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1,114 rows where experiment.library_selection = "cDNA" and tissue_curation = "Liver"

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technology 7

devstage_curation_coarse 6

devstage_curation 6

experiment.platform 4

experiment.library_source 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Liver · 1,114 ✖

experiment.library_strategy 1

experiment.library_selection 1

  • cDNA · 1,114 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.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
171 171 DRR075399 DRX069313 DRS075494 DRP004473 PRJDB5226 Effects of local gut tumor on whole organismal gene expressions in zebrafish DRP004473 Other How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.     The liver of control fish 7dpf Control liver SAMD00065413   sample name:3 control liver 150701 Hiseq3A l3 019|tissue type:Liver                 Illumina HiSeq 2500 sequencing of SAMD00065413 DRX069313 Control liver 1 Agilent SureSelect Strand Specific RNA Prep Kit   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP004473 Illumina HiSeq 2500 sequencing of SAMD00065413       951579036.0 26432751.0 DRR075399 0:36 A:231570583;C:228182815;G:227223430;T:264569214;N:32994 36       231570583 228182815 227223430 264569214 32994 DRX069313 DRS075494 DRA005199 ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International 1 0.8903   0.08667   0.7236   0.51557   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Japan 2018-09-19 Larval Larval Liver Liver and Biliary System
206 206 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
207 207 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
208 208 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
209 209 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
210 210 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
211 211 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
212 212 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
213 213 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
214 214 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
215 215 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
216 216 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
217 217 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
218 218 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
219 219 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
220 220 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
221 221 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
222 222 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
223 223 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
224 224 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
225 225 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
8104 8104 ERR2455366 ERX2474426 ERS2327331 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 4 SAMEA104725948 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725948|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:overfeeding|organism part:liver|sample name:E MTAB 6636:Sample 4|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 4 s Sample 4 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:overfeeding RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 OF-4_H7MWNALXX_L6_1.fq.gz fastq 4961276550.0 33075177.0 E MTAB 6636:Sample 4 0:150 1:0 A:1349413168;C:1135314970;G:1137935563;T:1338034716;N:578133 150 0     1349413168 1135314970 1137935563 1338034716 578133 ERX2474426 ERS2327331 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.90787   0.11999   0.66123   0.49072   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
8105 8105 ERR2455365 ERX2474425 ERS2327330 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 3 SAMEA104725947 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725947|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:fructose|organism part:liver|sample name:E MTAB 6636:Sample 3|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 3 s Sample 3 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:fructose RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 Fru-3_H7MWNALXX_L5_1.fq.gz fastq 5858273250.0 39055155.0 E MTAB 6636:Sample 3 0:150 1:0 A:1580150663;C:1353221682;G:1355865524;T:1568428138;N:607243 150 0     1580150663 1353221682 1355865524 1568428138 607243 ERX2474425 ERS2327330 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.91505   0.11036   0.65985   0.48443   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
8106 8106 ERR2455364 ERX2474424 ERS2327329 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 2 SAMEA104725946 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725946|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:cholesterol|organism part:liver|sample name:E MTAB 6636:Sample 2|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 2 s Sample 2 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:cholesterol RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 Cho-2_H7MWNALXX_L5_1.fq.gz fastq 5636304900.0 37575366.0 E MTAB 6636:Sample 2 0:150 1:0 A:1526862069;C:1295343770;G:1298751994;T:1514766898;N:580169 150 0     1526862069 1295343770 1298751994 1514766898 580169 ERX2474424 ERS2327329 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.91032   0.11644   0.66649   0.47766   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
