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
280,DRR161311,DRX151936,DRS095335,DRP005084,PRJDB7735,Gene expression profile in adult zebrafish liver,DRP005084,Transcriptome Analysis,Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.,,,,Transcriptome of female Danio rerio liver,SAMD00153247,,sample name:transcriptome zebrafish female|sex:female|strain:RIKEN WT|tissue:liver,,,,,,,,,NextSeq 500 paired end sequencing of SAMD00153247,DRX151936,f,1,1,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP005084,NextSeq 500 paired end sequencing of SAMD00153247,,,,2338564937.0,15498367.0,DRR161311,0:75.45 1:75.44,A:613899755;C:541756858;G:548366901;T:633083422;N:1458001,75,75,,,613899755,541756858,548366901,633083422,1458001,DRX151936,DRS095335,DRA007652,"OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine","Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine",2,0.95814,0.96362,0.05394,0.04517,0.77932,0.7834,0.37385,0.37264,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-05-20,Undetermined,Adult,Liver,Liver and Biliary System
281,DRR161310,DRX151935,DRS095334,DRP005084,PRJDB7735,Gene expression profile in adult zebrafish liver,DRP005084,Transcriptome Analysis,Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.,,,,Transcriptome of male Danio rerio liver,SAMD00153246,,sample name:transcriptome zebrafish male|sex:male|strain:RIKEN WT|tissue:liver,,,,,,,,,NextSeq 500 paired end sequencing of SAMD00153246,DRX151935,m,1,1,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP005084,NextSeq 500 paired end sequencing of SAMD00153246,,,,2506978527.0,16611154.0,DRR161310,0:75.48 1:75.44,A:672321355;C:568289588;G:569411670;T:695545626;N:1410288,75,75,,,672321355,568289588,569411670,695545626,1410288,DRX151935,DRS095334,DRA007652,"OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine","Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine",2,0.94746,0.95115,0.07899,0.06363,0.80837,0.8115,0.52008,0.58743,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,unknown,bulk,unknown,unknown,,Japan,2019-05-20,Undetermined,Adult,Liver,Liver and Biliary System
19471,ERR14031296,ERX13434262,ERS22545283,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq Control Replicate 1,Control Replicate 1,SAMEA117477679,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009305 Control Replicate 1|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009305 Control Replicate 1|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9483,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19069_Control_14_R1.fastq.gz 19070_Control_14_R2.fastq.gz,fastq fastq,10004171894.0,33126397.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9483,0:151 1:151,A:2747978244;C:2173369585;G:2355012585;T:2716465615;N:11345865,151,151,,,2747978244,2173369585,2355012585,2716465615,11345865,ERX13434262,ERS22545283,ERA31000109,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
19472,ERR14031290,ERX13434256,ERS22545281,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq Control Replicate 2,Control Replicate 2,SAMEA117477677,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009306 Control Replicate 2|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009306 Control Replicate 2|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9484,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19071_Control_9_R1.fastq.gz 19072_Control_9_R2.fastq.gz,fastq fastq,11659155450.0,38606475.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9484,0:151 1:151,A:3197012061;C:2522601146;G:2753110022;T:3173195478;N:13236743,151,151,,,3197012061,2522601146,2753110022,3173195478,13236743,ERX13434256,ERS22545281,ERA31000093,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
19473,ERR14031295,ERX13434261,ERS22545292,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq NAFLD Replicate 2,NAFLD Replicate 2,SAMEA117477688,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009308 NAFLD Replicate 2|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009308 NAFLD Replicate 2|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9486,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19075_NAFLD_8_R1.fastq.gz 19076_NAFLD_8_R2.fastq.gz,fastq fastq,11001354150.0,36428325.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9486,0:151 1:151,A:3036945132;C:2390487588;G:2547341716;T:3014093258;N:12486456,151,151,,,3036945132,2390487588,2547341716,3014093258,12486456,ERX13434261,ERS22545292,ERA31000106,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
19474,ERR14031298,ERX13434264,ERS22545288,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq NAFLD Replicate 3,NAFLD Replicate 3,SAMEA117477684,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009309 NAFLD Replicate 3|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009309 NAFLD Replicate 3|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9487,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19077_NAFLD_9_R1.fastq.gz 19078_NAFLD_9_R2.fastq.gz,fastq fastq,10367145694.0,34328297.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9487,0:151 1:151,A:2861355932;C:2257080818;G:2411788871;T:2828044975;N:8875098,151,151,,,2861355932,2257080818,2411788871,2828044975,8875098,ERX13434264,ERS22545288,ERA31000114,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
19475,ERR14031292,ERX13434258,ERS22545282,ERP166767,PRJEB83101,Fish tales of fatty liver A transcriptomic approach to understanding NAFLD,inda-STUDY-IIITD-2024-11-18 13:55:50.21-189,Other,Background: Non alcoholic fatty liver disease is a significant global health concern  affecting millions and characterized by its complexity as a multifaceted disease. Despite its prevalence  the underlying molecular mechanisms remain poorly understood. Methods: Here  we propose a novel diet induced zebrafish model to investigate NAFLD. We validate this model through a series of histological examinations and molecular assessments  allowing us to explore the intricate pathways involved in the disease. We employ transcriptomic analysis to identify novel players associated with NAFLD progression. Results:  Our findings demonstrate that zebrafish subjected to a high fat diet exhibit weight gain  while Oil Red O staining confirms significant fat deposition in the liver. Quantitative PCR analysis reveals increased expression of lipogenic genes such as acc  fasn  hmgcs1  hmgcra  alongside markers of endoplasmic reticulum stress such as atf6  xbp1  gadd45a  ddit3 and mitochondrial unfolded protein response genes such as hspd1  hspa9  clpp  lonp1  indicating mitochondrial dysfunction which includes increased expression of genes encoding oxphos complexes  uqcrc2  cox4i1  atp5f1b. Transcriptomic profiling uncovers novel markers such as inha  gck  ces2a  id3 and dysregulated pathways related to metabolism  insulin signaling  and cellular stress responses. Conclusions: This study successfully establishes a zebrafish model that replicates key features of NAFLD  including histopathological changes and metabolic dysregulation. The validation of our model allows for a deeper exploration of the molecular landscape of NAFLD. By revealing novel biomarkers and pathways through transcriptomic analysis  our research opens new avenues for understanding the pathogenesis of NAFLD and potential therapeutic targets.,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,,RNA Seq NAFLD Replicate 1,NAFLD Replicate 1,SAMEA117477678,"Kusuma School of Biological Sciences (KSBS),IIT-Delhi;Department of Computational Biology,IIITD;IISER-Bhopal;Centre for Integrative Genomics,Genopode, University of Lausanne, Lausanne 1015, Switzerland",ENA first public:2024 12 05|INSDC center name:Kusuma School of Biological Sciences KSBS IIT Delhi;Department of Computational Biology IIITD;IISER Bhopal;Centre for Integrative Genomics Genopode  University of Lausanne  Lausanne 1015  Switzerland|INSDC status:public|Submitter Id:SAMIN0009307 NAFLD Replicate 1|broker name:IBDC|collection date:2023 04 18|common name:zebrafish|geographic location country and/or sea:India|sample name:SAMIN0009307 NAFLD Replicate 1|scientific name:Danio rerio,,,,,,,,,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9485,1,1,NaN,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP166767,Illumina HiSeq X paired end sequencing; Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD,ENA FIRST PUBLIC:2024 12 05|ENA LAST UPDATE:2024 12 05,19073_NAFLD_11_R1.fastq.gz 19074_NAFLD_11_R2.fastq.gz,fastq fastq,11885531932.0,39356066.0,RUN Fish tales of fatty liver: a transcriptomic approach to understanding NAFLD 9485,0:151 1:151,A:3208478929;C:2671086650;G:2843156238;T:3153091073;N:9719042,151,151,,,3208478929,2671086650,2843156238,3153091073,9719042,ERX13434258,ERS22545282,ERA31000101,Indian Biological Data Centre|European Nucleotide Archive,Indian Biological Data Centre,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,India,2024-12-05,Undetermined,Undetermined,Liver,Liver and Biliary System
