 2:62	A:2759428468;C:2136767451;G:2019665363;T:2292438314;N:239554	8	30	62		2759428468	2136767451	2019665363	2292438314	239554	SRX11729083	SRS9757821	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.94827		0.05642		0.89658		0.75622		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65642	65642	SRR15427697	SRX11729083	SRS9757821	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		WT 2	GSM5515732	source name:Adult zebrafish liver dissection\|genotype:WT\|tissue:Liver	WT 2	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:WT\|tissue:Liver	GSM5515732	GSM5515732: WT 2; Danio rerio; RNA Seq	GSM5515732		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515732	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 WT4 0 G S4 L002 I1 001.fastq.gz read2PairFiles=JACH01 WT4 0 G S4 L002 R1 001.fastq.gz read3PairFiles=JACH01 WT4 0 G S4 L002 R2 001.fastq.gz	JACH01_WT4_0_G_S4_L002_I1_001.fastq.gz JACH01_WT4_0_G_S4_L002_R1_001.fastq.gz JACH01_WT4_0_G_S4_L002_R2_001.fastq.gz	fastq fastq fastq	14869012700.0	148690127.0	GSM5515732 r2	0:8 1:30 2:62	A:2762560965;C:2138448212;G:2021327816;T:2296295190;N:155691	8	30	62		2762560965	2138448212	2021327816	2296295190	155691	SRX11729083	SRS9757821	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.94954		0.05588		0.89438		0.75111		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65643	65643	SRR15427694	SRX11729082	SRS9757819	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		WT 1	GSM5515731	source name:Adult zebrafish liver dissection\|genotype:WT\|tissue:Liver	WT 1	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:WT\|tissue:Liver	GSM5515731	GSM5515731: WT 1; Danio rerio; RNA Seq	GSM5515731		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515731	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 WT2 0 G S3 L001 I1 001.fastq.gz read2PairFiles=JACH01 WT2 0 G S3 L001 R1 001.fastq.gz read3PairFiles=JACH01 WT2 0 G S3 L001 R2 001.fastq.gz	JACH01_WT2_0_G_S3_L001_I1_001.fastq.gz JACH01_WT2_0_G_S3_L001_R1_001.fastq.gz JACH01_WT2_0_G_S3_L001_R2_001.fastq.gz	fastq fastq fastq	14974124300.0	149741243.0	GSM5515731 r1	0:8 1:30 2:62	A:2755810823;C:2157907927;G:2041659391;T:2328338949;N:239976	8	30	62		2755810823	2157907927	2041659391	2328338949	239976	SRX11729082	SRS9757819	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.9462		0.05451		0.89832		0.7809		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
65644	65644	SRR15427695	SRX11729082	SRS9757819	SRP332278	PRJNA754150	Single cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and pathways with human liver	GSE181987	Other	Liver fibrosis is the excessive accumulation of extracellular matrix that can progress to cirrhosis and failure if untreated. The mechanisms of fibrogenesis are multi faceted and remain elusive with no approved antifibrotic treatments available. Here we use single cell RNA sequencing scRNA seq of the adult zebrafish liver to study the molecular and cellular dynamics of the liver at a single cell level and demonstrate the value of the adult zebrafish as a model for studying liver fibrosis. scRNA seq reveals transcriptionally unique populations of hepatic cell types that comprise the zebrafish liver. Joint clustering with human liver scRNA seq data demonstrates high conservation of transcriptional profiles and human marker genes in zebrafish cell types. Human and zebrafish hepatic stellate cells HSCs the driver cell in liver fibrosis specifically show conservation of transcriptional profiles and we uncover Colec11 as a novel conserved marker for zebrafish HSCs. To demonstrate the power of scRNA seq to study liver fibrosis we performed scRNA seq on our zebrafish model of a pediatric liver disease with characteristic early progressive liver fibrosis caused by mutation in mannose phosphate isomerase MPI. Comparison of differentially expressed genes from human and zebrafish MPI mutant HSC datasets demonstrated similar activation of fibrosis signaling pathways and upstream regulators. CellPhoneDB analysis revealed important