8107 8107 ERR2455363 ERX2474423 ERS2327328 ERP107743 PRJEB25789 RNA seq of zebrafish larvae fed with different diets E-MTAB-6636 Transcriptome Analysis We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development. ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29   Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Sample 1 SAMEA104725945 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725945|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:control|organism part:liver|sample name:E MTAB 6636:Sample 1|scientific name:Danio rerio                 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets E MTAB 6636:Sample 1 s Sample 1 s RNA seq of zebrafish larvae fed with different diets Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5μg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Experimental Factor: diet:control RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 4000   ERP107743 Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16 ND-1_H7MWNALXX_L5_1.fq.gz fastq 5197165350.0 34647769.0 E MTAB 6636:Sample 1 0:150 1:0 A:1430911816;C:1174811274;G:1175616551;T:1415284019;N:541690 150 0     1430911816 1174811274 1175616551 1415284019 541690 ERX2474423 ERS2327328 ERA1259907 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive 1 0.89838   0.13883   0.66129   0.48467   150   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified nebnext bulk unknown unknown   China 2018-03-29 Larval Larval Liver Liver and Biliary System
19471 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 33210 SRR29868290 SRX25365557 SRS22031297 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver PHx 11dpi GSM8403320   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing Liver PHx 11dpi A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy GSM8403320 GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq GSM8403320 r1 GSM8403320 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I1_001.fastq.gz fastq fastq fastq fastq 14533781976.0 86510607.0 GSM8403320 r1                       SRX25365557 SRS22031297 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92123   0.07848   0.87767   0.63307   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33211 33211 SRR29868291 SRX25365557 SRS22031297 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver PHx 11dpi GSM8403320   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing Liver PHx 11dpi A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy GSM8403320 GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq GSM8403320 r1 GSM8403320 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I1_001.fastq.gz fastq fastq fastq fastq 14988315888.0 89216166.0 GSM8403320 r2 0:10 1:10 2:28 3:120 A:3248904317;C:2406836003;G:2506118019;T:2544017722;N:63859 10 10 28 120 3248904317 2406836003 2506118019 2544017722 63859 SRX25365557 SRS22031297 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92258   0.07901   0.87805   0.61529   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33212 33212 SRR29868292 SRX25365557 SRS22031297 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver PHx 11dpi GSM8403320   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing Liver PHx 11dpi A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy GSM8403320 GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq GSM8403320 r1 GSM8403320 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I1_001.fastq.gz fastq fastq fastq fastq 15113782152.0 89962989.0 GSM8403320 r3 0:10 1:10 2:28 3:120 A:3272277396;C:2428985319;G:2529710055;T:2564489719;N:96191 10 10 28 120 3272277396 2428985319 2529710055 2564489719 96191 SRX25365557 SRS22031297 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92256   0.07848   0.87815   0.62057   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33213 33213 SRR29868293 SRX25365557 SRS22031297 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver PHx 11dpi GSM8403320   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing Liver PHx 11dpi A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy GSM8403320 GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq GSM8403320 r1 GSM8403320 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I1_001.fastq.gz fastq fastq fastq fastq 14872072488.0 88524241.0 GSM8403320 r4 0:10 1:10 2:28 3:120 A:3227423261;C:2385566347;G:2480919292;T:2528894334;N:105686 10 10 28 120 3227423261 2385566347 2480919292 2528894334 105686 SRX25365557 SRS22031297 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92066   0.07821   0.87941   0.63528   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33214 33214 SRR29868294 SRX25365556 SRS22031296 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver PHx 4dpi GSM8403319   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing Liver PHx 4dpi A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy GSM8403319 GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq GSM8403319 r1 GSM8403319 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R2_001.fastq.gz fastq fastq fastq