31986,SRR28894021,SRX24452441,SRS21206092,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,elovl2 4,,strain:elovl2 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,elovl2 4,8,8,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,elovl2-4,fastq,4367010000.0,29113400.0,elovl2 4.gz,0:150,A:1161921878;C:1015107709;G:1012841192;T:1177020487;N:118734,150,,,,1161921878,1015107709,1012841192,1177020487,118734,SRX24452441,SRS21206092,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31987,SRR28894022,SRX24452440,SRS21206091,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,elovl2 3,,strain:elovl2 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,elovl2 3,7,7,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,elovl2-3,fastq,5125533150.0,34170221.0,elovl2 3.gz,0:150,A:1365645170;C:1189846405;G:1184721703;T:1385180096;N:139776,150,,,,1365645170,1189846405,1184721703,1385180096,139776,SRX24452440,SRS21206091,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31988,SRR28894023,SRX24452439,SRS21206090,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,elovl2 2,,strain:elovl2 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,elovl2 2,6,6,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,elovl2-2,fastq,3261375750.0,21742505.0,elovl2 2.gz,0:150,A:878478836;C:747963062;G:743760185;T:891083235;N:90432,150,,,,878478836,747963062,743760185,891083235,90432,SRX24452439,SRS21206090,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31989,SRR28894024,SRX24452438,SRS21206089,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,elovl2 1,,strain:elovl2 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,elovl2 1,5,5,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,elovl2-1,fastq,3629422950.0,24196153.0,elovl2 1.gz,0:150,A:974034477;C:836070594;G:831068189;T:988151010;N:98680,150,,,,974034477,836070594,831068189,988151010,98680,SRX24452438,SRS21206089,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31990,SRR28894025,SRX24452437,SRS21206088,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,WT 4,,strain:WT 4|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,WT 4,4,4,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,WT-4,fastq,4037472900.0,26916486.0,WT 4.gz,0:150,A:1083383010;C:932278459;G:925831402;T:1095868616;N:111413,150,,,,1083383010,932278459,925831402,1095868616,111413,SRX24452437,SRS21206088,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31991,SRR28894026,SRX24452436,SRS21206087,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,WT 3,,strain:WT 3|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,WT 3,3,3,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,WT-3,fastq,3651994200.0,24346628.0,WT 3.gz,0:150,A:978819903;C:844506880;G:836704943;T:991863415;N:99059,150,,,,978819903,844506880,836704943,991863415,99059,SRX24452436,SRS21206087,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31992,SRR28894027,SRX24452435,SRS21206086,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,WT 2,,strain:WT 2|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,WT 2,2,2,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,WT-2,fastq,3845338950.0,25635593.0,WT 2.gz,0:150,A:1033991995;C:885977441;G:878907105;T:1046356459;N:105950,150,,,,1033991995,885977441,878907105,1046356459,105950,SRX24452435,SRS21206086,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
31993,SRR28894028,SRX24452434,SRS21206085,SRP505663,PRJNA1107798,liver,PRJNA1107798,Other,wt and elovl2 mutant liver,,,,,WT 1,,strain:WT 1|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:not collected|geo loc name:not collected|sex:male|tissue:liver|BioSampleModel:Model organism or animal,,,,,,,,,WT 1,1,1,liver,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,SINGLE,ILLUMINA,Illumina HiSeq X,,SRP505663,,,WT-1,fastq,3756883050.0,25045887.0,WT 1.gz,0:150,A:1005244721;C:868304979;G:865360007;T:1017811504;N:161839,150,,,,1005244721,868304979,865360007,1017811504,161839,SRX24452434,SRS21206085,SRA1858809,Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology,Chinese Academy of Sciences (CAS),,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-05-04,Undetermined,Undetermined,Liver,Liver and Biliary System
33210,SRR29868290,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L001_I1_001.fastq.gz,fastq fastq fastq fastq,14533781976.0,86510607.0,GSM8403320 r1,,,,,,,,,,,,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92123,,0.07848,,0.87767,,0.63307,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33211,SRR29868291,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L002_I1_001.fastq.gz,fastq fastq fastq fastq,14988315888.0,89216166.0,GSM8403320 r2,0:10 1:10 2:28 3:120,A:3248904317;C:2406836003;G:2506118019;T:2544017722;N:63859,10,10,28,120,3248904317,2406836003,2506118019,2544017722,63859,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92258,,0.07901,,0.87805,,0.61529,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33212,SRR29868292,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L003_I1_001.fastq.gz,fastq fastq fastq fastq,15113782152.0,89962989.0,GSM8403320 r3,0:10 1:10 2:28 3:120,A:3272277396;C:2428985319;G:2529710055;T:2564489719;N:96191,10,10,28,120,3272277396,2428985319,2529710055,2564489719,96191,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92256,,0.07848,,0.87815,,0.62057,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33213,SRR29868293,SRX25365557,SRS22031297,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 11dpi,GSM8403320,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 11dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403320,GSM8403320: Liver PHx 11dpi; Danio rerio; RNA Seq,GSM8403320 r1,GSM8403320,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-SEE-PHx-11dpi-GEM-11-04-24_S24_L004_I1_001.fastq.gz,fastq fastq fastq fastq,14872072488.0,88524241.0,GSM8403320 r4,0:10 1:10 2:28 3:120,A:3227423261;C:2385566347;G:2480919292;T:2528894334;N:105686,10,10,28,120,3227423261,2385566347,2480919292,2528894334,105686,SRX25365557,SRS22031297,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92066,,0.07821,,0.87941,,0.63528,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33214,SRR29868294,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L001_R2_001.fastq.gz,fastq fastq fastq fastq,17814930504.0,106041253.0,GSM8403319 r1,0:10 1:10 2:28 3:120,A:3778122253;C:2833144305;G:2888284601;T:3225338000;N:61201,10,10,28,120,3778122253,2833144305,2888284601,3225338000,61201,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92579,,0.07861,,0.82518,,0.61746,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33215,SRR29868295,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L002_R2_001.fastq.gz,fastq fastq fastq fastq,18469195752.0,109935689.0,GSM8403319 r2,0:10 1:10 2:28 3:120,A:3912835271;C:2940938740;G:3000841815;T:3337590023;N:76831,10,10,28,120,3912835271,2940938740,3000841815,3337590023,76831,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92613,,0.07975,,0.82599,,0.6186,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33216,SRR29868296,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L003_R2_001.fastq.gz,fastq fastq fastq fastq,18744044088.0,111571691.0,GSM8403319 r3,0:10 1:10 2:28 3:120,A:3967793098;C:2986585695;G:3048563710;T:3385544059;N:116358,10,10,28,120,3967793098,2986585695,3048563710,3385544059,116358,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9274,,0.07865,,0.82605,,0.61088,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33217,SRR29868297,SRX25365556,SRS22031296,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver PHx 4dpi,GSM8403319,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy|geo loc name:missing|collection date:missing,Liver PHx 4dpi,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Hepatectomy,GSM8403319,GSM8403319: Liver PHx 4dpi; Danio rerio; RNA Seq,GSM8403319 r1,GSM8403319,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-SEE-BBNTR-PHx-4dpi-GEM-04-04-24_S23_L004_R2_001.fastq.gz,fastq fastq fastq fastq,18250884624.0,108636218.0,GSM8403319 r4,0:10 1:10 2:28 3:120,A:3870590300;C:2903010183;G:2961077382;T:3301541312;N:126983,10,10,28,120,3870590300,2903010183,2961077382,3301541312,126983,SRX25365556,SRS22031296,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92712,,0.07894,,0.82509,,0.60912,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33218,SRR29868298,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L001_I1_001.fastq.gz,fastq fastq fastq fastq,17110767912.0,101849809.0,GSM8403318 r1,0:10 1:10 2:28 3:120,A:3788205667;C:2699657929;G:2699620981;T:3034435232;N:57271,10,10,28,120,3788205667,2699657929,2699620981,3034435232,57271,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91437,,0.05435,,0.86983,,0.62046,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33219,SRR29868299,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L003_I1_001.fastq.gz,fastq fastq fastq fastq,17981827752.0,107034689.0,GSM8403318 r3,0:10 1:10 2:28 3:120,A:3977642248;C:2840653787;G:2844602651;T:3181150070;N:113924,10,10,28,120,3977642248,2840653787,2844602651,3181150070,113924,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91394,,0.05332,,0.87,,0.61803,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33220,SRR29868300,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L004_I1_001.fastq.gz,fastq fastq fastq fastq,17550170232.0,104465299.0,GSM8403318 r4,0:10 1:10 2:28 3:120,A:3887199949;C:2768808747;G:2769733142;T:3109971563;N:122479,10,10,28,120,3887199949,2768808747,2769733142,3109971563,122479,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91342,,0.0541,,0.87046,,0.61388,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33221,SRR29868306,SRX25365555,SRS22031295,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 9dppa,GSM8403318,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 9dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403318,GSM8403318: Liver MTZ 9dppa; Danio rerio; RNA Seq,GSM8403318 r1,GSM8403318,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-SEE-MTZ-9dppa-GEM-26-04-24_S26_L002_I1_001.fastq.gz,fastq fastq fastq fastq,17719057944.0,105470583.0,GSM8403318 r2,0:10 1:10 2:28 3:120,A:3923720947;C:2796640453;G:2800418238;T:3135616927;N:73395,10,10,28,120,3923720947,2796640453,2800418238,3135616927,73395,SRX25365555,SRS22031295,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.91325,,0.05422,,0.86949,,0.6266,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33222,SRR29868301,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L001_R2_001.fastq.gz,fastq