rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
206,DRR162535,DRX153154,DRS083215,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 39 mpf zebrafish replicate5,SAMD00152483,,sample name:l39 5|age:39 month|biological replicate:5|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152483,DRX153154,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152483,,,,1222686600.0,6113433.0,DRR162535,0:100 1:100,A:332248505;C:277678269;G:280475826;T:332221614;N:62386,100,100,,,332248505,277678269,280475826,332221614,62386,DRX153154,DRS083215,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94973,0.95168,0.05815,0.0574,0.80714,0.80992,0.2996,0.29323,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
207,DRR162534,DRX153153,DRS083214,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 39 mpf zebrafish replicate4,SAMD00152482,,sample name:l39 4|age:39 month|biological replicate:4|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152482,DRX153153,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152482,,,,1640116400.0,8200582.0,DRR162534,0:100 1:100,A:453347555;C:365904202;G:366450625;T:454324883;N:89135,100,100,,,453347555,365904202,366450625,454324883,89135,DRX153153,DRS083214,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93653,0.93054,0.09033,0.08864,0.7417,0.74341,0.47622,0.47803,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
208,DRR162533,DRX153152,DRS083213,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 39 mpf zebrafish replicate3,SAMD00152481,,sample name:l39 3|age:39 month|biological replicate:3|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152481,DRX153152,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152481,,,,1676561000.0,8382805.0,DRR162533,0:100 1:100,A:458233101;C:380058901;G:378567207;T:459616427;N:85364,100,100,,,458233101,380058901,378567207,459616427,85364,DRX153152,DRS083213,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94088,0.93572,0.08357,0.08412,0.78516,0.79383,0.58177,0.569,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
209,DRR162532,DRX153151,DRS083212,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 39 mpf zebrafish replicate2,SAMD00152480,,sample name:l39 2|age:39 month|biological replicate:2|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152480,DRX153151,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152480,,,,1818896600.0,9094483.0,DRR162532,0:100 1:100,A:513353000;C:395752133;G:399719533;T:509976715;N:95219,100,100,,,513353000,395752133,399719533,509976715,95219,DRX153151,DRS083212,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.92557,0.90731,0.10552,0.10279,0.73655,0.73963,0.55463,0.53901,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
210,DRR162531,DRX153150,DRS083211,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 39 mpf zebrafish replicate1,SAMD00152479,,sample name:l39 1|age:39 month|biological replicate:1|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152479,DRX153150,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152479,,,,1365495000.0,6827475.0,DRR162531,0:100 1:100,A:397961331;C:285103195;G:285088182;T:397271923;N:70369,100,100,,,397961331,285103195,285088182,397271923,70369,DRX153150,DRS083211,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91718,0.9094,0.12236,0.12108,0.74905,0.75213,0.52227,0.52956,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
211,DRR162530,DRX153149,DRS083210,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 16 mpf zebrafish replicate5,SAMD00152478,,sample name:l16 5|age:16 month|biological replicate:5|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152478,DRX153149,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152478,,,,1350377800.0,6751889.0,DRR162530,0:100 1:100,A:386028757;C:288772838;G:290958369;T:384548737;N:69099,100,100,,,386028757,288772838,290958369,384548737,69099,DRX153149,DRS083210,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93516,0.92365,0.08362,0.08141,0.82446,0.82769,0.62055,0.62498,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
212,DRR162529,DRX153148,DRS083209,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 16 mpf zebrafish replicate4,SAMD00152477,,sample name:l16 4|age:16 month|biological replicate:4|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152477,DRX153148,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152477,,,,1336103200.0,6680516.0,DRR162529,0:100 1:100,A:382497123;C:284680985;G:285893391;T:382963813;N:67888,100,100,,,382497123,284680985,285893391,382963813,67888,DRX153148,DRS083209,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9394,0.94216,0.0736,0.07267,0.81909,0.82063,0.34071,0.35081,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
213,DRR162528,DRX153147,DRS083208,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 16 mpf zebrafish replicate3,SAMD00152476,,sample name:l16 3|age:16 month|biological replicate:3|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152476,DRX153147,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152476,,,,1382207400.0,6911037.0,DRR162528,0:100 1:100,A:389944369;C:300605191;G:301498468;T:390090609;N:68763,100,100,,,389944369,300605191,301498468,390090609,68763,DRX153147,DRS083208,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93205,0.92544,0.08167,0.0803,0.80164,0.80472,0.60042,0.52988,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
214,DRR162527,DRX153146,DRS083207,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 16 mpf zebrafish replicate2,SAMD00152475,,sample name:l16 2|age:16 month|biological replicate:2|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152475,DRX153146,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152475,,,,1420870200.0,7104351.0,DRR162527,0:100 1:100,A:390283357;C:318567042;G:320772328;T:391175121;N:72352,100,100,,,390283357,318567042,320772328,391175121,72352,DRX153146,DRS083207,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.95451,0.95673,0.03982,0.04064,0.83765,0.84053,0.16589,0.16881,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
215,DRR162526,DRX153145,DRS083206,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 16 mpf zebrafish replicate1,SAMD00152474,,sample name:l16 1|age:16 month|biological replicate:1|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152474,DRX153145,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152474,,,,1153415600.0,5767078.0,DRR162526,0:100 1:100,A:331352139;C:244998423;G:248301842;T:328704463;N:58733,100,100,,,331352139,244998423,248301842,328704463,58733,DRX153145,DRS083206,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.95303,0.95385,0.03203,0.03206,0.86592,0.86734,0.23054,0.23207,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
216,DRR162525,DRX153144,DRS083205,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 7 mpf zebrafish replicate5,SAMD00152473,,sample name:l07 5|age:7 month|biological replicate:5|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152473,DRX153144,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152473,,,,890770600.0,4453853.0,DRR162525,0:100 1:100,A:256905080;C:188672401;G:188524159;T:256621928;N:47032,100,100,,,256905080,188672401,188524159,256621928,47032,DRX153144,DRS083205,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.9268,0.9203,0.08741,0.08714,0.79013,0.80292,0.60305,0.60127,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
217,DRR162524,DRX153143,DRS083204,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 7 mpf zebrafish replicate4,SAMD00152472,,sample name:l07 4|age:7 month|biological replicate:4|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152472,DRX153143,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152472,,,,1483455800.0,7417279.0,DRR162524,0:100 1:100,A:436293893;C:304891230;G:308137580;T:434055810;N:77287,100,100,,,436293893,304891230,308137580,434055810,77287,DRX153143,DRS083204,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.91896,0.90192,0.0717,0.07014,0.81085,0.8132,0.58351,0.59366,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
218,DRR162523,DRX153142,DRS083203,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 7 mpf zebrafish replicate3,SAMD00152471,,sample name:l07 3|age:7 month|biological replicate:3|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152471,DRX153142,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152471,,,,1864489400.0,9322447.0,DRR162523,0:100 1:100,A:502417821;C:427210740;G:431014519;T:503749673;N:96647,100,100,,,502417821,427210740,431014519,503749673,96647,DRX153142,DRS083203,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.95976,0.96143,0.04395,0.04468,0.79448,0.79782,0.263,0.26714,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