fastq 17814930504.0 106041253.0 GSM8403319 r1 0:10 1:10 2:28 3:120 A:3778122253;C:2833144305;G:2888284601;T:3225338000;N:61201 10 10 28 120 3778122253 2833144305 2888284601 3225338000 61201 SRX25365556 SRS22031296 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92579   0.07861   0.82518   0.61746   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33215 33215 SRR29868295 SRX25365556 SRS22031296 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver PHx 4dpi GSM8403319   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing Liver PHx 4dpi A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy GSM8403319 GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq GSM8403319 r1 GSM8403319 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R2_001.fastq.gz fastq fastq fastq fastq 18469195752.0 109935689.0 GSM8403319 r2 0:10 1:10 2:28 3:120 A:3912835271;C:2940938740;G:3000841815;T:3337590023;N:76831 10 10 28 120 3912835271 2940938740 3000841815 3337590023 76831 SRX25365556 SRS22031296 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92613   0.07975   0.82599   0.6186   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33216 33216 SRR29868296 SRX25365556 SRS22031296 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver PHx 4dpi GSM8403319   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing Liver PHx 4dpi A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy GSM8403319 GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq GSM8403319 r1 GSM8403319 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R2_001.fastq.gz fastq fastq fastq fastq 18744044088.0 111571691.0 GSM8403319 r3 0:10 1:10 2:28 3:120 A:3967793098;C:2986585695;G:3048563710;T:3385544059;N:116358 10 10 28 120 3967793098 2986585695 3048563710 3385544059 116358 SRX25365556 SRS22031296 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.9274   0.07865   0.82605   0.61088   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33217 33217 SRR29868297 SRX25365556 SRS22031296 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver PHx 4dpi GSM8403319   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing Liver PHx 4dpi A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy GSM8403319 GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq GSM8403319 r1 GSM8403319 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R2_001.fastq.gz fastq fastq fastq fastq 18250884624.0 108636218.0 GSM8403319 r4 0:10 1:10 2:28 3:120 A:3870590300;C:2903010183;G:2961077382;T:3301541312;N:126983 10 10 28 120 3870590300 2903010183 2961077382 3301541312 126983 SRX25365556 SRS22031296 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92712   0.07894   0.82509   0.60912   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33218 33218 SRR29868298 SRX25365555 SRS22031295 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 9dppa GSM8403318   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 9dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403318 GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq GSM8403318 r1 GSM8403318 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I1_001.fastq.gz fastq fastq fastq fastq 17110767912.0 101849809.0 GSM8403318 r1 0:10 1:10 2:28 3:120 A:3788205667;C:2699657929;G:2699620981;T:3034435232;N:57271 10 10 28 120 3788205667 2699657929 2699620981 3034435232 57271 SRX25365555 SRS22031295 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.91437   0.05435   0.86983   0.62046   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33219 33219 SRR29868299 SRX25365555 SRS22031295 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 9dppa GSM8403318   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 9dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403318 GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq GSM8403318 r1 GSM8403318 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I1_001.fastq.gz fastq fastq fastq fastq 17981827752.0 107034689.0 GSM8403318 r3 0:10 1:10 2:28 3:120 A:3977642248;C:2840653787;G:2844602651;T:3181150070;N:113924 10 10 28 120 3977642248 2840653787 2844602651 3181150070 113924 SRX25365555 SRS22031295 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.91394   0.05332   0.87   0.61803   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33220 33220 SRR29868300 SRX25365555 SRS22031295 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 9dppa GSM8403318   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 9dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403318 GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq GSM8403318 r1 GSM8403318 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I1_001.fastq.gz fastq fastq fastq fastq 17550170232.0 104465299.0 GSM8403318 r4 0:10 1:10 2:28 3:120 A:3887199949;C:2768808747;G:2769733142;T:3109971563;N:122479 10 10 28 120 3887199949 2768808747 2769733142 3109971563 122479 SRX25365555 SRS22031295 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.91342   0.0541   0.87046   0.61388   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33221 33221 SRR29868306 SRX25365555 SRS22031295 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 9dppa GSM8403318   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 9dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403318 GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq GSM8403318 r1 GSM8403318 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I1_001.fastq.gz fastq fastq fastq fastq 17719057944.0 105470583.0 GSM8403318 r2 0:10 1:10 2:28 3:120 A:3923720947;C:2796640453;G:2800418238;T:3135616927;N:73395 10 10 28 120 3923720947 2796640453 2800418238 3135616927 73395 SRX25365555 SRS22031295 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.91325   0.05422   0.86949   0.6266   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33222 33222 SRR29868301 SRX25365554 SRS22031294 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 1dppa GSM8403317   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 1dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403317 GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq GSM8403317 r1 GSM8403317 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R2_001.fastq.gz fastq fastq fastq fastq 21323163288.0 126923591.0 GSM8403317 r1 0:10 1:10 2:28 3:120 A:4482829539;C:3366994739;G:3484245391;T:3896538980;N:222271 10 10 28 120 4482829539 3366994739 3484245391 3896538980 222271 SRX25365554 SRS22031294 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93349   0.07482   0.81925   0.57693   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33223 33223 SRR29868302 SRX25365554 SRS22031294 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 1dppa GSM8403317   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 1dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403317 GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq GSM8403317 r1 GSM8403317 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R1_001.fastq.gz fastq fastq fastq fastq 7887231744.0 46947808.0 GSM8403317 r5 0:10 1:10 2:28 3:120 A:1641421944;C:1251181706;G:1291844073;T:1449242410;N:46827 10 10 28 120 1641421944 1251181706 1291844073 1449242410 46827 SRX25365554 SRS22031294 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93251   0.07497   0.81763   0.58245   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33224 33224 SRR29868303 SRX25365554 SRS22031294 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 1dppa GSM8403317   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 1dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403317 GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq GSM8403317 r1 GSM8403317 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R2_001.fastq.gz fastq fastq fastq fastq 8028118896.0 47786422.0 GSM8403317 r6 0:10 1:10 2:28 3:120 A:1672066662;C:1273372069;G:1312792441;T:1476102756;N:36712 10 10 28 120 1672066662 1273372069 1312792441 1476102756 36712 SRX25365554 SRS22031294 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93266   0.07544   0.81675   0.57597   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33225 33225 SRR29868304 SRX25365554 SRS22031294 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 1dppa GSM8403317   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 1dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403317 GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq GSM8403317 r1 GSM8403317 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R2_001.fastq.gz fastq fastq fastq fastq 8223531120.0 48949590.0 GSM8403317 r7 0:10 1:10 2:28 3:120 A:1713836781;C:1304685662;G:1345155931;T:1510228105;N:44321 10 10 28 120 1713836781 1304685662 1345155931 1510228105 44321 SRX25365554 SRS22031294 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93273   0.07513   0.81546   0.58099   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33226 33226 SRR29868305 SRX25365554 SRS22031294 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 1dppa GSM8403317   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 1dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403317 GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq GSM8403317 r1 GSM8403317 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I1_001.fastq.gz fastq fastq fastq fastq 7715042160.0 45922870.0 GSM8403317 r8 0:10 1:10 2:28 3:120 A:1604997878;C:1222312105;G:1258545155;T:1424847802;N:41460 10 10 28 120 1604997878 1222312105 1258545155 1424847802 41460 SRX25365554 SRS22031294 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93359   0.07524   0.81479   0.57882   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33227 33227 SRR29868320 SRX25365554 SRS22031294 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 1dppa GSM8403317   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 1dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403317 GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq GSM8403317 r1 GSM8403317 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R2_001.fastq.gz fastq fastq fastq fastq 21662633664.0 128944248.0 GSM8403317 r2 0:10 1:10 2:28 3:120 A:4553543446;C:3422125565;G:3539342477;T:3957989911;N:308361 10 10 28 120 4553543446 3422125565 3539342477 3957989911 308361 SRX25365554 SRS22031294 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93227   0.07246   0.81696   0.50066   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33228 33228 SRR29868321 