fastq fastq fastq,21323163288.0,126923591.0,GSM8403317 r1,0:10 1:10 2:28 3:120,A:4482829539;C:3366994739;G:3484245391;T:3896538980;N:222271,10,10,28,120,4482829539,3366994739,3484245391,3896538980,222271,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93349,,0.07482,,0.81925,,0.57693,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33223,SRR29868302,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L001_R1_001.fastq.gz,fastq fastq fastq fastq,7887231744.0,46947808.0,GSM8403317 r5,0:10 1:10 2:28 3:120,A:1641421944;C:1251181706;G:1291844073;T:1449242410;N:46827,10,10,28,120,1641421944,1251181706,1291844073,1449242410,46827,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93251,,0.07497,,0.81763,,0.58245,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33224,SRR29868303,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8028118896.0,47786422.0,GSM8403317 r6,0:10 1:10 2:28 3:120,A:1672066662;C:1273372069;G:1312792441;T:1476102756;N:36712,10,10,28,120,1672066662,1273372069,1312792441,1476102756,36712,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93266,,0.07544,,0.81675,,0.57597,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33225,SRR29868304,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L003_R2_001.fastq.gz,fastq fastq fastq fastq,8223531120.0,48949590.0,GSM8403317 r7,0:10 1:10 2:28 3:120,A:1713836781;C:1304685662;G:1345155931;T:1510228105;N:44321,10,10,28,120,1713836781,1304685662,1345155931,1510228105,44321,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93273,,0.07513,,0.81546,,0.58099,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33226,SRR29868305,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-1dppa-GEM-240122_S35_L004_I1_001.fastq.gz,fastq fastq fastq fastq,7715042160.0,45922870.0,GSM8403317 r8,0:10 1:10 2:28 3:120,A:1604997878;C:1222312105;G:1258545155;T:1424847802;N:41460,10,10,28,120,1604997878,1222312105,1258545155,1424847802,41460,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93359,,0.07524,,0.81479,,0.57882,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33227,SRR29868320,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L002_R2_001.fastq.gz,fastq fastq fastq fastq,21662633664.0,128944248.0,GSM8403317 r2,0:10 1:10 2:28 3:120,A:4553543446;C:3422125565;G:3539342477;T:3957989911;N:308361,10,10,28,120,4553543446,3422125565,3539342477,3957989911,308361,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93227,,0.07246,,0.81696,,0.50066,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33228,SRR29868321,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L003_I1_001.fastq.gz,fastq fastq fastq fastq,22267198800.0,132542850.0,GSM8403317 r3,0:10 1:10 2:28 3:120,A:4677084299;C:3522052285;G:3641789558;T:4063831592;N:384266,10,10,28,120,4677084299,3522052285,3641789558,4063831592,384266,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93308,,0.07402,,0.82035,,0.58114,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33229,SRR29868322,SRX25365554,SRS22031294,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 1dppa,GSM8403317,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 1dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403317,GSM8403317: Liver MTZ 1dppa; Danio rerio; RNA Seq,GSM8403317 r1,GSM8403317,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-reload-EES3-1dppa-GEM-240122_S18_L004_I1_001.fastq.gz,fastq fastq fastq fastq,21946980216.0,130636787.0,GSM8403317 r4,0:10 1:10 2:28 3:120,A:4613356051;C:3469396471;G:3586452720;T:4006684161;N:525037,10,10,28,120,4613356051,3469396471,3586452720,4006684161,525037,SRX25365554,SRS22031294,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.932,,0.07454,,0.8199,,0.57856,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33230,SRR29868307,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L001_I1_001.fastq.gz,fastq fastq fastq fastq,9879931488.0,58809116.0,GSM8403315 r1,0:10 1:10 2:28 3:120,A:2083561937;C:1579881891;G:1601331938;T:1792234199;N:83955,10,10,28,120,2083561937,1579881891,1601331938,1792234199,83955,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9245,,0.07832,,0.83207,,0.59038,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33231,SRR29868308,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L001_I1_001.fastq.gz,fastq fastq fastq fastq,11728809288.0,69814341.0,GSM8403315 r5,0:10 1:10 2:28 3:120,A:2469898525;C:1869748167;G:1900689647;T:2137258339;N:126242,10,10,28,120,2469898525,1869748167,1900689647,2137258339,126242,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92438,,0.08084,,0.83181,,0.58855,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33232,SRR29868309,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L002_I1_001.fastq.gz,fastq fastq fastq fastq,11877483744.0,70699308.0,GSM8403315 r6,0:10 1:10 2:28 3:120,A:2501780371;C:1893908685;G:1923797061;T:2164259893;N:170950,10,10,28,120,2501780371,1893908685,1923797061,2164259893,170950,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92477,,0.07874,,0.83321,,0.5933,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33233,SRR29868310,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L003_I1_001.fastq.gz,fastq fastq fastq fastq,12148826256.0,72314442.0,GSM8403315 r7,0:10 1:10 2:28 3:120,A:2557348707;C:1939726759;G:1969388742;T:2211056576;N:212256,10,10,28,120,2557348707,1939726759,1969388742,2211056576,212256,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9241,,0.07899,,0.83246,,0.59733,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33234,SRR29868311,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES4-reload-EES2-larvlivCTL213dpf-GEM-230727_S20_L004_I1_001.fastq.gz,fastq fastq fastq fastq,12000520224.0,71431668.0,GSM8403315 r8,0:10 1:10 2:28 3:120,A:2527907019;C:1914860315;G:1943708096;T:2185034081;N:290649,10,10,28,120,2527907019,1914860315,1943708096,2185034081,290649,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92467,,0.07869,,0.83274,,0.59327,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33235,SRR29868331,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10005892344.0,59558883.0,GSM8403315 r2,0:10 1:10 2:28 3:120,A:2111541927;C:1599222457;G:1620308600;T:1815908968;N:84008,10,10,28,120,2111541927,1599222457,1620308600,1815908968,84008,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.925,,0.07865,,0.83435,,0.60287,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33236,SRR29868332,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10016183856.0,59620142.0,GSM8403315 r3,0:10 1:10 2:28 3:120,A:2111419802;C:1602592297;G:1623486867;T:1816842279;N:75795,10,10,28,120,2111419802,1602592297,1623486867,1816842279,75795,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9252,,0.07706,,0.83311,,0.58482,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33237,SRR29868333,SRX25365553,SRS22031298,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control2,GSM8403315,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control2,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403315,GSM8403315: Liver Control2; Danio rerio; RNA Seq,GSM8403315 r1,GSM8403315,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-larvalliver-CTL213dpf-GEM-230727_S11_L004_I1_001.fastq.gz,fastq fastq fastq fastq,9972679080.0,59361185.0,GSM8403315 r4,0:10 1:10 2:28 3:120,A:2102584213;C:1595356295;G:1615800606;T:1809513301;N:87785,10,10,28,120,2102584213,1595356295,1615800606,1809513301,87785,SRX25365553,SRS22031298,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92471,,0.07908,,0.83368,,0.59597,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33238,SRR29868312,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L001_I1_001.fastq.gz,fastq fastq fastq fastq,21831966072.0,129952179.0,GSM8403316 r1,0:10 1:10 2:28 3:120,A:4479350098;C:3460914438;G:3623235900;T:4030530673;N:230371,10,10,28,120,4479350098,3460914438,3623235900,4030530673,230371,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93487,,0.07462,,0.81168,,0.58593,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33239,SRR29868313,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L002_R2_001.fastq.gz,fastq fastq fastq fastq,22210988016.0,132208262.0,GSM8403316 r2,0:10 1:10 2:28 3:120,A:4554555932;C:3523295618;G:3687384727;T:4099433293;N:321870,10,10,28,120,4554555932,3523295618,3687384727,4099433293,321870,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93515,,0.07425,,0.81251,,0.56065,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33240,SRR29868314,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L003_R2_001.fastq.gz,fastq fastq fastq fastq,22964241384.0,136691913.0,GSM8403316 r3,0:10 1:10 2:28 3:120,A:4705118723;C:3647298654;G:3815152922;T:4235059775;N:399486,10,10,28,120,4705118723,3647298654,3815152922,4235059775,399486,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93515,,0.07425,,0.81085,,0.58414,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33241,SRR29868315,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-reload-EES2-0dppa-GEM-240122_S17_L004_R2_001.fastq.gz,fastq fastq fastq fastq,22572116784.0,134357838.0,GSM8403316 r4,0:10 1:10 2:28 3:120,A:4628982434;C:3582861623;G:3746732678;T:4163813221;N:550604,10,10,28,120,4628982434,3582861623,3746732678,4163813221,550604,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93487,,0.07514,,0.80862,,0.57745,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33242,SRR29868316,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9319118424.0,55470943.0,GSM8403316 r5,0:10 1:10 2:28 