219,DRR162522,DRX153141,DRS083202,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 7 mpf zebrafish replicate2,SAMD00152470,,sample name:l07 2|age:7 month|biological replicate:2|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152470,DRX153141,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152470,,,,2033108200.0,10165541.0,DRR162522,0:100 1:100,A:551635703;C:463271027;G:463695854;T:554401182;N:104434,100,100,,,551635703,463271027,463695854,554401182,104434,DRX153141,DRS083202,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94795,0.94217,0.05903,0.0589,0.79131,0.79462,0.54196,0.5496,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
220,DRR162521,DRX153140,DRS083201,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 7 mpf zebrafish replicate1,SAMD00152469,,sample name:l07 1|age:7 month|biological replicate:1|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152469,DRX153140,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152469,,,,1468954400.0,7344772.0,DRR162521,0:100 1:100,A:395399684;C:336608951;G:340607200;T:396263402;N:75163,100,100,,,395399684,336608951,340607200,396263402,75163,DRX153140,DRS083201,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.95562,0.95778,0.02931,0.02966,0.86667,0.8686,0.15375,0.16038,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Adult,Adult,Liver,Liver and Biliary System
221,DRR162520,DRX153139,DRS083200,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate5,SAMD00152468,,sample name:l02 5|age:2 month|biological replicate:5|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152468,DRX153139,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152468,,,,1264817800.0,6324089.0,DRR162520,0:100 1:100,A:351295111;C:280181229;G:281044764;T:352232836;N:63860,100,100,,,351295111,280181229,281044764,352232836,63860,DRX153139,DRS083200,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93687,0.93419,0.07774,0.07776,0.7587,0.7609,0.56082,0.56748,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
222,DRR162519,DRX153138,DRS083199,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate4,SAMD00152467,,sample name:l02 4|age:2 month|biological replicate:4|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152467,DRX153138,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152467,,,,1762366200.0,8811831.0,DRR162519,0:100 1:100,A:481999545;C:397566169;G:399183135;T:483526493;N:90858,100,100,,,481999545,397566169,399183135,483526493,90858,DRX153138,DRS083199,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.93994,0.93528,0.06039,0.05936,0.75037,0.75394,0.52945,0.52961,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
223,DRR162518,DRX153137,DRS083198,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate3,SAMD00152466,,sample name:l02 3|age:2 month|biological replicate:3|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152466,DRX153137,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152466,,,,1464434200.0,7322171.0,DRR162518,0:100 1:100,A:400972247;C:330316514;G:329635959;T:403435022;N:74458,100,100,,,400972247,330316514,329635959,403435022,74458,DRX153137,DRS083198,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94169,0.93517,0.075,0.07408,0.78541,0.78796,0.56483,0.56426,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
224,DRR162517,DRX153136,DRS083197,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate2,SAMD00152465,,sample name:l02 2|age:2 month|biological replicate:2|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152465,DRX153136,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152465,,,,1953667000.0,9768335.0,DRR162517,0:100 1:100,A:525411621;C:450279523;G:450410879;T:527464993;N:99984,100,100,,,525411621,450279523,450410879,527464993,99984,DRX153136,DRS083197,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94424,0.93692,0.06451,0.06582,0.78358,0.79557,0.56036,0.57581,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
225,DRR162516,DRX153135,DRS083196,DRP004696,PRJDB7713,Age associated transcriptome analysis in 5 tissues of zebrafish,DRP004696,Transcriptome Analysis,We performed transcriptome analysis for brain  gill  heart  liver and muscle from 2 month   7 month   16 month  and 39 mpf zebrafish. We analyzed age associated gene expression pattern in zebrafish and compared with similar public transcriptome data of rat Yu et al.  2014.,,,,liver sample from 2 mpf zebrafish replicate1,SAMD00152464,,sample name:l02 1|age:2 month|biological replicate:1|tissue:liver,,,,,,,,,Illumina HiSeq 2000 paired end sequencing of SAMD00152464,DRX153135,1,1,Illumina TruSeq Stranded mRNA HT Kit,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP004696,Illumina HiSeq 2000 paired end sequencing of SAMD00152464,,,,1541676600.0,7708383.0,DRR162516,0:100 1:100,A:414776600;C:354650822;G:357258514;T:414910092;N:80572,100,100,,,414776600,354650822,357258514,414910092,80572,DRX153135,DRS083196,DRA007711,UT-AQUA|Laboratory of Aquatic Molecular Biology and Biotechnology,"Department of Aquatic Bioscience, Graduate School of Agriculture and Life Sciences, The University of Tokyo",2,0.94346,0.93048,0.06888,0.06759,0.79086,0.79452,0.56037,0.55727,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Japan,2018-12-24,Juvenile,Juvenile,Liver,Liver and Biliary System
19471,ERR14031296,ERX13434262,ERS22545283,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq Control Replicate 1,Control Replicate 1,SAMEA117477679,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009305 Control Replicate 1|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009305 Control Replicate 1|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9483,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19069_Control_14_R1.fastq.gz 19070_Control_14_R2.fastq.gz,fastq fastq,10004171894.0,33126397.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9483,0:151 1:151,A:2747978244;C:2173369585;G:2355012585;T:2716465615;N:11345865,151,151,,,2747978244,2173369585,2355012585,2716465615,11345865,ERX13434262,ERS22545283,ERA31000109,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
19472,ERR14031290,ERX13434256,ERS22545281,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq Control Replicate 2,Control Replicate 2,SAMEA117477677,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009306 Control Replicate 2|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009306 Control Replicate 2|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9484,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19071_Control_9_R1.fastq.gz 19072_Control_9_R2.fastq.gz,fastq fastq,11659155450.0,38606475.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9484,0:151 1:151,A:3197012061;C:2522601146;G:2753110022;T:3173195478;N:13236743,151,151,,,3197012061,2522601146,2753110022,3173195478,13236743,ERX13434256,ERS22545281,ERA31000093,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
19473,ERR14031295,ERX13434261,ERS22545292,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq NAFLD Replicate 2,NAFLD Replicate 2,SAMEA117477688,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009308 NAFLD Replicate 2|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009308 NAFLD Replicate 2|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9486,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19075_NAFLD_8_R1.fastq.gz 19076_NAFLD_8_R2.fastq.gz,fastq fastq,11001354150.0,36428325.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9486,0:151 1:151,A:3036945132;C:2390487588;G:2547341716;T:3014093258;N:12486456,151,151,,,3036945132,2390487588,2547341716,3014093258,12486456,ERX13434261,ERS22545292,ERA31000106,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
19474,ERR14031298,ERX13434264,ERS22545288,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq NAFLD Replicate 3,NAFLD Replicate 3,SAMEA117477684,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009309 NAFLD Replicate 3|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009309 NAFLD Replicate 3|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9487,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19077_NAFLD_9_R1.fastq.gz 19078_NAFLD_9_R2.fastq.gz,fastq fastq,10367145694.0,34328297.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9487,0:151 1:151,A:2861355932;C:2257080818;G:2411788871;T:2828044975;N:8875098,151,151,,,2861355932,2257080818,2411788871,2828044975,8875098,ERX13434264,ERS22545288,ERA31000114,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