SRX25365554 SRS22031294 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 1dppa GSM8403317   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 1dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403317 GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq GSM8403317 r1 GSM8403317 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I1_001.fastq.gz fastq fastq fastq fastq 22267198800.0 132542850.0 GSM8403317 r3 0:10 1:10 2:28 3:120 A:4677084299;C:3522052285;G:3641789558;T:4063831592;N:384266 10 10 28 120 4677084299 3522052285 3641789558 4063831592 384266 SRX25365554 SRS22031294 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93308   0.07402   0.82035   0.58114   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33229 33229 SRR29868322 SRX25365554 SRS22031294 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 1dppa GSM8403317   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 1dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403317 GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq GSM8403317 r1 GSM8403317 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I1_001.fastq.gz fastq fastq fastq fastq 21946980216.0 130636787.0 GSM8403317 r4 0:10 1:10 2:28 3:120 A:4613356051;C:3469396471;G:3586452720;T:4006684161;N:525037 10 10 28 120 4613356051 3469396471 3586452720 4006684161 525037 SRX25365554 SRS22031294 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.932   0.07454   0.8199   0.57856   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33230 33230 SRR29868307 SRX25365553 SRS22031298 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control2 GSM8403315   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control2 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403315 GSM8403315: Liver Control2; Danio rerio; RNA Seq GSM8403315 r1 GSM8403315 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I1_001.fastq.gz fastq fastq fastq fastq 9879931488.0 58809116.0 GSM8403315 r1 0:10 1:10 2:28 3:120 A:2083561937;C:1579881891;G:1601331938;T:1792234199;N:83955 10 10 28 120 2083561937 1579881891 1601331938 1792234199 83955 SRX25365553 SRS22031298 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.9245   0.07832   0.83207   0.59038   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33231 33231 SRR29868308 SRX25365553 SRS22031298 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control2 GSM8403315   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control2 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403315 GSM8403315: Liver Control2; Danio rerio; RNA Seq GSM8403315 r1 GSM8403315 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I1_001.fastq.gz fastq fastq fastq fastq 11728809288.0 69814341.0 GSM8403315 r5 0:10 1:10 2:28 3:120 A:2469898525;C:1869748167;G:1900689647;T:2137258339;N:126242 10 10 28 120 2469898525 1869748167 1900689647 2137258339 126242 SRX25365553 SRS22031298 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92438   0.08084   0.83181   0.58855   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33232 33232 SRR29868309 SRX25365553 SRS22031298 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control2 GSM8403315   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control2 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403315 GSM8403315: Liver Control2; Danio rerio; RNA Seq GSM8403315 r1 GSM8403315 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I1_001.fastq.gz fastq fastq fastq fastq 11877483744.0 70699308.0 GSM8403315 r6 0:10 1:10 2:28 3:120 A:2501780371;C:1893908685;G:1923797061;T:2164259893;N:170950 10 10 28 120 2501780371 1893908685 1923797061 2164259893 170950 SRX25365553 SRS22031298 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92477   0.07874   0.83321   0.5933   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33233 33233 SRR29868310 SRX25365553 SRS22031298 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control2 GSM8403315   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control2 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403315 GSM8403315: Liver Control2; Danio rerio; RNA Seq GSM8403315 r1 GSM8403315 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I1_001.fastq.gz fastq fastq fastq fastq 12148826256.0 72314442.0 GSM8403315 r7 0:10 1:10 2:28 3:120 A:2557348707;C:1939726759;G:1969388742;T:2211056576;N:212256 10 10 28 120 2557348707 1939726759 1969388742 2211056576 212256 SRX25365553 SRS22031298 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.9241   0.07899   0.83246   0.59733   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33234 33234 SRR29868311 SRX25365553 SRS22031298 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control2 GSM8403315   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control2 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403315 GSM8403315: Liver Control2; Danio rerio; RNA Seq GSM8403315 r1 GSM8403315 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I1_001.fastq.gz fastq fastq fastq fastq 12000520224.0 71431668.0 GSM8403315 r8 0:10 1:10 2:28 3:120 A:2527907019;C:1914860315;G:1943708096;T:2185034081;N:290649 10 10 28 120 2527907019 1914860315 1943708096 2185034081 290649 SRX25365553 SRS22031298 