receptor ligand interactions within normal and fibrotic states. This study establishes the first scRNA seq atlas of the adult zebrafish liver highlights the high degree of similarity to the human liver and strengthens its value as a model to study liver fibrosis. Overall design: Single cell RNA sequencing analysis of adult zebrafish liver tissue from mpi+/ mss7 and WT siblings Please note that the Series supplementary files were generated from multiple samples as following: zf WT MPIMT EC HSC subset GSM5515731 GSM5515736 zf WT MPIMT liver GSM5515731 GSM5515736 zf liver atlas GSM5515731 …		pubmed:35315595		WT 1	GSM5515731	source name:Adult zebrafish liver dissection\|genotype:WT\|tissue:Liver	WT 1	FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11	Adult zebrafish liver dissection		Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	Adult fish were maintained on a 14:10 light/dark cycle at 28°C.	genotype:WT\|tissue:Liver	GSM5515731	GSM5515731: WT 1; Danio rerio; RNA Seq	GSM5515731		1	Livers were dissected from 18 mpf adult zebrafish. Single cell suspensions were generated as described in Materials and Methods. Cells were dissociated and digested using standard collagenase and DNAse protocols and single cell suspensions were filtered through a 70um filter. Suspensions were loaded into 10X Chromium gel beads. Library construction was performed as per 10X Genomics v3 chemistry kit. 10X chromium	GEO Accession:GSM5515731	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP332278	loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=JACH01 WT2 0 G S3 L002 I1 001.fastq.gz read2PairFiles=JACH01 WT2 0 G S3 L002 R1 001.fastq.gz read3PairFiles=JACH01 WT2 0 G S3 L002 R2 001.fastq.gz	JACH01_WT2_0_G_S3_L002_I1_001.fastq.gz JACH01_WT2_0_G_S3_L002_R1_001.fastq.gz JACH01_WT2_0_G_S3_L002_R2_001.fastq.gz	fastq fastq fastq	14981913300.0	149819133.0	GSM5515731 r2	0:8 1:30 2:62	A:2757221756;C:2158264290;G:2042268570;T:2330874969;N:156661	8	30	62		2757221756	2158264290	2042268570	2330874969	156661	SRX11729082	SRS9757819	SRA1277309	GEO	Jaime Chu Lab, Pediatrics, Icahn School of Medicine at Mount Sinai	1	0.94701		0.05368		0.89591		0.57205		62		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-08-12	Adult	Adult	Liver	Liver and Biliary System
67832	67832	SRR17375072	SRX13549231	SRS11443005	SRP352824	PRJNA793009	Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells	GSE192740	Other	Analysis of CITE seq data Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45 cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat cholesterol and sugar from healthy and steatotic human livers from hamster liver pig liver chicken liver monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers NAFLD mouse livers healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45 cells derived from mice fed a standard diet SD or western diet WD; fat cholesterol and sugar. Liver CD45+ and CD45 cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver mouse StSt capsule mouse NAFLD liver human non steatotic liver human steatotic liver	parent bioproject:PRJNA793005	pubmed:35021063;pubmed:36304458		Zebrafish 002 Whole Liver Cells Zebrafish	GSM5764413	tissue:Liver\|shortfilename:CS131\|strain:Tgmpeg1:EGFPgl22\|platform:10x Genomics – v3\|digestion method:Ex Vivo\|number of added abs:0\|number of cells:1241	Zebrafish 002 Whole Liver Cells Zebrafish	Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse hg19 Human GRCz10 Zebrafish MesAur1.0.100 Hamster GRCg6a.96 Chicken Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object	Liver		All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.		shortfilename:CS131\|strain:Tgmpeg1:EGFPgl22\|platform:10x Genomics – v3\|digestion method:Ex Vivo\|number of added abs:0\|number of cells:1241	GSM5764413	GSM5764413: Zebrafish 002 Whole Liver Cells Zebrafish; Danio rerio; RNA Seq	GSM5764413		1	All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.	GEO Accession:GSM5764413	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP352824		CS131_R1.fastq.gz CS131_R2.fastq.gz	fastq fastq	27410113115.0	230337085.0	GSM5764413 r1	0:28 1:91	A:7502899227;C:6375936516;G:6281396027;T:7241238684;N:8642661	28	91			7502899227	6375936516	6281396027	7241238684	8642661	SRX13549231	SRS11443005	SRA1349905	GEO	VIB Inflammation Research Center, VIB-University of Ghent	2	0.00522	0.93004	0.00164	0.0692	0.99476	0.85098	0.48648	0.60903	28	91	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2021-12-29	Undetermined	Undetermined	Liver	Liver and Biliary System