3:120,A:1895887547;C:1477863924;G:1543846946;T:1738857665;N:57078,10,10,28,120,1895887547,1477863924,1543846946,1738857665,57078,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93507,,0.07612,,0.80862,,0.5708,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33243,SRR29868317,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9433874184.0,56154013.0,GSM8403316 r6,0:10 1:10 2:28 3:120,A:1919903956;C:1496318299;G:1560772790;T:1761443349;N:43166,10,10,28,120,1919903956,1496318299,1560772790,1761443349,43166,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93514,,0.07597,,0.80937,,0.5877,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33244,SRR29868318,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L003_I1_001.fastq.gz,fastq fastq fastq fastq,9674650944.0,57587208.0,GSM8403316 r7,0:10 1:10 2:28 3:120,A:1969538339;C:1535292977;G:1601577456;T:1804003343;N:52845,10,10,28,120,1969538339,1535292977,1601577456,1804003343,52845,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93521,,0.07665,,0.80876,,0.57512,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33245,SRR29868319,SRX25365552,SRS22031293,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver MTZ 0dppa,GSM8403316,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation|geo loc name:missing|collection date:missing,Liver MTZ 0dppa,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Partial Ablation,GSM8403316,GSM8403316: Liver MTZ 0dppa; Danio rerio; RNA Seq,GSM8403316 r1,GSM8403316,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES2-0dppa-GEM-240122_S34_L004_R2_001.fastq.gz,fastq fastq fastq fastq,9063172776.0,53947457.0,GSM8403316 r8,0:10 1:10 2:28 3:120,A:1844279220;C:1435218712;G:1495137465;T:1699009389;N:50054,10,10,28,120,1844279220,1435218712,1495137465,1699009389,50054,SRX25365552,SRS22031293,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93431,,0.07653,,0.80803,,0.57631,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33246,SRR29868323,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L001_I1_001.fastq.gz,fastq fastq fastq fastq,10244575656.0,60979617.0,GSM8403314 r1,0:10 1:10 2:28 3:120,A:2119295536;C:1665865582;G:1726802243;T:1805507036;N:83643,10,10,28,120,2119295536,1665865582,1726802243,1805507036,83643,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92821,,0.09448,,0.83725,,0.60089,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33247,SRR29868324,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L002_I1_001.fastq.gz,fastq fastq fastq fastq,10380032880.0,61785910.0,GSM8403314 r2,0:10 1:10 2:28 3:120,A:2148125611;C:1687299842;G:1748516982;T:1830286430;N:80335,10,10,28,120,2148125611,1687299842,1748516982,1830286430,80335,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.93012,,0.0931,,0.83621,,0.60089,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33248,SRR29868325,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L003_I1_001.fastq.gz,fastq fastq fastq fastq,10397790648.0,61891611.0,GSM8403314 r3,0:10 1:10 2:28 3:120,A:2150008358;C:1691781234;G:1752867785;T:1832258443;N:77500,10,10,28,120,2150008358,1691781234,1752867785,1832258443,77500,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.9284,,0.09293,,0.83605,,0.59853,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33249,SRR29868326,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES1-larvalliver-CTL113dpf-GEM-230727_S10_L004_I1_001.fastq.gz,fastq fastq fastq fastq,10333943592.0,61511569.0,GSM8403314 r4,0:10 1:10 2:28 3:120,A:2138003833;C:1680536471;G:1740834135;T:1821926938;N:86903,10,10,28,120,2138003833,1680536471,1740834135,1821926938,86903,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92828,,0.09437,,0.83611,,0.58915,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33250,SRR29868327,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L001_I2_001.fastq.gz,fastq fastq fastq fastq,11552239440.0,68763330.0,GSM8403314 r5,0:10 1:10 2:28 3:120,A:2384461898;C:1875086137;G:1950680109;T:2041249149;N:122307,10,10,28,120,2384461898,1875086137,1950680109,2041249149,122307,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92842,,0.09581,,0.83591,,0.59709,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33251,SRR29868328,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L002_I1_001.fastq.gz,fastq fastq fastq fastq,11713305912.0,69722059.0,GSM8403314 r6,0:10 1:10 2:28 3:120,A:2418305019;C:1901514145;G:1976625286;T:2070035096;N:167534,10,10,28,120,2418305019,1901514145,1976625286,2070035096,167534,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92987,,0.09528,,0.8352,,0.60535,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33252,SRR29868329,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L003_I1_001.fastq.gz,fastq fastq fastq fastq,12060725208.0,71790031.0,GSM8403314 r7,0:10 1:10 2:28 3:120,A:2488941083;C:1959911465;G:2036435394;T:2129304281;N:211497,10,10,28,120,2488941083,1959911465,2036435394,2129304281,211497,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92896,,0.09426,,0.83867,,0.53757,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
33253,SRR29868330,SRX25365551,SRS22031292,SRP520597,PRJNA1136957,Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish,GSE272484,Transcriptome Analysis,Liver possesses robust regenerative ability  characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries  hepatocytes  the primary liver cells  undergo self duplication to replenish the liver mass. In contrast  when the damage is extensive  or hepatocyte proliferation is impaired  cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However  the regenerative mechanisms during periods of growth in young animals remain unexplored. Here  we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing  we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1  Control2  post partial ablation MTZ 0dppa  MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT  and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.,,pubmed:40480975,,Liver Control1,GSM8403314,,source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT|geo loc name:missing|collection date:missing,Liver Control1,A custom Cell Ranger index was generated from the Ensembl GRCz11 genome sequence and annotation filtered with ‘mkgtf’ command of Cell Ranger options: ‘—attribute = gene biotype:lincRNA –attribute = gene biotype:antisense  as well as the pseudo mTagBFP2  H2B mGL  mCherry NTR sequences in these cells using the mkref command. This index was used to map reads and generate gene expression matrices using the ‘count’ command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option “–include  introns” set to False all other options were used as per default. Assembly: GRCz11 Supplementary files format and content: Count Matrix as h5ad file Supplementary files format and content: Metadata listing the cell annotations as csv file,Liver,,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer’s instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3’ v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer’s protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control – No 4 OHT,GSM8403314,GSM8403314: Liver Control1; Danio rerio; RNA Seq,GSM8403314 r1,GSM8403314,1,Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich  E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools  11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly  the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher  12563029 at 37°C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation  TrypLE was inactivated with goat serum. To remove undissociated chunks and debris  the solution was passed through a 40 μm cell strainer Miltenyi Biotec  130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4°C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 μl of PBS. To remove dead cells  Calcein violet Thermo Fisher  C34858 or Draq7 Thermo Fisher  D15105 was added at a final concentration of 1 µM and 3 µM  respectively  and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates  including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7   respectively. FACS was performed  using a 100 µm nozzle  and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform  the cell suspension was adjusted with PBS to a density of 300 cells/µl and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 cells. Subsequently  the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell three prime v3. post the gel emulsion bead suspension underwent the reverse transcription reaction  emulsion was broken and DNA purified using Silane beads. The complementary DNA was amplified with 12 cycles  following the guidelines of the 10x Genomics user manual. The 10x Genomics single cell RNA seq library preparation—involving fragmentation  dA tailing  adapter ligation  and indexing PCR—was performed based on the manufacturer's protocol. post quantification  the libraries were sequenced on an Illumina NextSeq 550 machine.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP520597,,loader:fastq load.py,ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_I2_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R1_001.fastq.gz ULB-CB-cr-zf-EES3-reload-EES1-larvlivCTL113dpf-GEM-230727_S19_L004_R2_001.fastq.gz,fastq fastq fastq fastq,11892922944.0,70791208.0,GSM8403314 r8,0:10 1:10 2:28 3:120,A:2456445818;C:1931328609;G:2006328383;T:2100554789;N:287361,10,10,28,120,2456445818,1931328609,2006328383,2100554789,287361,SRX25365551,SRS22031292,SRA1926595,"Regeneration and Stress Biology, IRIBHM, ULB","Regeneration and Stress Biology, IRIBHM, ULB",1,0.92946,,0.09343,,0.83704,,0.59688,,120,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-07-17,Undetermined,Larval,Liver,Liver and Biliary System