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92467   0.07869   0.83274   0.59327   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33235 33235 SRR29868331 SRX25365553 SRS22031298 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control2 GSM8403315   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control2 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403315 GSM8403315: Liver Control2; Danio rerio; RNA Seq GSM8403315 r1 GSM8403315 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R2_001.fastq.gz fastq fastq fastq fastq 10005892344.0 59558883.0 GSM8403315 r2 0:10 1:10 2:28 3:120 A:2111541927;C:1599222457;G:1620308600;T:1815908968;N:84008 10 10 28 120 2111541927 1599222457 1620308600 1815908968 84008 SRX25365553 SRS22031298 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.925   0.07865   0.83435   0.60287   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33236 33236 SRR29868332 SRX25365553 SRS22031298 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control2 GSM8403315   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control2 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403315 GSM8403315: Liver Control2; Danio rerio; RNA Seq GSM8403315 r1 GSM8403315 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R2_001.fastq.gz fastq fastq fastq fastq 10016183856.0 59620142.0 GSM8403315 r3 0:10 1:10 2:28 3:120 A:2111419802;C:1602592297;G:1623486867;T:1816842279;N:75795 10 10 28 120 2111419802 1602592297 1623486867 1816842279 75795 SRX25365553 SRS22031298 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.9252   0.07706   0.83311   0.58482   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33237 33237 SRR29868333 SRX25365553 SRS22031298 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control2 GSM8403315   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control2 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403315 GSM8403315: Liver Control2; Danio rerio; RNA Seq GSM8403315 r1 GSM8403315 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I1_001.fastq.gz fastq fastq fastq fastq 9972679080.0 59361185.0 GSM8403315 r4 0:10 1:10 2:28 3:120 A:2102584213;C:1595356295;G:1615800606;T:1809513301;N:87785 10 10 28 120 2102584213 1595356295 1615800606 1809513301 87785 SRX25365553 SRS22031298 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92471   0.07908   0.83368   0.59597   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33238 33238 SRR29868312 SRX25365552 SRS22031293 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 0dppa GSM8403316   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 0dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403316 GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq GSM8403316 r1 GSM8403316 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I1_001.fastq.gz fastq fastq fastq fastq 21831966072.0 129952179.0 GSM8403316 r1 0:10 1:10 2:28 3:120 A:4479350098;C:3460914438;G:3623235900;T:4030530673;N:230371 10 10 28 120 4479350098 3460914438 3623235900 4030530673 230371 SRX25365552 SRS22031293 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93487   0.07462   0.81168   0.58593   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33239 33239 SRR29868313 SRX25365552 SRS22031293 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 0dppa GSM8403316   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 0dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403316 GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq GSM8403316 r1 GSM8403316 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R2_001.fastq.gz fastq fastq fastq fastq 22210988016.0 132208262.0 GSM8403316 r2 0:10 1:10 2:28 3:120 A:4554555932;C:3523295618;G:3687384727;T:4099433293;N:321870 10 10 28 120 4554555932 3523295618 3687384727 4099433293 321870 SRX25365552 SRS22031293 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93515   0.07425   0.81251   0.56065   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33240 33240 SRR29868314 SRX25365552 SRS22031293 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 0dppa GSM8403316   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 0dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403316 GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq GSM8403316 r1 GSM8403316 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R2_001.fastq.gz fastq fastq fastq fastq 22964241384.0 136691913.0 GSM8403316 r3 0:10 1:10 2:28 3:120 A:4705118723;C:3647298654;G:3815152922;T:4235059775;N:399486 10 10 28 120 4705118723 3647298654 3815152922 4235059775 399486 SRX25365552 SRS22031293 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93515   0.07425   0.81085   0.58414   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33241 33241 SRR29868315 SRX25365552 SRS22031293 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 0dppa GSM8403316   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 0dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403316 GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq GSM8403316 r1 GSM8403316 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R2_001.fastq.gz fastq fastq fastq fastq 22572116784.0 134357838.0 GSM8403316 r4 0:10 1:10 2:28 3:120 