19475,ERR14031292,ERX13434258,ERS22545282,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq NAFLD Replicate 1,NAFLD Replicate 1,SAMEA117477678,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009307 NAFLD Replicate 1|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009307 NAFLD Replicate 1|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9485,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19073_NAFLD_11_R1.fastq.gz 19074_NAFLD_11_R2.fastq.gz,fastq fastq,11885531932.0,39356066.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9485,0:151 1:151,A:3208478929;C:2671086650;G:2843156238;T:3153091073;N:9719042,151,151,,,3208478929,2671086650,2843156238,3153091073,9719042,ERX13434258,ERS22545282,ERA31000101,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
28955,SRR26862014,SRX22556964,SRS19565505,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,atf4a / ;atf4b / ;sec31anju221 7dpf liver rep3,GSM7905882,,source name:liver|tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,atf4a / ;atf4b / ;sec31anju221 7dpf liver rep3,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905882,GSM7905882: atf4a / ;atf4b / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq,GSM7905882 r1,GSM7905882,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,atf4a_atf4b_sec31a_7dpf_liver_3_R1.fastq.gz atf4a_atf4b_sec31a_7dpf_liver_3_R2.fastq.gz,fastq fastq,5909169300.0,19697231.0,GSM7905882 r1,0:150 1:150,A:1814217313;C:1062889607;G:1281434828;T:1750535462;N:92090,150,150,,,1814217313,1062889607,1281434828,1750535462,92090,SRX22556964,SRS19565505,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.76999,0.77426,0.42801,0.42392,0.8016,0.80275,0.54736,0.56955,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28956,SRR26862015,SRX22556963,SRS19565504,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,atf4a / ;atf4b / ;sec31anju221 7dpf liver rep2,GSM7905881,,source name:liver|tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,atf4a / ;atf4b / ;sec31anju221 7dpf liver rep2,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905881,GSM7905881: atf4a / ;atf4b / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq,GSM7905881 r1,GSM7905881,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,atf4a_atf4b_sec31a_7dpf_liver_2_R2.fastq.gz atf4a_atf4b_sec31a_7dpf_liver_2_R1.fastq.gz,fastq fastq,5909169300.0,19697231.0,GSM7905881 r1,0:150 1:150,A:1814304871;C:1062851267;G:1281344920;T:1750575670;N:92572,150,150,,,1814304871,1062851267,1281344920,1750575670,92572,SRX22556963,SRS19565504,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.77,0.77338,0.42787,0.42319,0.80137,0.80314,0.56997,0.57195,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28957,SRR26862016,SRX22556962,SRS19565503,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,atf4a / ;atf4b / ;sec31anju221 7dpf liver rep1,GSM7905880,,source name:liver|tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,atf4a / ;atf4b / ;sec31anju221 7dpf liver rep1,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905880,GSM7905880: atf4a / ;atf4b / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq,GSM7905880 r1,GSM7905880,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,atf4a_atf4b_sec31a_7dpf_liver_1_R1.fastq.gz atf4a_atf4b_sec31a_7dpf_liver_1_R2.fastq.gz,fastq fastq,5909169600.0,19697232.0,GSM7905880 r1,0:150 1:150,A:1814273460;C:1062781687;G:1281372048;T:1750650699;N:91706,150,150,,,1814273460,1062781687,1281372048,1750650699,91706,SRX22556962,SRS19565503,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.76973,0.77461,0.42583,0.42416,0.80154,0.80501,0.56619,0.57103,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28958,SRR26862017,SRX22556961,SRS19565502,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,atf6 / ;sec31anju221 7dpf liver rep3,GSM7905879,,source name:liver|tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,atf6 / ;sec31anju221 7dpf liver rep3,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905879,GSM7905879: atf6 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq,GSM7905879 r1,GSM7905879,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,atf6_sec31a_7dpf_liver_3_R1.fastq.gz atf6_sec31a_7dpf_liver_3_R2.fastq.gz,fastq fastq,5861267700.0,19537559.0,GSM7905879 r1,0:150 1:150,A:1784341701;C:1072473445;G:1285100764;T:1719260200;N:91590,150,150,,,1784341701,1072473445,1285100764,1719260200,91590,SRX22556961,SRS19565502,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.75325,0.76151,0.45725,0.45689,0.78798,0.78922,0.56218,0.56438,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28959,SRR26862018,SRX22556960,SRS19565501,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,atf6 / ;sec31anju221 7dpf liver rep2,GSM7905878,,source name:liver|tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,atf6 / ;sec31anju221 7dpf liver rep2,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905878,GSM7905878: atf6 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq,GSM7905878 r1,GSM7905878,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,atf6_sec31a_7dpf_liver_2_R1.fastq.gz atf6_sec31a_7dpf_liver_2_R2.fastq.gz,fastq fastq,5861267700.0,19537559.0,GSM7905878 r1,0:150 1:150,A:1784326758;C:1072428588;G:1285145147;T:1719275142;N:92065,150,150,,,1784326758,1072428588,1285145147,1719275142,92065,SRX22556960,SRS19565501,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.75399,0.76366,0.46023,0.46101,0.79153,0.79243,0.56082,0.56109,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28960,SRR26862019,SRX22556959,SRS19565500,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,atf6 / ;sec31anju221 7dpf liver rep1,GSM7905877,,source name:liver|tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,atf6 / ;sec31anju221 7dpf liver rep1,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905877,GSM7905877: atf6 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq,GSM7905877 r1,GSM7905877,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,atf6_sec31a_7dpf_liver_1_R1.fastq.gz atf6_sec31a_7dpf_liver_1_R2.fastq.gz,fastq fastq,5861267700.0,19537559.0,GSM7905877 r1,0:150 1:150,A:1784239507;C:1072424839;G:1285216751;T:1719294746;N:91857,150,150,,,1784239507,1072424839,1285216751,1719294746,91857,SRX22556959,SRS19565500,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.75279,0.76268,0.45792,0.46002,0.79251,0.79482,0.55778,0.55965,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28961,SRR26862020,SRX22556958,SRS19565499,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,srebf2 / ;sec31anju221 7dpf liver rep3,GSM7905876,,source name:liver|tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,srebf2 / ;sec31anju221 7dpf liver rep3,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905876,GSM7905876: srebf2 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq,GSM7905876 r1,GSM7905876,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,srebf2_sec31a_7dpf_liver_3_R2.fastq.gz srebf2_sec31a_7dpf_liver_3_R1.fastq.gz,fastq fastq,5510352000.0,18367840.0,GSM7905876 r1,0:150 1:150,A:1627756472;C:1023474678;G:1300851324;T:1558184587;N:84939,150,150,,,1627756472,1023474678,1300851324,1558184587,84939,SRX22556958,SRS19565499,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.80994,0.82412,0.13867,0.1397,0.84264,0.84228,0.58499,0.58509,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28962,SRR26862021,SRX22556957,SRS19565498,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,srebf2 / ;sec31anju221 7dpf liver rep2,GSM7905875,,source name:liver|tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,srebf2 / ;sec31anju221 7dpf liver rep2,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905875,GSM7905875: srebf2 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq,GSM7905875 r1,GSM7905875,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,srebf2_sec31a_7dpf_liver_2_R1.fastq.gz srebf2_sec31a_7dpf_liver_2_R2.fastq.gz,fastq fastq,5510352000.0,18367840.0,GSM7905875 r1,0:150 1:150,A:1627771682;C:1023494582;G:1300898781;T:1558101507;N:85448,150,150,,,1627771682,1023494582,1300898781,1558101507,85448,SRX22556957,SRS19565498,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.81036,0.82384,0.14055,0.13973,0.84151,0.84145,0.58974,0.57294,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28963,SRR26862022,SRX22556956,SRS19565497,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,srebf2 / ;sec31anju221 7dpf liver rep1,GSM7905874,,source name:liver|tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,srebf2 / ;sec31anju221 7dpf liver rep1,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905874,GSM7905874: srebf2 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq,GSM7905874 r1,GSM7905874,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,srebf2_sec31a_7dpf_liver_1_R1.fastq.gz srebf2_sec31a_7dpf_liver_1_R2.fastq.gz,fastq fastq,5510352300.0,18367841.0,GSM7905874 r1,0:150 1:150,A:1627704384;C:1023445689;G:1301022904;T:1558092507;N:86816,150,150,,,1627704384,1023445689,1301022904,1558092507,86816,SRX22556956,SRS19565497,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.81137,0.82447,0.13931,0.13977,0.84104,0.84129,0.58031,0.57864,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28964,SRR26862023,SRX22556955,SRS19565496,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,srebf1 / ;sec31anju221 7dpf liver rep3,GSM7905873,,source name:liver|tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,srebf1 / ;sec31anju221 7dpf liver rep3,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905873,GSM7905873: srebf1 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq,GSM7905873 r1,GSM7905873,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,srebf1_sec31a_7dpf_liver_3_R1.fastq.gz srebf1_sec31a_7dpf_liver_3_R2.fastq.gz,fastq fastq,6400097700.0,21333659.0,GSM7905873 r1,0:150 1:150,A:1899190871;C:1190525037;G:1467138729;T:1843142069;N:100994,150,150,,,1899190871,1190525037,1467138729,1843142069,100994,SRX22556955,SRS19565496,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.81425,0.82461,0.21108,0.21197,0.82221,0.82323,0.56957,0.594,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28965,SRR26862024,SRX22556954,SRS19565495,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,srebf1 / ;sec31anju221 7dpf liver rep2,GSM7905872,,source name:liver|tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,srebf1 / ;sec31anju221 7dpf liver rep2,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905872,GSM7905872: srebf1 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq,GSM7905872 r1,GSM7905872,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,srebf1_sec31a_7dpf_liver_2_R1.fastq.gz srebf1_sec31a_7dpf_liver_2_R2.fastq.gz,fastq fastq,6400098000.0,21333660.0,GSM7905872 r1,0:150 1:150,A:1898994954;C:1190735681;G:1467311615;T:1842955236;N:100514,150,150,,,1898994954,1190735681,1467311615,1842955236,100514,SRX22556954,SRS19565495,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.81439,0.82458,0.20976,0.20983,0.82252,0.82278,0.57027,0.58785,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28966,SRR26862025,SRX22556953,SRS19565494,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,srebf1 / ;sec31anju221 7dpf liver rep1,GSM7905871,,source name:liver|tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,srebf1 / ;sec31anju221 7dpf liver rep1,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905871,GSM7905871: srebf1 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq,GSM7905871 r1,GSM7905871,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,srebf1_sec31a_7dpf_liver_1_R1.fastq.gz srebf1_sec31a_7dpf_liver_1_R2.fastq.gz,fastq fastq,6400098000.0,21333660.0,GSM7905871 r1,0:150 1:150,A:1899112598;C:1190526850;G:1467278074;T:1843080128;N:100350,150,150,,,1899112598,1190526850,1467278074,1843080128,100350,SRX22556953,SRS19565494,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.81419,0.82464,0.20997,0.21061,0.82317,0.82296,0.57794,0.57323,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28967,SRR26862026,SRX22556952,SRS19565493,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,xbp1 / ;sec31anju221 7dpf liver rep3,GSM7905870,,source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,xbp1 / ;sec31anju221 7dpf liver rep3,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905870,GSM7905870: xbp1 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq,GSM7905870 r1,GSM7905870,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,xbp1_sec31a_7dpf_liver_3_R1.fastq.gz xbp1_sec31a_7dpf_liver_3_R2.fastq.gz,fastq fastq,6187152600.0,20623842.0,GSM7905870 r1,0:150 1:150,A:1877363692;C:1115080777;G:1381299595;T:1812977195;N:431341,150,150,,,1877363692,1115080777,1381299595,1812977195,431341,SRX22556952,SRS19565493,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.76954,0.76951,0.43867,0.43143,0.77993,0.78291,0.54133,0.5381,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28968,SRR26862027,SRX22556951,SRS19565492,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,xbp1 / ;sec31anju221 7dpf liver rep2,GSM7905869,,source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,xbp1 / ;sec31anju221 7dpf liver rep2,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905869,GSM7905869: xbp1 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq,GSM7905869 r1,GSM7905869,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,xbp1_sec31a_7dpf_liver_2_R1.fastq.gz xbp1_sec31a_7dpf_liver_2_R2.fastq.gz,fastq fastq,6187152600.0,20623842.0,GSM7905869 r1,0:150 1:150,A:1877413505;C:1115113811;G:1381185230;T:1813009192;N:430862,150,150,,,1877413505,1115113811,1381185230,1813009192,430862,SRX22556951,SRS19565492,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.77052,0.77186,0.4375,0.43158,0.77857,0.78376,0.54778,0.54495,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28969,SRR26862028,SRX22556950,SRS19565491,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,xbp1 / ;sec31anju221 7dpf liver rep1,GSM7905868,,source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,xbp1 / ;sec31anju221 7dpf liver rep1,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905868,GSM7905868: xbp1 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq,GSM7905868 r1,GSM7905868,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,xbp1_sec31a_7dpf_liver_1_R1.fastq.gz xbp1_sec31a_7dpf_liver_1_R2.fastq.gz,fastq fastq,6187152900.0,20623843.0,GSM7905868 r1,0:150 1:150,A:1877304250;C:1115136591;G:1381366555;T:1812912124;N:433380,150,150,,,1877304250,1115136591,1381366555,1812912124,433380,SRX22556950,SRS19565491,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.77014,0.76961,0.43869,0.43265,0.77863,0.78293,0.54465,0.54127,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28970,SRR26862029,SRX22556949,SRS19565490,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,sec31anju221 7dpf liver rep3,GSM7905867,,source name:liver|tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,sec31anju221 7dpf liver rep3,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905867,GSM7905867: sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq,GSM7905867 r1,GSM7905867,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,sec31a_7dpf_liver_3_R1.fastq.gz sec31a_7dpf_liver_3_R2.fastq.gz,fastq fastq,7290483000.0,24301610.0,GSM7905867 r1,0:150 1:150,A:2201443580;C:1310250352;G:1667114316;T:2111120776;N:553976,150,150,,,2201443580,1310250352,1667114316,2111120776,553976,SRX22556949,SRS19565490,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.80458,0.80677,0.27528,0.27217,0.8228,0.82507,0.58018,0.57745,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28971,SRR26862030,SRX22556948,SRS19565489,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,sec31anju221 7dpf liver rep2,GSM7905866,,source name:liver|tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,sec31anju221 7dpf liver rep2,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905866,GSM7905866: sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq,GSM7905866 r1,GSM7905866,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,sec31a_7dpf_liver_2_R1.fastq.gz sec31a_7dpf_liver_2_R2.fastq.gz,fastq fastq,7290483300.0,24301611.0,GSM7905866 r1,0:150 1:150,A:2201546187;C:1310316929;G:1666786006;T:2111279666;N:554512,150,150,,,2201546187,1310316929,1666786006,2111279666,554512,SRX22556948,SRS19565489,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.80528,0.80845,0.27376,0.27196,0.82286,0.82451,0.58075,0.57876,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28972,SRR26862031,SRX22556947,SRS19565488,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,sec31anju221 7dpf liver rep1,GSM7905865,,source name:liver|tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,sec31anju221 7dpf liver rep1,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin,GSM7905865,GSM7905865: sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq,GSM7905865 r1,GSM7905865,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,sec31a_7dpf_liver_1_R2.fastq.gz sec31a_7dpf_liver_1_R1.fastq.gz,fastq fastq,7290483300.0,24301611.0,GSM7905865 r1,0:150 1:150,A:2201492232;C:1310255361;G:1666931918;T:2111261791;N:541998,150,150,,,2201492232,1310255361,1666931918,2111261791,541998,SRX22556947,SRS19565488,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.80672,0.80946,0.27449,0.27121,0.82026,0.82238,0.58542,0.58114,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28973,SRR26862032,SRX22556946,SRS19565487,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,WT 7dpf liver rep3,GSM7905864,,source name:liver|tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,WT 7dpf liver rep3,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin,GSM7905864,GSM7905864: WT 7dpf liver rep3; Danio rerio; RNA Seq,GSM7905864 r1,GSM7905864,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,ctrl_7dpf_liver_3_R1.fastq.gz ctrl_7dpf_liver_3_R2.fastq.gz,fastq fastq,6492651600.0,21642172.0,GSM7905864 r1,0:150 1:150,A:1911454132;C:1210565181;G:1559325152;T:1810846037;N:461098,150,150,,,1911454132,1210565181,1559325152,1810846037,461098,SRX22556946,SRS19565487,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.83482,0.84576,0.18949,0.18912,0.84853,0.84914,0.67518,0.67721,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28974,SRR26862033,SRX22556945,SRS19565486,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,WT 7dpf liver rep2,GSM7905863,,source name:liver|tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,WT 7dpf liver rep2,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin,GSM7905863,GSM7905863: WT 7dpf liver rep2; Danio rerio; RNA Seq,GSM7905863 r1,GSM7905863,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,ctrl_7dpf_liver_2_R1.fastq.gz ctrl_7dpf_liver_2_R2.fastq.gz,fastq fastq,6492651600.0,21642172.0,GSM7905863 r1,0:150 1:150,A:1911298884;C:1210698281;G:1559339763;T:1810859879;N:454793,150,150,,,1911298884,1210698281,1559339763,1810859879,454793,SRX22556945,SRS19565486,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.83478,0.84217,0.19106,0.18909,0.84642,0.84717,0.67888,0.67654,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