34933,SRR32455887,SRX27770376,SRS24149655,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 R 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol and RSL3|replicate:replicate=Biological Replicate 10|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol and RSL3,a6 R 1,a6 R 1,Zebrafish hepatocytes treated with hexagingerol and RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100779-a6_R_1.R1.raw.fastq.gz L1EIG0100779-a6_R_1.R2.raw.fastq.gz,fastq fastq,6312642580.0,20902790.0,L1EIG0100779 a6 R 1.R1.raw.fastq.gz,0:151 1:151,A:1737087421;C:1412742895;G:1434786235;T:1727525167;N:500862,151,151,,,1737087421,1412742895,1434786235,1727525167,500862,SRX27770376,SRS24149655,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34934,SRR32455888,SRX27770375,SRS24149654,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol|replicate:replicate=Biological Replicate 9|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol,a6 3,a6 3,Zebrafish hepatocytes treated with hexagingerol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100778-a6_3.R1.raw.fastq.gz L1EIG0100778-a6_3.R2.raw.fastq.gz,fastq fastq,7105238258.0,23527279.0,L1EIG0100778 a6 3.R1.raw.fastq.gz,0:151 1:151,A:1967054238;C:1576589056;G:1603457184;T:1957568817;N:568963,151,151,,,1967054238,1576589056,1603457184,1957568817,568963,SRX27770375,SRS24149654,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34935,SRR32455889,SRX27770374,SRS24149653,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol|replicate:replicate=Biological Replicate 8|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol,a6 2,a6 2,Zebrafish hepatocytes treated with hexagingerol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100777-a6_2.R1.raw.fastq.gz L1EIG0100777-a6_2.R2.raw.fastq.gz,fastq fastq,6411725760.0,21230880.0,L1EIG0100777 a6 2.R1.raw.fastq.gz,0:151 1:151,A:1774737720;C:1423197995;G:1445462269;T:1767813232;N:514544,151,151,,,1774737720,1423197995,1445462269,1767813232,514544,SRX27770374,SRS24149653,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34936,SRR32455890,SRX27770373,SRS24149652,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a6 1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol|replicate:replicate=Biological Replicate 7|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol,a6 1,a6 1,Zebrafish hepatocytes treated with hexagingerol,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100776-a6_1.R1.raw.fastq.gz L1EIG0100776-a6_1.R2.raw.fastq.gz,fastq fastq,6755539170.0,22369335.0,L1EIG0100776 a6 1.R1.raw.fastq.gz,0:151 1:151,A:1872149169;C:1498908791;G:1521034783;T:1862905844;N:540583,151,151,,,1872149169,1498908791,1521034783,1862905844,540583,SRX27770373,SRS24149652,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34937,SRR32455891,SRX27770372,SRS24149651,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,R 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with RSL3|replicate:replicate=Biological Replicate 6|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with RSL3,R 3,R 3,Zebrafish hepatocytes treated with RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100775-R_3.R1.raw.fastq.gz L1EIG0100775-R_3.R2.raw.fastq.gz,fastq fastq,6942710314.0,22989107.0,L1EIG0100775 R 3.R1.raw.fastq.gz,0:151 1:151,A:1902580151;C:1560207132;G:1591149353;T:1888209871;N:563807,151,151,,,1902580151,1560207132,1591149353,1888209871,563807,SRX27770372,SRS24149651,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34938,SRR32455892,SRX27770371,SRS24149650,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,R 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with RSL3|replicate:replicate=Biological Replicate 5|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with RSL3,R 2,R 2,Zebrafish hepatocytes treated with RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100774-R_2.R1.raw.fastq.gz L1EIG0100774-R_2.R2.raw.fastq.gz,fastq fastq,6762005292.0,22390746.0,L1EIG0100774 R 2.R1.raw.fastq.gz,0:151 1:151,A:1853419911;C:1519952383;G:1546410472;T:1841314407;N:908119,151,151,,,1853419911,1519952383,1546410472,1841314407,908119,SRX27770371,SRS24149650,SRA2082274,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-02-23,Undetermined,Undetermined,Liver,Liver and Biliary System
34939,SRR32455893,SRX27770370,SRS24149649,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,R 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 RSL3|replicate:replicate=Biological Replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with RSL3,R 1,R 1,Zebrafish hepatocytes treated with RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100773-R_1.R1.raw.fastq.gz L1EIG0100773-R_1.R2.raw.fastq.gz,fastq fastq,6895808204.0,22833802.0,L1EIG0100773 R 1.R1.raw.fastq.gz,0:151 1:151,A:1893971807;C:1546715304;G:1570984307;T:1883580575;N:556211,151,151,,,1893971807,1546715304,1570984307,1883580575,556211,SRX27770370,SRS24149649,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
34940,SRR32455894,SRX27770369,SRS24149648,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a0 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Untreated zebrafish hepatocytes|replicate:replicate=Biological Replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,Untreated zebrafish hepatocytes,a0 3,a0 3,Untreated zebrafish hepatocytes,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100772-a0_3.R1.raw.fastq.gz L1EIG0100772-a0_3.R2.raw.fastq.gz,fastq fastq,7075697524.0,23429462.0,L1EIG0100772 a0 3.R1.raw.fastq.gz,0:151 1:151,A:1948593052;C:1578581045;G:1609493554;T:1938462155;N:567718,151,151,,,1948593052,1578581045,1609493554,1938462155,567718,SRX27770369,SRS24149648,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
34941,SRR32455895,SRX27770368,SRS24149647,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 3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol and RSL3|replicate:replicate=Biological Replicate 12|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol and RSL3,a6 R 3,a6 R 3,Zebrafish hepatocytes treated with hexagingerol and RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100781-a6_R_3.R1.raw.fastq.gz L1EIG0100781-a6_R_3.R2.raw.fastq.gz,fastq fastq,7116518260.0,23564630.0,L1EIG0100781 a6 R 3.R1.raw.fastq.gz,0:151 1:151,A:1964563996;C:1585337517;G:1611230029;T:1954816245;N:570473,151,151,,,1964563996,1585337517,1611230029,1954816245,570473,SRX27770368,SRS24149647,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
34942,SRR32455896,SRX27770367,SRS24149646,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 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Zebrafish hepatocytes treated with hexagingerol and RSL3|replicate:replicate=Biological Replicate 11|BioSampleModel:Model organism or animal,,,,,,,,,Zebrafish hepatocytes treated with hexagingerol and RSL3,a6 R 2,a6 R 2,Zebrafish hepatocytes treated with hexagingerol and RSL3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100780-a6_R_2.R1.raw.fastq.gz L1EIG0100780-a6_R_2.R2.raw.fastq.gz,fastq fastq,6799607916.0,22515258.0,L1EIG0100780 a6 R 2.R1.raw.fastq.gz,0:151 1:151,A:1876556721;C:1516219722;G:1543095947;T:1863186684;N:548842,151,151,,,1876556721,1516219722,1543095947,1863186684,548842,SRX27770367,SRS24149646,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
34943,SRR32455897,SRX27770366,SRS24149645,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a0 2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:2023 06 01|geo loc name:China:Wuhan|sex:not applicable|tissue:Untreated zebrafish hepatocytes|replicate:replicate=Biological Replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,Untreated zebrafish hepatocytes,a0 2,a0 2,Untreated zebrafish hepatocytes,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100771-a0_2.R1.raw.fastq.gz L1EIG0100771-a0_2.R2.raw.fastq.gz,fastq fastq,7445923854.0,24655377.0,L1EIG0100771 a0 2.R1.raw.fastq.gz,0:151 1:151,A:2041975942;C:1667033398;G:1714016742;T:2022303021;N:594751,151,151,,,2041975942,1667033398,1714016742,2022303021,594751,SRX27770366,SRS24149645,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
34944,SRR32455898,SRX27770365,SRS24149644,SRP565693,PRJNA1227000,Effect of hexagingerenol on ferroptosis,PRJNA1227000,Other,To investigate the effect of hexagingerol on ferroptosis in zebrafish hepatocytes by adding ferroptosis agonist,,,,,a0 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:Untreated zebrafish hepatocytes|replicate:replicate=Biological Replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,Untreated zebrafish hepatocytes,a0 1,a0 1,Untreated zebrafish hepatocytes,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP565693,,,L1EIG0100770-a0_1.R1.raw.fastq.gz L1EIG0100770-a0_1.R2.raw.fastq.gz,fastq fastq,7695172910.0,25480705.0,L1EIG0100770 a0 1.R1.raw.fastq.gz,0:151 1:151,A:2126497578;C:1711136637;G:1741192106;T:2115729594;N:616995,151,151,,,2126497578,1711136637,1741192106,2115729594,616995,SRX27770365,SRS24149644,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