A:4628982434;C:3582861623;G:3746732678;T:4163813221;N:550604 10 10 28 120 4628982434 3582861623 3746732678 4163813221 550604 SRX25365552 SRS22031293 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93487   0.07514   0.80862   0.57745   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33242 33242 SRR29868316 SRX25365552 SRS22031293 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 0dppa GSM8403316   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 0dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403316 GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq GSM8403316 r1 GSM8403316 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R2_001.fastq.gz fastq fastq fastq fastq 9319118424.0 55470943.0 GSM8403316 r5 0:10 1:10 2:28 3:120 A:1895887547;C:1477863924;G:1543846946;T:1738857665;N:57078 10 10 28 120 1895887547 1477863924 1543846946 1738857665 57078 SRX25365552 SRS22031293 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93507   0.07612   0.80862   0.5708   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33243 33243 SRR29868317 SRX25365552 SRS22031293 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 0dppa GSM8403316   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 0dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403316 GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq GSM8403316 r1 GSM8403316 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R2_001.fastq.gz fastq fastq fastq fastq 9433874184.0 56154013.0 GSM8403316 r6 0:10 1:10 2:28 3:120 A:1919903956;C:1496318299;G:1560772790;T:1761443349;N:43166 10 10 28 120 1919903956 1496318299 1560772790 1761443349 43166 SRX25365552 SRS22031293 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93514   0.07597   0.80937   0.5877   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33244 33244 SRR29868318 SRX25365552 SRS22031293 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 0dppa GSM8403316   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 0dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403316 GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq GSM8403316 r1 GSM8403316 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I1_001.fastq.gz fastq fastq fastq fastq 9674650944.0 57587208.0 GSM8403316 r7 0:10 1:10 2:28 3:120 A:1969538339;C:1535292977;G:1601577456;T:1804003343;N:52845 10 10 28 120 1969538339 1535292977 1601577456 1804003343 52845 SRX25365552 SRS22031293 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93521   0.07665   0.80876   0.57512   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33245 33245 SRR29868319 SRX25365552 SRS22031293 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver MTZ 0dppa GSM8403316   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing Liver MTZ 0dppa A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation GSM8403316 GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq GSM8403316 r1 GSM8403316 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R2_001.fastq.gz fastq fastq fastq fastq 9063172776.0 53947457.0 GSM8403316 r8 0:10 1:10 2:28 3:120 A:1844279220;C:1435218712;G:1495137465;T:1699009389;N:50054 10 10 28 120 1844279220 1435218712 1495137465 1699009389 50054 SRX25365552 SRS22031293 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93431   0.07653   0.80803   0.57631   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33246 33246 SRR29868323 SRX25365551 SRS22031292 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control1 GSM8403314   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control1 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403314 GSM8403314: Liver Control1; Danio rerio; RNA Seq GSM8403314 r1 GSM8403314 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I1_001.fastq.gz fastq fastq fastq fastq 10244575656.0 60979617.0 GSM8403314 r1 0:10 1:10 2:28 3:120 A:2119295536;C:1665865582;G:1726802243;T:1805507036;N:83643 10 10 28 120 2119295536 1665865582 1726802243 1805507036 83643 SRX25365551 SRS22031292 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92821   0.09448   0.83725   0.60089   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33247 33247 SRR29868324 SRX25365551 SRS22031292 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control1 GSM8403314   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control1 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403314 GSM8403314: Liver Control1; Danio rerio; RNA Seq GSM8403314 r1 GSM8403314 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I1_001.fastq.gz fastq fastq fastq fastq 10380032880.0 61785910.0 GSM8403314 r2 0:10 1:10 2:28 3:120 A:2148125611;C:1687299842;G:1748516982;T:1830286430;N:80335 10 10 28 120 2148125611 1687299842 1748516982 1830286430 80335 SRX25365551 SRS22031292 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.93012   0.0931   0.83621   0.60089   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33248 33248 SRR29868325 SRX25365551 SRS22031292 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control1 GSM8403314   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control1 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403314 GSM8403314: Liver Control1; Danio rerio; RNA Seq GSM8403314 r1 