28975,SRR26862034,SRX22556944,SRS19565485,SRP472550,PRJNA1041773,Transcriptome profiles of liver from 7dpf zebrafish larvae from control  sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing,GSE248098,Transcriptome Analysis,We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation  critical effectors of the UPR xbp1  atf4a/4b  atf6  srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape  livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 and sequenced on Illumina Novaseq platform.,,pubmed:39139065,,WT 7dpf liver rep1,GSM7905862,,source name:liver|tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing,WT 7dpf liver rep1,Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample,liver,,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin,GSM7905862,GSM7905862: WT 7dpf liver rep1; Danio rerio; RNA Seq,GSM7905862 r1,GSM7905862,1,At 7dpf   zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB  Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP472550,,,ctrl_7dpf_liver_1_R1.fastq.gz ctrl_7dpf_liver_1_R2.fastq.gz,fastq fastq,6492651600.0,21642172.0,GSM7905862 r1,0:150 1:150,A:1911338464;C:1210670533;G:1559401753;T:1810786876;N:453974,150,150,,,1911338464,1210670533,1559401753,1810786876,453974,SRX22556944,SRS19565485,SRA1753371,"Xin Lou Lab, Medical School, Nanjing University","Xin Lou Lab, Medical School, Nanjing University",2,0.83368,0.84388,0.18806,0.18877,0.84713,0.84932,0.67925,0.67975,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,China,2023-11-17,Larval,Larval,Liver,Liver and Biliary System
29816,SRR27496346,SRX23167489,SRS20117077,SRP483191,PRJNA1063616,Protection from starvation induced liver atrophy.,GSE252997,Transcriptome Analysis,Starvation causes the accumulation of lipid droplets in the liver  a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding  hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here  we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation  the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover  cavefish are resistant to liver atrophy during starvation  providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish  surface fish  and cavefish  we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further  down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis  suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall  our study identifies a conserved  druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment  no exogenous food was added. At 6 dpf  the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.,,pubmed:38467419,,Liver 6dpf DMSO rep1,GSM8012203,,source name:Liver|tissue:Liver|genotype:AB|treatment:DMSO|geo loc name:missing|collection date:missing,Liver 6dpf DMSO rep1,Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome  and counted using FeatureCounts. For normalization  differential gene expression analysis  and GO analysis  iDEP version 0.951 was utilized with default parameters. For differential gene expression  a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.,Liver,Lipofermata or DMSO treatment for 48 hours,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,Zebrafish larvae at 6 dpf.,tissue:Liver|genotype:AB|treatment:DMSO,GSM8012203,GSM8012203: Liver 6dpf DMSO rep1; Danio rerio; RNA Seq,GSM8012203 r1,GSM8012203,1,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483191,,loader:fastq load.py,DMSO_1_R1.fastq.gz DMSO_1_R2.fastq.gz,fastq fastq,3947938488.0,13072644.0,GSM8012203 r1,0:151 1:151,A:1068152483;C:899059502;G:921482728;T:1059209932;N:33843,151,151,,,1068152483,899059502,921482728,1059209932,33843,SRX23167489,SRS20117077,SRA1784007,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Belgium,2024-01-11,Larval,Larval,Liver,Liver and Biliary System
29817,SRR27496347,SRX23167488,SRS20117076,SRP483191,PRJNA1063616,Protection from starvation induced liver atrophy.,GSE252997,Transcriptome Analysis,Starvation causes the accumulation of lipid droplets in the liver  a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding  hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here  we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation  the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover  cavefish are resistant to liver atrophy during starvation  providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish  surface fish  and cavefish  we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further  down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis  suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall  our study identifies a conserved  druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment  no exogenous food was added. At 6 dpf  the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.,,pubmed:38467419,,Liver 6dpf Lipofermata rep2,GSM8012206,,source name:Liver|tissue:Liver|genotype:AB|treatment:Lipofermata|geo loc name:missing|collection date:missing,Liver 6dpf Lipofermata rep2,Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome  and counted using FeatureCounts. For normalization  differential gene expression analysis  and GO analysis  iDEP version 0.951 was utilized with default parameters. For differential gene expression  a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.,Liver,Lipofermata or DMSO treatment for 48 hours,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,Zebrafish larvae at 6 dpf.,tissue:Liver|genotype:AB|treatment:Lipofermata,GSM8012206,GSM8012206: Liver 6dpf Lipofermata rep2; Danio rerio; RNA Seq,GSM8012206 r1,GSM8012206,1,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483191,,loader:fastq load.py,Lipofermata_2_R1.fastq.gz Lipofermata_2_R2.fastq.gz,fastq fastq,3365739868.0,11144834.0,GSM8012206 r1,0:151 1:151,A:904693218;C:775639535;G:792394997;T:892981123;N:30995,151,151,,,904693218,775639535,792394997,892981123,30995,SRX23167488,SRS20117076,SRA1784007,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Belgium,2024-01-11,Larval,Larval,Liver,Liver and Biliary System
29818,SRR27496348,SRX23167487,SRS20117075,SRP483191,PRJNA1063616,Protection from starvation induced liver atrophy.,GSE252997,Transcriptome Analysis,Starvation causes the accumulation of lipid droplets in the liver  a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding  hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here  we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation  the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover  cavefish are resistant to liver atrophy during starvation  providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish  surface fish  and cavefish  we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further  down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis  suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall  our study identifies a conserved  druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment  no exogenous food was added. At 6 dpf  the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.,,pubmed:38467419,,Liver 6dpf Lipofermata rep1,GSM8012205,,source name:Liver|tissue:Liver|genotype:AB|treatment:Lipofermata|geo loc name:missing|collection date:missing,Liver 6dpf Lipofermata rep1,Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome  and counted using FeatureCounts. For normalization  differential gene expression analysis  and GO analysis  iDEP version 0.951 was utilized with default parameters. For differential gene expression  a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.,Liver,Lipofermata or DMSO treatment for 48 hours,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,Zebrafish larvae at 6 dpf.,tissue:Liver|genotype:AB|treatment:Lipofermata,GSM8012205,GSM8012205: Liver 6dpf Lipofermata rep1; Danio rerio; RNA Seq,GSM8012205 r1,GSM8012205,1,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483191,,loader:fastq load.py,Lipofermata_1_R1.fastq.gz Lipofermata_1_R2.fastq.gz,fastq fastq,3645146040.0,12070020.0,GSM8012205 r1,0:151 1:151,A:981366033;C:836975744;G:858564002;T:968208667;N:31594,151,151,,,981366033,836975744,858564002,968208667,31594,SRX23167487,SRS20117075,SRA1784007,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Belgium,2024-01-11,Larval,Larval,Liver,Liver and Biliary System