36336,SRR390721,SRX112005,SRS282726,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from HBx+HCP transgenic line,GSM850201,,source name:zebrafish liver|phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver,mRNA from HBx+HCP transgenic line,HBx+HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:intrahepatic cholangiocarcinoma|strain:HBx+HCP transgenic|tissue:liver,GSM850201,GSM850201: mRNA from HBx+HCP transgenic line; Danio rerio; RNA Seq,GSM850201 1,GSM850201: mRNA from HBx+HCP transgenic line,1,,GEO Accession:GSM850201,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP009863,,,HBx+HCP.qual HBx+HCP.csfasta,SOLiD_native SOLiD_native,3946087000.0,78921740.0,GSM850201 r1,0:50,0:926148003;1:1112848138;2:1139608445;3:763770020;.:3712394,50,,,,,,,,,SRX112005,SRS282726,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.71816,,0.05681,,0.91727,,0.25279,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36337,SRR390720,SRX112004,SRS282725,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from HCP transgenic line,GSM850200,,source name:zebrafish liver|phenotype:n1|strain:HCP transgenic|tissue:liver,mRNA from HCP transgenic line,HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:n1|strain:HCP transgenic|tissue:liver,GSM850200,GSM850200: mRNA from HCP transgenic line; Danio rerio; RNA Seq,GSM850200 1,GSM850200: mRNA from HCP transgenic line,1,,GEO Accession:GSM850200,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP009863,,,HCP.qual HCP.csfasta,SOLiD_native SOLiD_native,4104044600.0,82080892.0,GSM850200 r1,0:50,0:944238890;1:1172273582;2:1207771613;3:775967445;.:3793070,50,,,,,,,,,SRX112004,SRS282725,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.70132,,0.05286,,0.94422,,0.26785,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36338,SRR390719,SRX112003,SRS282724,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from HBx transgenic line,GSM850199,,source name:zebrafish liver|phenotype:n1|strain:HBx transgenic|tissue:liver,mRNA from HBx transgenic line,HBx count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:n1|strain:HBx transgenic|tissue:liver,GSM850199,GSM850199: mRNA from HBx transgenic line; Danio rerio; RNA Seq,GSM850199 1,GSM850199: mRNA from HBx transgenic line,1,,GEO Accession:GSM850199,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP009863,,,HBx.qual HBx.csfasta,SOLiD_native SOLiD_native,3783924950.0,75678499.0,GSM850199 r1,0:50,0:909506019;1:1055965468;2:1075994223;3:739008253;.:3450987,50,,,,,,,,,SRX112003,SRS282724,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.70675,,0.04174,,0.94146,,0.22954,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
36339,SRR390718,SRX112002,SRS282723,SRP009863,PRJNA151317,A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver,GSE34493,Transcriptome Analysis,We sequenced mRNA from each transgenic zebrafish line including WT  HBx  HCP  and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age.,,,,mRNA from AB strain,GSM850198,,source name:zebrafish liver|phenotype:n1|strain:AB|tissue:liver,mRNA from AB strain,WT count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.,zebrafish liver,Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis,The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing  the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation  the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.,Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.,phenotype:n1|strain:AB|tissue:liver,GSM850198,GSM850198: mRNA from AB strain; Danio rerio; RNA Seq,GSM850198 1,GSM850198: mRNA from AB strain,1,,GEO Accession:GSM850198,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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>,SRP009863,,,WT.csfasta WT.qual,SOLiD_native SOLiD_native,5129652800.0,102593056.0,GSM850198 r1,0:50,0:1167298346;1:1421158274;2:1551481320;3:984758434;.:4956426,50,,,,,,,,,SRX112002,SRS282723,SRA048698,GEO,"Institute of Cellular and Organismic Biology, Academia Sinica",1,0.73072,,0.04843,,0.95574,,0.21796,,50,,B,,usable mapping rate,legacy,early,full_length,random_priming,unknown,bulk,unknown,unknown,,Taiwan,2011-12-16,Undetermined,Adult,Liver,Liver and Biliary System
37277,SRR1057959,SRX398517,SRS518969,SRP034710,PRJNA232516,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE53630,Transcriptome Analysis,The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing  using three prime' RNA SAGE on SOLiD system,,pubmed:24633177,,6T2,GSM1297515,,source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis,6T2,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor,one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis,GSM1297515,GSM1297515: 6T2; Danio rerio; RNA Seq,GSM1297515,,1,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1297515,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP034710,,,6T2.csfasta.gz 6T2.qual.gz,SOLiD_native SOLiD_native,818910190.0,23397434.0,GSM1297515 r1,0:35,0:347259734;1:164743259;2:162029194;3:130508344;.:14369659,35,,,,,,,,,SRX398517,SRS518969,SRA122333,GEO,National University of Singapore,1,0.03756,,0.0064,,0.99931,,0.92063,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-24,Undetermined,Adult,Liver,Liver and Biliary System
37278,SRR1057958,SRX398516,SRS518968,SRP034710,PRJNA232516,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE53630,Transcriptome Analysis,The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing  using three prime' RNA SAGE on SOLiD system,,pubmed:24633177,,6T1,GSM1297514,,source name:liver tumor|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis,6T1,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,liver tumor,one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:mifeprist1|outcome:liver tumorigenesis,GSM1297514,GSM1297514: 6T1; Danio rerio; RNA Seq,GSM1297514,,1,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1297514,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP034710,,,6T1.csfasta.gz 6T1.qual.gz,SOLiD_native SOLiD_native,761241005.0,21749743.0,GSM1297514 r1,0:35,0:306840116;1:164725874;2:160786359;3:126370697;.:2517959,35,,,,,,,,,SRX398516,SRS518968,SRA122333,GEO,National University of Singapore,1,0.0542,,0.00664,,0.99876,,0.95184,,35,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-24,Undetermined,Adult,Liver,Liver and Biliary System
37279,SRR1057957,SRX398515,SRS518967,SRP034710,PRJNA232516,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE53630,Transcriptome Analysis,The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing  using three prime' RNA SAGE on SOLiD system,,pubmed:24633177,,6M2,GSM1297513,,source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control,6M2,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control,GSM1297513,GSM1297513: 6M2; Danio rerio; RNA Seq,GSM1297513,,1,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1297513,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP034710,,,6M2.csfasta.gz 6M2.qual.gz,SOLiD_native SOLiD_native,627546330.0,20918211.0,GSM1297513 r1,0:30,0:265606277;1:113800100;2:158432886;3:89099865;.:607202,30,,,,,,,,,SRX398515,SRS518967,SRA122333,GEO,National University of Singapore,1,0.28369,,0.05854,,0.97611,,0.92541,,30,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-24,Undetermined,Adult,Liver,Liver and Biliary System
37280,SRR1057956,SRX398514,SRS518966,SRP034710,PRJNA232516,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE53630,Transcriptome Analysis,The kras transgenic line was generated by using a mifepristone inducible transgenic system in combination with a Cre loxP system. Most of the induced transgenic fish developed hepatocellular carcinoma at 6 month post induction. Overall design: Transcriptome profiling of Kras tumor sample 6T1 and 6T2 and control samples 6M1 and 6M2 were generated by deep sequencing  using three prime' RNA SAGE on SOLiD system,,pubmed:24633177,,6M1,GSM1297512,,source name:control liver|tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control,6M1,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database allowing maxium mismatches. The expression levels of mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: danRer7 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.,control liver,one mpf transgenic fish was treated at 1uM mifepriston for 36 hours to induce liver tumorigenesis.,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,,tissue:liver|genotype/variation:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line|agent:n1|outcome:control,GSM1297512,GSM1297512: 6M1; Danio rerio; RNA Seq,GSM1297512,,1,Total RNA was extracted using TRIzol Reagent Invitrogen  USA and treated with DNase I to remove genomic DNA contamination. Library construction was conducted by Mission Biotech Taiwan following standard ABI SOLiD protocol.,GEO Accession:GSM1297512,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD 3 Plus System,,SRP034710,,,6M1.csfasta.gz 6M1.qual.gz,SOLiD_native SOLiD_native,670343910.0,22344797.0,GSM1297512 r1,0:30,0:270812672;1:123662771;2:177982653;3:97335698;.:550116,30,,,,,,,,,SRX398514,SRS518966,SRA122333,GEO,National University of Singapore,1,0.28477,,0.05061,,0.9735,,0.86701,,30,,B,,usable mapping rate,legacy,early,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2013-12-24,Undetermined,Adult,Liver,Liver and Biliary System
38003,SRR1265754,SRX529148,SRS598845,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Female Liver Replicate 3 sRNAseq,GSM1376637,,source name:Female Liver|gender:female|tissue:Liver|genetic background:Wild type   Singapore strain,Female Liver Replicate 3 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Female Liver,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Female|tissue:Liver|genetic background:Wild type   Singapore strain,GSM1376637,GSM1376637: Female Liver Replicate 3 sRNAseq; Danio rerio; miRNA Seq,GSM1376637,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376637,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZL012_GCCAAT_L008_R1.fastq.gz,fastq,105717543.0,2072893.0,GSM1376637 r1,0:51,A:22408978;C:25732405;G:31681641;T:25880225;N:14294,51,,,,22408978,25732405,31681641,25880225,14294,SRX529148,SRS598845,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.05572,,0.0017,,0.99691,,0.56539,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Liver,Liver and Biliary System