67833	67833	SRR17375071	SRX13549230	SRS11443004	SRP352824	PRJNA793009	Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells	GSE192740	Other	Analysis of CITE seq data Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45 cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat cholesterol and sugar from healthy and steatotic human livers from hamster liver pig liver chicken liver monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers NAFLD mouse livers healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45 cells derived from mice fed a standard diet SD or western diet WD; fat cholesterol and sugar. Liver CD45+ and CD45 cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver mouse StSt capsule mouse NAFLD liver human non steatotic liver human steatotic liver	parent bioproject:PRJNA793005	pubmed:35021063;pubmed:36304458		Zebrafish 001 Whole Liver Cells Zebrafish	GSM5764412	tissue:Liver\|shortfilename:CS130\|strain:Tgmpeg1:EGFPgl22\|platform:10x Genomics – v3\|digestion method:Ex Vivo\|number of added abs:0\|number of cells:2256	Zebrafish 001 Whole Liver Cells Zebrafish	Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse hg19 Human GRCz10 Zebrafish MesAur1.0.100 Hamster GRCg6a.96 Chicken Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object	Liver		All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.		shortfilename:CS130\|strain:Tgmpeg1:EGFPgl22\|platform:10x Genomics – v3\|digestion method:Ex Vivo\|number of added abs:0\|number of cells:2256	GSM5764412	GSM5764412: Zebrafish 001 Whole Liver Cells Zebrafish; Danio rerio; RNA Seq	GSM5764412		1	All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.	GEO Accession:GSM5764412	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP352824		CS130_R1.fastq.gz CS130_R2.fastq.gz	fastq fastq	29028764681.0	243939199.0	GSM5764412 r1	0:28 1:91	A:7990080958;C:6832189305;G:6802247428;T:7395232074;N:9014916	28	91			7990080958	6832189305	6802247428	7395232074	9014916	SRX13549230	SRS11443004	SRA1349905	GEO	VIB Inflammation Research Center, VIB-University of Ghent	2	0.00621	0.93648	0.00152	0.07051	0.99466	0.85036	0.33907	0.45636	28	91	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2021-12-29	Undetermined	Undetermined	Liver	Liver and Biliary System
67834	67834	SRR17375070	SRX13549229	SRS11443003	SRP352824	PRJNA793009	Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells	GSE192740	Other	Analysis of CITE seq data Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45 cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat cholesterol and sugar from healthy and steatotic human livers from hamster liver pig liver chicken liver monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers NAFLD mouse livers healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45 cells derived from mice fed a standard diet SD or western diet WD; fat cholesterol and sugar. Liver CD45+ and CD45 cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver mouse StSt capsule mouse NAFLD liver human non steatotic liver human steatotic liver	parent bioproject:PRJNA793005	pubmed:35021063;pubmed:36304458		Zebrafish 002 Liver mpeg1.1+ cells Zebrafish	GSM5764411	tissue:Liver\|shortfilename:CS129\|strain:Tgmpeg1:EGFPgl22\|platform:10x Genomics – v3\|digestion method:Ex Vivo\|number of added abs:0\|number of cells:4126	Zebrafish 002 Liver mpeg1.1+ cells Zebrafish	Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse hg19 Human GRCz10 Zebrafish MesAur1.0.100 Hamster GRCg6a.96 Chicken Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object	Liver		All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.		