29819,SRR27496349,SRX23167486,SRS20117074,SRP483191,PRJNA1063616,Protection from starvation induced liver atrophy.,GSE252997,Transcriptome Analysis,Starvation causes the accumulation of lipid droplets in the liver  a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding  hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here  we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation  the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover  cavefish are resistant to liver atrophy during starvation  providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish  surface fish  and cavefish  we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further  down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis  suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall  our study identifies a conserved  druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment  no exogenous food was added. At 6 dpf  the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.,,pubmed:38467419,,Liver 6dpf DMSO rep2,GSM8012204,,source name:Liver|tissue:Liver|genotype:AB|treatment:DMSO|geo loc name:missing|collection date:missing,Liver 6dpf DMSO rep2,Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome  and counted using FeatureCounts. For normalization  differential gene expression analysis  and GO analysis  iDEP version 0.951 was utilized with default parameters. For differential gene expression  a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.,Liver,Lipofermata or DMSO treatment for 48 hours,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,Zebrafish larvae at 6 dpf.,tissue:Liver|genotype:AB|treatment:DMSO,GSM8012204,GSM8012204: Liver 6dpf DMSO rep2; Danio rerio; RNA Seq,GSM8012204 r1,GSM8012204,1,For RNA Seq  mRNA was isolated from livers at 6 dpf. For this  livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega  Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis  library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods  e.g. measurement of volume and quantity  gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology  using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation  post first strand synthesis  the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next  the sequencing adapters were ligated to the DNA fragments  and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP483191,,loader:fastq load.py,DMSO_2_R1.fastq.gz DMSO_2_R2.fastq.gz,fastq fastq,3062768334.0,10141617.0,GSM8012204 r1,0:151 1:151,A:815902447;C:711030547;G:726159250;T:809648102;N:27988,151,151,,,815902447,711030547,726159250,809648102,27988,SRX23167486,SRS20117074,SRA1784007,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,Belgium,2024-01-11,Larval,Larval,Liver,Liver and Biliary System
33210,SRR29868290,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I1_001.fastq.gz,fastq fastq fastq fastq,14533781976.0,86510607.0,GSM8403320 r1,,,,,,,,,,,,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92123,,0.07848,,0.87767,,0.63307,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33211,SRR29868291,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I1_001.fastq.gz,fastq fastq fastq fastq,14988315888.0,89216166.0,GSM8403320 r2,0:10 1:10 2:28 3:120,A:3248904317;C:2406836003;G:2506118019;T:2544017722;N:63859,10,10,28,120,3248904317,2406836003,2506118019,2544017722,63859,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92258,,0.07901,,0.87805,,0.61529,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33212,SRR29868292,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I1_001.fastq.gz,fastq fastq fastq fastq,15113782152.0,89962989.0,GSM8403320 r3,0:10 1:10 2:28 3:120,A:3272277396;C:2428985319;G:2529710055;T:2564489719;N:96191,10,10,28,120,3272277396,2428985319,2529710055,2564489719,96191,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92256,,0.07848,,0.87815,,0.62057,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33213,SRR29868293,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I1_001.fastq.gz,fastq fastq fastq fastq,14872072488.0,88524241.0,GSM8403320 r4,0:10 1:10 2:28 3:120,A:3227423261;C:2385566347;G:2480919292;T:2528894334;N:105686,10,10,28,120,3227423261,2385566347,2480919292,2528894334,105686,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92066,,0.07821,,0.87941,,0.63528,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33214,SRR29868294,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R2_001.fastq.gz,fastq fastq fastq fastq,17814930504.0,106041253.0,GSM8403319 r1,0:10 1:10 2:28 3:120,A:3778122253;C:2833144305;G:2888284601;T:3225338000;N:61201,10,10,28,120,3778122253,2833144305,2888284601,3225338000,61201,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92579,,0.07861,,0.82518,,0.61746,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33215,SRR29868295,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R2_001.fastq.gz,fastq fastq fastq fastq,18469195752.0,109935689.0,GSM8403319 r2,0:10 1:10 2:28 3:120,A:3912835271;C:2940938740;G:3000841815;T:3337590023;N:76831,10,10,28,120,3912835271,2940938740,3000841815,3337590023,76831,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92613,,0.07975,,0.82599,,0.6186,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33216,SRR29868296,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R2_001.fastq.gz,fastq fastq fastq fastq,18744044088.0,111571691.0,GSM8403319 r3,0:10 1:10 2:28 3:120,A:3967793098;C:2986585695;G:3048563710;T:3385544059;N:116358,10,10,28,120,3967793098,2986585695,3048563710,3385544059,116358,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9274,,0.07865,,0.82605,,0.61088,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33217,SRR29868297,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R2_001.fastq.gz,fastq fastq fastq fastq,18250884624.0,108636218.0,GSM8403319 r4,0:10 1:10 2:28 3:120,A:3870590300;C:2903010183;G:2961077382;T:3301541312;N:126983,10,10,28,120,3870590300,2903010183,2961077382,3301541312,126983,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92712,,0.07894,,0.82509,,0.60912,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33218,SRR29868298,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I1_001.fastq.gz,fastq fastq fastq fastq,17110767912.0,101849809.0,GSM8403318 r1,0:10 1:10 2:28 3:120,A:3788205667;C:2699657929;G:2699620981;T:3034435232;N:57271,10,10,28,120,3788205667,2699657929,2699620981,3034435232,57271,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91437,,0.05435,,0.86983,,0.62046,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33219,SRR29868299,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I1_001.fastq.gz,fastq fastq fastq fastq,17981827752.0,107034689.0,GSM8403318 r3,0:10 1:10 2:28 3:120,A:3977642248;C:2840653787;G:2844602651;T:3181150070;N:113924,10,10,28,120,3977642248,2840653787,2844602651,3181150070,113924,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91394,,0.05332,,0.87,,0.61803,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33220,SRR29868300,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I1_001.fastq.gz,fastq fastq fastq fastq,17550170232.0,104465299.0,GSM8403318 r4,0:10 1:10 2:28 3:120,A:3887199949;C:2768808747;G:2769733142;T:3109971563;N:122479,10,10,28,120,3887199949,2768808747,2769733142,3109971563,122479,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91342,,0.0541,,0.87046,,0.61388,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33221,SRR29868306,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I1_001.fastq.gz,fastq fastq fastq fastq,17719057944.0,105470583.0,GSM8403318 r2,0:10 1:10 2:28 3:120,A:3923720947;C:2796640453;G:2800418238;T:3135616927;N:73395,10,10,28,120,3923720947,2796640453,2800418238,3135616927,73395,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91325,,0.05422,,0.86949,,0.6266,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33222,SRR29868301,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R2_001.fastq.gz,fastq fastq fastq fastq,21323163288.0,126923591.0,GSM8403317 r1,0:10 1:10 2:28 