38004,SRR1265753,SRX529147,SRS598844,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Female Liver Replicate 2 sRNAseq,GSM1376636,,source name:Female Liver|gender:female|tissue:Liver|genetic background:Wild type   Singapore strain,Female Liver Replicate 2 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Female Liver,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Female|tissue:Liver|genetic background:Wild type   Singapore strain,GSM1376636,GSM1376636: Female Liver Replicate 2 sRNAseq; Danio rerio; miRNA Seq,GSM1376636,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376636,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZL011_ACAGTG_L008_R1.fastq.gz,fastq,484614546.0,9502246.0,GSM1376636 r1,0:51,A:98373224;C:113894197;G:148444486;T:123841427;N:61212,51,,,,98373224,113894197,148444486,123841427,61212,SRX529147,SRS598844,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.01517,,0.00112,,0.9964,,0.61558,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Liver,Liver and Biliary System
38005,SRR1265752,SRX529146,SRS598843,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Female Liver Replicate 1 sRNAseq,GSM1376635,,source name:Female Liver|gender:female|tissue:Liver|genetic background:Wild type   Singapore strain,Female Liver Replicate 1 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Female Liver,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Female|tissue:Liver|genetic background:Wild type   Singapore strain,GSM1376635,GSM1376635: Female Liver Replicate 1 sRNAseq; Danio rerio; miRNA Seq,GSM1376635,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376635,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZL010_TGACCA_L008_R1.fastq.gz,fastq,304949706.0,5979406.0,GSM1376635 r1,0:51,A:62732698;C:71083849;G:92267430;T:78825237;N:40492,51,,,,62732698,71083849,92267430,78825237,40492,SRX529146,SRS598843,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.01218,,0.001,,0.99709,,0.55264,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Liver,Liver and Biliary System
38006,SRR1265751,SRX529145,SRS598842,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Male Liver Replicate 3 sRNAseq,GSM1376634,,source name:Male Liver|gender:male|tissue:Liver|genetic background:Wild type   Singapore strain,Male Liver Replicate 3 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Male Liver,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Male|tissue:Liver|genetic background:Wild type   Singapore strain,GSM1376634,GSM1376634: Male Liver Replicate 3 sRNAseq; Danio rerio; miRNA Seq,GSM1376634,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376634,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZL009_GATCAG_L007_R1.fastq.gz,fastq,287383266.0,5634966.0,GSM1376634 r1,0:51,A:54829818;C:73200212;G:89994996;T:69332773;N:25467,51,,,,54829818,73200212,89994996,69332773,25467,SRX529145,SRS598842,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00273,,0.00026,,0.99791,,0.69537,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Liver,Liver and Biliary System
38007,SRR1265750,SRX529144,SRS598841,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Male Liver Replicate 2 sRNAseq,GSM1376633,,source name:Male Liver|gender:male|tissue:Liver|genetic background:Wild type   Singapore strain,Male Liver Replicate 2 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Male Liver,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Male|tissue:Liver|genetic background:Wild type   Singapore strain,GSM1376633,GSM1376633: Male Liver Replicate 2 sRNAseq; Danio rerio; miRNA Seq,GSM1376633,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376633,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZL008_ACTTGA_L007_R1.fastq.gz,fastq,595761753.0,11681603.0,GSM1376633 r1,0:51,A:111507488;C:155297338;G:186229891;T:142672923;N:54113,51,,,,111507488,155297338,186229891,142672923,54113,SRX529144,SRS598841,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00597,,0.00067,,0.99679,,0.72807,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Liver,Liver and Biliary System
38008,SRR1265749,SRX529143,SRS598840,SRP041544,PRJNA245824,Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish,GSE57169,Transcriptome Analysis,The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.,,pubmed:26574018,,Male Liver Replicate 1 sRNAseq,GSM1376632,,source name:Male Liver|gender:male|tissue:Liver|genetic background:Wild type   Singapore strain,Male Liver Replicate 1 sRNAseq,Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.,Male Liver,N/A,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,Fishes were purchased from a local supplier and acclimatized before tissue extraction.,gender:Male|tissue:Liver|genetic background:Wild type   Singapore strain,GSM1376632,GSM1376632: Male Liver Replicate 1 sRNAseq; Danio rerio; miRNA Seq,GSM1376632,,1,Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.,GEO Accession:GSM1376632,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP041544,,,MZL007_CAGATC_L007_R1.fastq.gz,fastq,976402599.0,19145149.0,GSM1376632 r1,,,,,,,,,,,,SRX529143,SRS598840,SRA160430,GEO,"Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore",1,0.00348,,0.00035,,0.99742,,0.69292,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,size_fractionation,trueseq,bulk,unknown,unknown,,Singapore,2014-04-29,Undetermined,Embryo,Liver,Liver and Biliary System
41593,SRR392106,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,c1-2_1.fq c1-2_2.fq,fastq fastq,855494000.0,4502600.0,Control Sampe 1,0:100 1:90,A:217839807;C:202017646;G:207454208;T:227797566;N:384773,100,90,,,217839807,202017646,207454208,227797566,384773,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.87575,0.93454,0.06936,0.08546,0.82513,0.82306,0.49603,0.49334,100,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41594,SRR392108,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,c2-2_1.fq c2-2_2.fq,fastq fastq,1238874100.0,6520390.0,Control Sampe 2,0:100 1:90,A:316162781;C:292160612;G:299402161;T:330578118;N:570428,100,90,,,316162781,292160612,299402161,330578118,570428,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.89891,0.94864,0.03863,0.04738,0.8673,0.86531,0.28488,0.27076,100,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41595,SRR392109,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,c3-2_2.fq c3-2_1.fq,fastq fastq,2412101476.0,12830327.0,Control Sampe 3,0:100 1:88,A:611075174;C:569003408;G:589175071;T:641747898;N:1099925,100,88,,,611075174,569003408,589175071,641747898,1099925,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.87563,0.94341,0.03506,0.0441,0.83063,0.82795,0.41995,0.41226,100,88,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41596,SRR392110,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,v1_2.fq v1_1.fq,fastq fastq,1549099640.0,8153156.0,Case sampe 1,0:100 1:90,A:412607118;C:353282622;G:359371048;T:423373718;N:465134,100,90,,,412607118,353282622,359371048,423373718,465134,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.92368,0.9462,0.0604,0.06838,0.81249,0.81578,0.47008,0.4761,100,90,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41597,SRR392111,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,v2_1.fq v2_2.fq,fastq fastq,1465445712.0,7794924.0,Case sampe 2,0:100 1:88,A:387149663;C:337675800;G:340143929;T:400109622;N:366698,100,88,,,387149663,337675800,340143929,400109622,366698,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.92047,0.94711,0.05494,0.06325,0.81255,0.8143,0.48839,0.47383,100,88,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41598,SRR402758,SRX111567,SRS282484,SRP009841,PRJNA3560,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNAseq,Transcriptome Analysis,The zebrafish Danio rerio is a prominent vertebrate development model  has been extensively utilized as the pathogen host interaction to be studied in recent yrs. However  the mechanisms involved in the immune response of the zebrafish to vaccine are not fully understood. For clarify the high immune relative protection in zebrafish following the immunization of the putative Edwardsiella tarda E. tarda live attenuate vaccine  we performed a comparative gene expression analysis of mocked and immunized zebrafish using the RNA seq technology and DEGseq to identify differential expressed genes  chiefly for gaining deep insight into the liver immunogenetics post WEDplas vaccinated zebrafish.,,,RNA sequencinag of mRNAs from zebrafish liver following live attenuate vaccine immunized 2 days.,RNA seq based liver transcriptome analysis revealed an activated MHC I pathway and an inhibited MHC II pathway at the early stage of vaccine immunization in zebrafish,ZF RNA sequence,,,,,,,,,,,ZF RNA sequence,ZF RNA sequence,wt1,1,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,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>,SRP009841,,,v3_2.fq v3_1.fq,fastq fastq,1025249164.0,5453453.0,Case sampe 3,0:100 1:88,A:261599009;C:242254683;G:249423008;T:271717829;N:254635,100,88,,,261599009,242254683,249423008,271717829,254635,SRX111567,SRS282484,SRA048658,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,East China University Of Science And Technology|State Key Laboratory of Pathogen and Biosecurity,2,0.93668,0.95934,0.02982,0.03449,0.81347,0.8196,0.47392,0.47176,100,88,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2012-08-01,Undetermined,Undetermined,Liver,Liver and Biliary System