GSM8403314 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I1_001.fastq.gz fastq fastq fastq fastq 10397790648.0 61891611.0 GSM8403314 r3 0:10 1:10 2:28 3:120 A:2150008358;C:1691781234;G:1752867785;T:1832258443;N:77500 10 10 28 120 2150008358 1691781234 1752867785 1832258443 77500 SRX25365551 SRS22031292 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.9284   0.09293   0.83605   0.59853   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33249 33249 SRR29868326 SRX25365551 SRS22031292 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control1 GSM8403314   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control1 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403314 GSM8403314: Liver Control1; Danio rerio; RNA Seq GSM8403314 r1 GSM8403314 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I1_001.fastq.gz fastq fastq fastq fastq 10333943592.0 61511569.0 GSM8403314 r4 0:10 1:10 2:28 3:120 A:2138003833;C:1680536471;G:1740834135;T:1821926938;N:86903 10 10 28 120 2138003833 1680536471 1740834135 1821926938 86903 SRX25365551 SRS22031292 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92828   0.09437   0.83611   0.58915   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33250 33250 SRR29868327 SRX25365551 SRS22031292 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control1 GSM8403314   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control1 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403314 GSM8403314: Liver Control1; Danio rerio; RNA Seq GSM8403314 r1 GSM8403314 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I2_001.fastq.gz fastq fastq fastq fastq 11552239440.0 68763330.0 GSM8403314 r5 0:10 1:10 2:28 3:120 A:2384461898;C:1875086137;G:1950680109;T:2041249149;N:122307 10 10 28 120 2384461898 1875086137 1950680109 2041249149 122307 SRX25365551 SRS22031292 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92842   0.09581   0.83591   0.59709   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33251 33251 SRR29868328 SRX25365551 SRS22031292 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control1 GSM8403314   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control1 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403314 GSM8403314: Liver Control1; Danio rerio; RNA Seq GSM8403314 r1 GSM8403314 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I1_001.fastq.gz fastq fastq fastq fastq 11713305912.0 69722059.0 GSM8403314 r6 0:10 1:10 2:28 3:120 A:2418305019;C:1901514145;G:1976625286;T:2070035096;N:167534 10 10 28 120 2418305019 1901514145 1976625286 2070035096 167534 SRX25365551 SRS22031292 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92987   0.09528   0.8352   0.60535   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33252 33252 SRR29868329 SRX25365551 SRS22031292 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control1 GSM8403314   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control1 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403314 GSM8403314: Liver Control1; Danio rerio; RNA Seq GSM8403314 r1 GSM8403314 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I1_001.fastq.gz fastq fastq fastq fastq 12060725208.0 71790031.0 GSM8403314 r7 0:10 1:10 2:28 3:120 A:2488941083;C:1959911465;G:2036435394;T:2129304281;N:211497 10 10 28 120 2488941083 1959911465 2036435394 2129304281 211497 SRX25365551 SRS22031292 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92896   0.09426   0.83867   0.53757   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
33253 33253 SRR29868330 SRX25365551 SRS22031292 SRP520597 PRJNA1136957 Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish GSE272484 Transcriptome Analysis Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.   pubmed:40480975   Liver Control1 GSM8403314   source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing Liver Control1 A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense as well as the pseudo mTagBFP2 H2B mGL mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file Liver   Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 …   tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT GSM8403314 GSM8403314: Liver Control1; Danio rerio; RNA Seq GSM8403314 r1 GSM8403314 1 Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 μm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 µM and 3 µM respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 µm nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 550   SRP520597   loader:fastq load.py ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R2_001.fastq.gz fastq fastq fastq fastq 11892922944.0 70791208.0 GSM8403314 r8 0:10 1:10 2:28 3:120 A:2456445818;C:1931328609;G:2006328383;T:2100554789;N:287361 10 10 28 120 2456445818 1931328609 2006328383 2100554789 287361 SRX25365551 SRS22031292 SRA1926595 Regeneration and Stress Biology, IRIBHM, ULB Regeneration and Stress Biology, IRIBHM, ULB 1 0.92946   0.09343   0.83704   0.59688   120   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_droplet 10x   Belgium 2024-07-17 Undetermined Larval Liver Liver and Biliary System
34933 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

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