3:120,A:4482829539;C:3366994739;G:3484245391;T:3896538980;N:222271,10,10,28,120,4482829539,3366994739,3484245391,3896538980,222271,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93349,,0.07482,,0.81925,,0.57693,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33223,SRR29868302,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R1_001.fastq.gz,fastq fastq fastq fastq,7887231744.0,46947808.0,GSM8403317 r5,0:10 1:10 2:28 3:120,A:1641421944;C:1251181706;G:1291844073;T:1449242410;N:46827,10,10,28,120,1641421944,1251181706,1291844073,1449242410,46827,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93251,,0.07497,,0.81763,,0.58245,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33224,SRR29868303,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8028118896.0,47786422.0,GSM8403317 r6,0:10 1:10 2:28 3:120,A:1672066662;C:1273372069;G:1312792441;T:1476102756;N:36712,10,10,28,120,1672066662,1273372069,1312792441,1476102756,36712,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93266,,0.07544,,0.81675,,0.57597,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33225,SRR29868304,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8223531120.0,48949590.0,GSM8403317 r7,0:10 1:10 2:28 3:120,A:1713836781;C:1304685662;G:1345155931;T:1510228105;N:44321,10,10,28,120,1713836781,1304685662,1345155931,1510228105,44321,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93273,,0.07513,,0.81546,,0.58099,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33226,SRR29868305,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I1_001.fastq.gz,fastq fastq fastq fastq,7715042160.0,45922870.0,GSM8403317 r8,0:10 1:10 2:28 3:120,A:1604997878;C:1222312105;G:1258545155;T:1424847802;N:41460,10,10,28,120,1604997878,1222312105,1258545155,1424847802,41460,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93359,,0.07524,,0.81479,,0.57882,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33227,SRR29868320,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R2_001.fastq.gz,fastq fastq fastq fastq,21662633664.0,128944248.0,GSM8403317 r2,0:10 1:10 2:28 3:120,A:4553543446;C:3422125565;G:3539342477;T:3957989911;N:308361,10,10,28,120,4553543446,3422125565,3539342477,3957989911,308361,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93227,,0.07246,,0.81696,,0.50066,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33228,SRR29868321,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I1_001.fastq.gz,fastq fastq fastq fastq,22267198800.0,132542850.0,GSM8403317 r3,0:10 1:10 2:28 3:120,A:4677084299;C:3522052285;G:3641789558;T:4063831592;N:384266,10,10,28,120,4677084299,3522052285,3641789558,4063831592,384266,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93308,,0.07402,,0.82035,,0.58114,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33229,SRR29868322,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I1_001.fastq.gz,fastq fastq fastq fastq,21946980216.0,130636787.0,GSM8403317 r4,0:10 1:10 2:28 3:120,A:4613356051;C:3469396471;G:3586452720;T:4006684161;N:525037,10,10,28,120,4613356051,3469396471,3586452720,4006684161,525037,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.932,,0.07454,,0.8199,,0.57856,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33230,SRR29868307,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I1_001.fastq.gz,fastq fastq fastq fastq,9879931488.0,58809116.0,GSM8403315 r1,0:10 1:10 2:28 3:120,A:2083561937;C:1579881891;G:1601331938;T:1792234199;N:83955,10,10,28,120,2083561937,1579881891,1601331938,1792234199,83955,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9245,,0.07832,,0.83207,,0.59038,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33231,SRR29868308,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I1_001.fastq.gz,fastq fastq fastq fastq,11728809288.0,69814341.0,GSM8403315 r5,0:10 1:10 2:28 3:120,A:2469898525;C:1869748167;G:1900689647;T:2137258339;N:126242,10,10,28,120,2469898525,1869748167,1900689647,2137258339,126242,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92438,,0.08084,,0.83181,,0.58855,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33232,SRR29868309,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I1_001.fastq.gz,fastq fastq fastq fastq,11877483744.0,70699308.0,GSM8403315 r6,0:10 1:10 2:28 3:120,A:2501780371;C:1893908685;G:1923797061;T:2164259893;N:170950,10,10,28,120,2501780371,1893908685,1923797061,2164259893,170950,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92477,,0.07874,,0.83321,,0.5933,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33233,SRR29868310,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I1_001.fastq.gz,fastq fastq fastq fastq,12148826256.0,72314442.0,GSM8403315 r7,0:10 1:10 2:28 3:120,A:2557348707;C:1939726759;G:1969388742;T:2211056576;N:212256,10,10,28,120,2557348707,1939726759,1969388742,2211056576,212256,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9241,,0.07899,,0.83246,,0.59733,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33234,SRR29868311,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I1_001.fastq.gz,fastq fastq fastq fastq,12000520224.0,71431668.0,GSM8403315 r8,0:10 1:10 2:28 3:120,A:2527907019;C:1914860315;G:1943708096;T:2185034081;N:290649,10,10,28,120,2527907019,1914860315,1943708096,2185034081,290649,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92467,,0.07869,,0.83274,,0.59327,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33235,SRR29868331,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10005892344.0,59558883.0,GSM8403315 r2,0:10 1:10 2:28 3:120,A:2111541927;C:1599222457;G:1620308600;T:1815908968;N:84008,10,10,28,120,2111541927,1599222457,1620308600,1815908968,84008,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.925,,0.07865,,0.83435,,0.60287,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33236,SRR29868332,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10016183856.0,59620142.0,GSM8403315 r3,0:10 1:10 2:28 3:120,A:2111419802;C:1602592297;G:1623486867;T:1816842279;N:75795,10,10,28,120,2111419802,1602592297,1623486867,1816842279,75795,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9252,,0.07706,,0.83311,,0.58482,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33237,SRR29868333,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I1_001.fastq.gz,fastq fastq fastq fastq,9972679080.0,59361185.0,GSM8403315 r4,0:10 1:10 2:28 3:120,A:2102584213;C:1595356295;G:1615800606;T:1809513301;N:87785,10,10,28,120,2102584213,1595356295,1615800606,1809513301,87785,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92471,,0.07908,,0.83368,,0.59597,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33238,SRR29868312,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I1_001.fastq.gz,fastq fastq fastq fastq,21831966072.0,129952179.0,GSM8403316 r1,0:10 1:10 2:28 3:120,A:4479350098;C:3460914438;G:3623235900;T:4030530673;N:230371,10,10,28,120,4479350098,3460914438,3623235900,4030530673,230371,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93487,,0.07462,,0.81168,,0.58593,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33239,SRR29868313,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R2_001.fastq.gz,fastq fastq fastq fastq,22210988016.0,132208262.0,GSM8403316 r2,0:10 1:10 2:28 3:120,A:4554555932;C:3523295618;G:3687384727;T:4099433293;N:321870,10,10,28,120,4554555932,3523295618,3687384727,4099433293,321870,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93515,,0.07425,,0.81251,,0.56065,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33240,SRR29868314,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R2_001.fastq.gz,fastq fastq fastq fastq,22964241384.0,136691913.0,GSM8403316 r3,0:10 1:10 2:28 3:120,A:4705118723;C:3647298654;G:3815152922;T:4235059775;N:399486,10,10,28,120,4705118723,3647298654,3815152922,4235059775,399486,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93515,,0.07425,,0.81085,,0.58414,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33241,SRR29868315,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R2_001.fastq.gz,fastq fastq fastq fastq,22572116784.0,134357838.0,GSM8403316 r4,0:10 1:10 2:28 3:120,A:4628982434;C:3582861623;G:3746732678;T:4163813221;N:550604,10,10,28,120,4628982434,3582861623,3746732678,4163813221,550604,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93487,,0.07514,,0.80862,,0.57745,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33242,SRR29868316,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9319118424.0,55470943.0,GSM8403316 r5,0:10 1:10 2:28 3:120,A:1895887547;C:1477863924;G:1543846946;T:1738857665;N:57078,10,10,28,120,1895887547,1477863924,1543846946,1738857665,57078,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93507,,0.07612,,0.80862,,0.5708,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33243,SRR29868317,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9433874184.0,56154013.0,GSM8403316 