shortfilename:CS129\|strain:Tgmpeg1:EGFPgl22\|platform:10x Genomics – v3\|digestion method:Ex Vivo\|number of added abs:0\|number of cells:4126	GSM5764411	GSM5764411: Zebrafish 002 Liver mpeg1.1+ cells Zebrafish; Danio rerio; RNA Seq	GSM5764411		1	All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.	GEO Accession:GSM5764411	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP352824		CS129_R1.fastq.gz CS129_R2.fastq.gz	fastq fastq	37123150869.0	311959251.0	GSM5764411 r1	0:28 1:91	A:10576275333;C:7976755033;G:8122940005;T:10435522767;N:11657731	28	91			10576275333	7976755033	8122940005	10435522767	11657731	SRX13549229	SRS11443003	SRA1349905	GEO	VIB Inflammation Research Center, VIB-University of Ghent	2	0.00585	0.89093	0.00199	0.20548	0.99269	0.82597	0.42801	0.61509	28	91	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2021-12-29	Undetermined	Undetermined	Liver	Liver and Biliary System
67835	67835	SRR17375069	SRX13549228	SRS11443002	SRP352824	PRJNA793009	Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches single cells	GSE192740	Other	Analysis of CITE seq data Nuclei RNA seq data and single cell RNA seq data on CD45+ and CD45 cells isolated from the livers of mice fed a standard diet SD or western diet WD; fat cholesterol and sugar from healthy and steatotic human livers from hamster liver pig liver chicken liver monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers NAFLD mouse livers healthy human livers and steatotic human livers. Overall design: Single cell RNA Seq = Liver CD45+ and CD45 cells derived from mice fed a standard diet SD or western diet WD; fat cholesterol and sugar. Liver CD45+ and CD45 cells derived from healthy and obese humans. 10 Visium Spatial Seq = mouse StSt liver mouse StSt capsule mouse NAFLD liver human non steatotic liver human steatotic liver	parent bioproject:PRJNA793005	pubmed:35021063;pubmed:36304458		Zebrafish 001 Liver mpeg1.1+ cells Zebrafish	GSM5764410	tissue:Liver\|shortfilename:CS128\|strain:Tgmpeg1:EGFPgl22\|platform:10x Genomics – v3\|digestion method:Ex Vivo\|number of added abs:0\|number of cells:1229	Zebrafish 001 Liver mpeg1.1+ cells Zebrafish	Raw data bcl files were first demultiplexed using Cell Ranger mkfastq version 3.1.0 or version 3.0.2 Demultiplexed data was then processed using the Cell Ranger count pipeline version 3.1.0 or version 3.0.2. Cite seq samples were mapped against the TotalSeqA whitelist. Genome build: mm10 Mouse hg19 Human GRCz10 Zebrafish MesAur1.0.100 Hamster GRCg6a.96 Chicken Sscrofa11.1.96 Pig or Macaca facicularis 5.0.100 Macaque Supplementary files format and content: h5 or txt files including raw gene – and if present – antibody counts output CellRanger Count Supplementary files format and content: rds file: Seurat object	Liver		All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.		shortfilename:CS128\|strain:Tgmpeg1:EGFPgl22\|platform:10x Genomics – v3\|digestion method:Ex Vivo\|number of added abs:0\|number of cells:1229	GSM5764410	GSM5764410: Zebrafish 001 Liver mpeg1.1+ cells Zebrafish; Danio rerio; RNA Seq	GSM5764410		1	All Methods listed in Guilliams et al. Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches. Cell. 2022.	GEO Accession:GSM5764410	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP352824		CS128_R1.fastq.gz CS128_R2.fastq.gz	fastq fastq	38316694094.0	321989026.0	GSM5764410 r1	0:28 1:91	A:10814226120;C:8293271134;G:8575797871;T:10621330197;N:12068772	28	91			10814226120	8293271134	8575797871	10621330197	12068772	SRX13549228	SRS11443002	SRA1349905	GEO	VIB Inflammation Research Center, VIB-University of Ghent	2	0.00626	0.88237	0.00215	0.18876	0.99249	0.83049	0.41451	0.59559	28	91	T	B	sc-like readlen	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	Belgium	2021-12-29	Undetermined	Undetermined	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

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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");;