41813,SRR5196073,SRX2511744,SRS1935437,SRP097636,PRJNA362941,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE93965,Transcriptome Analysis,The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably  complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma  livers of  transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.,,pubmed:31827597,,NormM,GSM2465777,,source name:Normal liver of transgenic fishes under mifeprist1|tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,NormM,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample,Normal liver of transgenic fishes under mifepristone,One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water.,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,,tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,GSM2465777,GSM2465777: NormM; Danio rerio; RNA Seq,GSM2465777,,1,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,GEO Accession:GSM2465777,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP097636,,,solid_SAGE3_6M2_F3.csfasta.gz solid_SAGE3_6M2_F3_QV.qual.gz,SOLiD_native SOLiD_native,627546330.0,20918211.0,GSM2465777 r1,0:30,0:265606277;1:113800100;2:158432886;3:89099865;.:607202,30,,,,,,,,,SRX2511744,SRS1935437,SRA530985,GEO,The Biomedical Center,1,0.28369,,0.05854,,0.97605,,0.92502,,30,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2017-01-23,Undetermined,Adult,Liver,Liver and Biliary System
41814,SRR5196072,SRX2511743,SRS1935436,SRP097636,PRJNA362941,Transcriptomic analyses of Kras induced zebrafish liver cancer,GSE93965,Transcriptome Analysis,The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably  complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma  livers of  transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.,,pubmed:31827597,,Norm,GSM2465776,,source name:Normal liver of transgenic fishes|tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,Norm,The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample,Normal liver of transgenic fishes,One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water.,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,,tissue:Normal liver|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line,GSM2465776,GSM2465776: Norm; Danio rerio; RNA Seq,GSM2465776,,1,mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample,GEO Accession:GSM2465776,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ABI_SOLID,AB SOLiD System 3.0,,SRP097636,,,solid_SAGE3_6M1_F3.csfasta.gz solid_SAGE3_6M1_F3_QV.qual.gz,SOLiD_native SOLiD_native,670343910.0,22344797.0,GSM2465776 r1,0:30,0:270812672;1:123662771;2:177982653;3:97335698;.:550116,30,,,,,,,,,SRX2511743,SRS1935436,SRA530985,GEO,The Biomedical Center,1,0.28477,,0.05056,,0.97348,,0.86678,,30,,B,,usable mapping rate,legacy,early,unknown,poly_a,unknown,bulk,unknown,unknown,,Unknown,2017-01-23,Undetermined,Adult,Liver,Liver and Biliary System
42533,SRR5742065,SRX2947031,SRS2306327,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL68,GSM2679611,,tissue:Liver|agent:5.8 nM 2 ethylhexyl phthalate,CL68,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:5.8 nM 2 ethylhexyl phthalate,GSM2679611,GSM2679611: CL68; Danio rerio; RNA Seq,GSM2679611,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679611,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL68.fa.fastq.gz,fastq,65053254.0,1548887.0,GSM2679611 r1,0:42,A:16875146;C:13379903;G:16312762;T:18482630;N:2813,42,,,,16875146,13379903,16312762,18482630,2813,SRX2947031,SRS2306327,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42534,SRR5742064,SRX2947030,SRS2306326,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL67,GSM2679610,,tissue:Liver|agent:5.8 nM 2 ethylhexyl phthalate,CL67,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:5.8 nM 2 ethylhexyl phthalate,GSM2679610,GSM2679610: CL67; Danio rerio; RNA Seq,GSM2679610,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679610,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL67.fa.fastq.gz,fastq,97951518.0,2332179.0,GSM2679610 r1,0:42,A:25604873;C:20781116;G:24203084;T:27358188;N:4257,42,,,,25604873,20781116,24203084,27358188,4257,SRX2947030,SRS2306326,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42535,SRR5742063,SRX2947029,SRS2306325,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL66,GSM2679609,,tissue:Liver|agent:0.65 nM Ethinylestradiol EE2,CL66,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:0.65 nM Ethinylestradiol EE2,GSM2679609,GSM2679609: CL66; Danio rerio; RNA Seq,GSM2679609,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679609,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL66.fa.fastq.gz,fastq,79555644.0,1894182.0,GSM2679609 r1,0:42,A:20840478;C:16298564;G:19354919;T:23058169;N:3514,42,,,,20840478,16298564,19354919,23058169,3514,SRX2947029,SRS2306325,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42536,SRR5742062,SRX2947028,SRS2306324,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL65,GSM2679608,,tissue:Liver|agent:0.65 nM Ethinylestradiol EE2,CL65,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:0.65 nM Ethinylestradiol EE2,GSM2679608,GSM2679608: CL65; Danio rerio; RNA Seq,GSM2679608,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679608,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL65.fa.fastq.gz,fastq,74658444.0,1777582.0,GSM2679608 r1,0:42,A:19262431;C:15422889;G:18345920;T:21623880;N:3324,42,,,,19262431,15422889,18345920,21623880,3324,SRX2947028,SRS2306324,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42537,SRR5742061,SRX2947027,SRS2306322,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL64,GSM2679607,,tissue:Liver|agent:Control,CL64,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:Control,GSM2679607,GSM2679607: CL64; Danio rerio; RNA Seq,GSM2679607,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679607,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL64e.fa.fastq.gz,fastq,81941412.0,1950986.0,GSM2679607 r1,0:42,A:21427784;C:17542697;G:20002613;T:22964734;N:3584,42,,,,21427784,17542697,20002613,22964734,3584,SRX2947027,SRS2306322,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42538,SRR5742060,SRX2947026,SRS2306323,SRP110156,PRJNA391468,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE PLASTICIZER 2 ETHYLHEXYL PHTHALATE DEHP.,GSE100367,Transcriptome Analysis,We report the effects of exposure to the endocrine disurptor 2 ethylhexyl phthalate DEHP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and insulin resistance  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:29391432,,CL63,GSM2679606,,tissue:Liver|agent:Control,CL63,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 0.65 nM of 17α ethinylestradiol EE2  one tank contained 5.8 nM of 2 ethylhexyl phthalate DEHP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:Control,GSM2679606,GSM2679606: CL63; Danio rerio; RNA Seq,GSM2679606,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679606,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110156,,,M-CL63e.fa.fastq.gz,fastq,99418914.0,2367117.0,GSM2679606 r1,0:42,A:25465262;C:20166931;G:24797943;T:28984279;N:4499,42,,,,25465262,20166931,24797943,28984279,4499,SRX2947026,SRS2306323,SRA579533,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System
42539,SRR5742109,SRX2947056,SRS2306352,SRP110158,PRJNA391470,SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON IONIC SURFACTANT NONYLPHENOL NP.,GSE100369,Transcriptome Analysis,We report the effects of exposure to the endocrine disruptor nonylphenol NP on transcriptome modification in the livers of  in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation  pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common  environmental compound.,,pubmed:30563618,,CL62,GSM2679636,,tissue:Liver|agent:100 nM Nonylphenol NP|Sex:male,CL62,Sequencing was carried out on an Illumina GAIIx. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence  and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics  San Diego  CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data  including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p value or q value  which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content:   tab delimited .txt files include the DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean  log2FoldChange  lfcSE  stat  pvalue  padj  are all derived from DESeq2,Liver,Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater  and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial  flaked fish food Tetra  Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments  80 L tanks were prepared for each of the experimental groups  housing 40 fish per tank. One tank contained water with 1000 nM of 17β estradiol E2  one tank contained 100 nM of nonylphenol NP  and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH  and stock working solutions were prepared  from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system  and all exposures lasted for three weeks. post the end of the experimental period  the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch  St. Louis  MO; 10 g/L tap water and sacrificed for removal of their livers  which were immediately frozen in liquid nitrogen and stored at  70ºC for molecular biology analysis.,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,,agent:100 nM Nonylphenol NP|Sex:Male,GSM2679636,GSM2679636: CL62; Danio rerio; RNA Seq,GSM2679636,,1,Isolation of total liver RNA was performed using TRIzol reagent Invitrogen  and the extracted RNA were further purified using the RNeasy Mini kit Qiagen  Valencia  California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina  San Diego  CA  100 200 ng of total RNA was used following the protocol described by the manufacturer.,GEO Accession:GSM2679636,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina Genome Analyzer IIx,,SRP110158,,,M-CL62.fa.fastq.gz,fastq,122493672.0,2916516.0,GSM2679636 r1,0:42,A:31987859;C:24358295;G:32088563;T:34053478;N:5477,42,,,,31987859,24358295,32088563,34053478,5477,SRX2947056,SRS2306352,SRA579535,GEO,"Walton RS311, Pathology, Medical University of South Carolina",,,,,,,,,,,,,,,illumina,early_illumina,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United States,2017-06-22,Undetermined,Undetermined,Liver,Liver and Biliary System