r6,0:10 1:10 2:28 3:120,A:1919903956;C:1496318299;G:1560772790;T:1761443349;N:43166,10,10,28,120,1919903956,1496318299,1560772790,1761443349,43166,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93514,,0.07597,,0.80937,,0.5877,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33244,SRR29868318,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I1_001.fastq.gz,fastq fastq fastq fastq,9674650944.0,57587208.0,GSM8403316 r7,0:10 1:10 2:28 3:120,A:1969538339;C:1535292977;G:1601577456;T:1804003343;N:52845,10,10,28,120,1969538339,1535292977,1601577456,1804003343,52845,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93521,,0.07665,,0.80876,,0.57512,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33245,SRR29868319,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R2_001.fastq.gz,fastq fastq fastq fastq,9063172776.0,53947457.0,GSM8403316 r8,0:10 1:10 2:28 3:120,A:1844279220;C:1435218712;G:1495137465;T:1699009389;N:50054,10,10,28,120,1844279220,1435218712,1495137465,1699009389,50054,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93431,,0.07653,,0.80803,,0.57631,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33246,SRR29868323,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I1_001.fastq.gz,fastq fastq fastq fastq,10244575656.0,60979617.0,GSM8403314 r1,0:10 1:10 2:28 3:120,A:2119295536;C:1665865582;G:1726802243;T:1805507036;N:83643,10,10,28,120,2119295536,1665865582,1726802243,1805507036,83643,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92821,,0.09448,,0.83725,,0.60089,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33247,SRR29868324,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I1_001.fastq.gz,fastq fastq fastq fastq,10380032880.0,61785910.0,GSM8403314 r2,0:10 1:10 2:28 3:120,A:2148125611;C:1687299842;G:1748516982;T:1830286430;N:80335,10,10,28,120,2148125611,1687299842,1748516982,1830286430,80335,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93012,,0.0931,,0.83621,,0.60089,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33248,SRR29868325,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I1_001.fastq.gz,fastq fastq fastq fastq,10397790648.0,61891611.0,GSM8403314 r3,0:10 1:10 2:28 3:120,A:2150008358;C:1691781234;G:1752867785;T:1832258443;N:77500,10,10,28,120,2150008358,1691781234,1752867785,1832258443,77500,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9284,,0.09293,,0.83605,,0.59853,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33249,SRR29868326,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I1_001.fastq.gz,fastq fastq fastq fastq,10333943592.0,61511569.0,GSM8403314 r4,0:10 1:10 2:28 3:120,A:2138003833;C:1680536471;G:1740834135;T:1821926938;N:86903,10,10,28,120,2138003833,1680536471,1740834135,1821926938,86903,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92828,,0.09437,,0.83611,,0.58915,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33250,SRR29868327,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I2_001.fastq.gz,fastq fastq fastq fastq,11552239440.0,68763330.0,GSM8403314 r5,0:10 1:10 2:28 3:120,A:2384461898;C:1875086137;G:1950680109;T:2041249149;N:122307,10,10,28,120,2384461898,1875086137,1950680109,2041249149,122307,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92842,,0.09581,,0.83591,,0.59709,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33251,SRR29868328,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I1_001.fastq.gz,fastq fastq fastq fastq,11713305912.0,69722059.0,GSM8403314 r6,0:10 1:10 2:28 3:120,A:2418305019;C:1901514145;G:1976625286;T:2070035096;N:167534,10,10,28,120,2418305019,1901514145,1976625286,2070035096,167534,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92987,,0.09528,,0.8352,,0.60535,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33252,SRR29868329,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I1_001.fastq.gz,fastq fastq fastq fastq,12060725208.0,71790031.0,GSM8403314 r7,0:10 1:10 2:28 3:120,A:2488941083;C:1959911465;G:2036435394;T:2129304281;N:211497,10,10,28,120,2488941083,1959911465,2036435394,2129304281,211497,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92896,,0.09426,,0.83867,,0.53757,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33253,SRR29868330,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R2_001.fastq.gz,fastq fastq fastq fastq,11892922944.0,70791208.0,GSM8403314 r8,0:10 1:10 2:28 3:120,A:2456445818;C:1931328609;G:2006328383;T:2100554789;N:287361,10,10,28,120,2456445818,1931328609,2006328383,2100554789,287361,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92946,,0.09343,,0.83704,,0.59688,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
34933,SRR32455887,SRX27770376,SRS24149655,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 R 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol and RSL3|replicate:replicate=Biological Replicate 10|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol and RSL3,a6 R 1,a6 R 1,Zebrafish hepatocytes treated with hexagingerol and RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100779-a6_R_1.R1.raw.fastq.gz L1EIG0100779-a6_R_1.R2.raw.fastq.gz,fastq fastq,6312642580.0,20902790.0,L1EIG0100779 a6 R 1.R1.raw.fastq.gz,0:151 1:151,A:1737087421;C:1412742895;G:1434786235;T:1727525167;N:500862,151,151,,,1737087421,1412742895,1434786235,1727525167,500862,SRX27770376,SRS24149655,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34934,SRR32455888,SRX27770375,SRS24149654,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol|replicate:replicate=Biological Replicate 9|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol,a6 3,a6 3,Zebrafish hepatocytes treated with hexagingerol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100778-a6_3.R1.raw.fastq.gz L1EIG0100778-a6_3.R2.raw.fastq.gz,fastq fastq,7105238258.0,23527279.0,L1EIG0100778 a6 3.R1.raw.fastq.gz,0:151 1:151,A:1967054238;C:1576589056;G:1603457184;T:1957568817;N:568963,151,151,,,1967054238,1576589056,1603457184,1957568817,568963,SRX27770375,SRS24149654,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34935,SRR32455889,SRX27770374,SRS24149653,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol|replicate:replicate=Biological Replicate 8|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol,a6 2,a6 2,Zebrafish hepatocytes treated with hexagingerol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100777-a6_2.R1.raw.fastq.gz L1EIG0100777-a6_2.R2.raw.fastq.gz,fastq fastq,6411725760.0,21230880.0,L1EIG0100777 a6 2.R1.raw.fastq.gz,0:151 1:151,A:1774737720;C:1423197995;G:1445462269;T:1767813232;N:514544,151,151,,,1774737720,1423197995,1445462269,1767813232,514544,SRX27770374,SRS24149653,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34936,SRR32455890,SRX27770373,SRS24149652,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol|replicate:replicate=Biological Replicate 7|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol,a6 1,a6 1,Zebrafish hepatocytes treated with hexagingerol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100776-a6_1.R1.raw.fastq.gz L1EIG0100776-a6_1.R2.raw.fastq.gz,fastq fastq,6755539170.0,22369335.0,L1EIG0100776 a6 1.R1.raw.fastq.gz,0:151 1:151,A:1872149169;C:1498908791;G:1521034783;T:1862905844;N:540583,151,151,,,1872149169,1498908791,1521034783,1862905844,540583,SRX27770373,SRS24149652,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34937,SRR32455891,SRX27770372,SRS24149651,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,R 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with RSL3|replicate:replicate=Biological Replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with RSL3,R 3,R 3,Zebrafish hepatocytes treated with RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100775-R_3.R1.raw.fastq.gz L1EIG0100775-R_3.R2.raw.fastq.gz,fastq fastq,6942710314.0,22989107.0,L1EIG0100775 R 3.R1.raw.fastq.gz,0:151 1:151,A:1902580151;C:1560207132;G:1591149353;T:1888209871;N:563807,151,151,,,1902580151,1560207132,1591149353,1888209871,563807,SRX27770372,SRS24149651,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34938,SRR32455892,SRX27770371,SRS24149650,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,R 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with RSL3|replicate:replicate=Biological Replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with RSL3,R 2,R 2,Zebrafish hepatocytes treated with RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100774-R_2.R1.raw.fastq.gz L1EIG0100774-R_2.R2.raw.fastq.gz,fastq fastq,6762005292.0,22390746.0,L1EIG0100774 R 2.R1.raw.fastq.gz,0:151 1:151,A:1853419911;C:1519952383;G:1546410472;T:1841314407;N:908119,151,151,,,1853419911,1519952383,1546410472,1841314407,908119,SRX27770371,SRS24149650,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System