{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Undetermined\" and tissue_curation_coarse = \"Liver and Biliary System\"", "rows": [[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.", null, null, null, "Transcriptome of female Danio rerio liver", "SAMD00153247", null, "sample name:transcriptome zebrafish female|sex:female|strain:RIKEN WT|tissue:liver", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing of SAMD00153247", "DRX151936", "f", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", "1520Application ReadForward11Application ReadReverse77", "DRP005084", "NextSeq 500 paired end sequencing of SAMD00153247", null, null, null, 2338564937.0, 15498367.0, "DRR161311", "0:75.45 1:75.44", "A:613899755;C:541756858;G:548366901;T:633083422;N:1458001", 75, 75, null, null, 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", null, "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.", null, null, null, "Transcriptome of male Danio rerio liver", "SAMD00153246", null, "sample name:transcriptome zebrafish male|sex:male|strain:RIKEN WT|tissue:liver", null, null, null, null, null, null, null, null, "NextSeq 500 paired end sequencing of SAMD00153246", "DRX151935", "m", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 500", "1520Application ReadForward11Application ReadReverse77", "DRP005084", "NextSeq 500 paired end sequencing of SAMD00153246", null, null, null, 2506978527.0, 16611154.0, "DRR161310", "0:75.48 1:75.44", "A:672321355;C:568289588;G:569411670;T:695545626;N:1410288", 75, 75, null, null, 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", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 2747978244, 2173369585, 2355012585, 2716465615, 11345865, "ERX13434262", "ERS22545283", "ERA31000109", "Indian Biological Data Centre|European Nucleotide Archive", "Indian Biological Data Centre", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 3197012061, 2522601146, 2753110022, 3173195478, 13236743, "ERX13434256", "ERS22545281", "ERA31000093", "Indian Biological Data Centre|European Nucleotide Archive", "Indian Biological Data Centre", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 3036945132, 2390487588, 2547341716, 3014093258, 12486456, "ERX13434261", "ERS22545292", "ERA31000106", "Indian Biological Data Centre|European Nucleotide Archive", "Indian Biological Data Centre", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 2861355932, 2257080818, 2411788871, 2828044975, 8875098, "ERX13434264", "ERS22545288", "ERA31000114", "Indian Biological Data Centre|European Nucleotide Archive", "Indian Biological Data Centre", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "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", null, null, null, null, null, null, null, null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "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, null, null, 3208478929, 2671086650, 2843156238, 3153091073, 9719042, "ERX13434258", "ERS22545282", "ERA31000101", "Indian Biological Data Centre|European Nucleotide Archive", "Indian Biological Data Centre", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "elovl2 4", null, "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", null, null, null, null, null, null, null, null, "elovl2 4", "8", "8", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "elovl2-4", "fastq", 4367010000.0, 29113400.0, "elovl2 4.gz", "0:150", "A:1161921878;C:1015107709;G:1012841192;T:1177020487;N:118734", 150, null, null, null, 1161921878, 1015107709, 1012841192, 1177020487, 118734, "SRX24452441", "SRS21206092", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "elovl2 3", null, "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", null, null, null, null, null, null, null, null, "elovl2 3", "7", "7", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "elovl2-3", "fastq", 5125533150.0, 34170221.0, "elovl2 3.gz", "0:150", "A:1365645170;C:1189846405;G:1184721703;T:1385180096;N:139776", 150, null, null, null, 1365645170, 1189846405, 1184721703, 1385180096, 139776, "SRX24452440", "SRS21206091", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "elovl2 2", null, "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", null, null, null, null, null, null, null, null, "elovl2 2", "6", "6", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "elovl2-2", "fastq", 3261375750.0, 21742505.0, "elovl2 2.gz", "0:150", "A:878478836;C:747963062;G:743760185;T:891083235;N:90432", 150, null, null, null, 878478836, 747963062, 743760185, 891083235, 90432, "SRX24452439", "SRS21206090", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "elovl2 1", null, "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", null, null, null, null, null, null, null, null, "elovl2 1", "5", "5", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "elovl2-1", "fastq", 3629422950.0, 24196153.0, "elovl2 1.gz", "0:150", "A:974034477;C:836070594;G:831068189;T:988151010;N:98680", 150, null, null, null, 974034477, 836070594, 831068189, 988151010, 98680, "SRX24452438", "SRS21206089", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "WT 4", null, "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", null, null, null, null, null, null, null, null, "WT 4", "4", "4", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "WT-4", "fastq", 4037472900.0, 26916486.0, "WT 4.gz", "0:150", "A:1083383010;C:932278459;G:925831402;T:1095868616;N:111413", 150, null, null, null, 1083383010, 932278459, 925831402, 1095868616, 111413, "SRX24452437", "SRS21206088", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "WT 3", null, "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", null, null, null, null, null, null, null, null, "WT 3", "3", "3", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "WT-3", "fastq", 3651994200.0, 24346628.0, "WT 3.gz", "0:150", "A:978819903;C:844506880;G:836704943;T:991863415;N:99059", 150, null, null, null, 978819903, 844506880, 836704943, 991863415, 99059, "SRX24452436", "SRS21206087", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "WT 2", null, "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", null, null, null, null, null, null, null, null, "WT 2", "2", "2", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "WT-2", "fastq", 3845338950.0, 25635593.0, "WT 2.gz", "0:150", "A:1033991995;C:885977441;G:878907105;T:1046356459;N:105950", 150, null, null, null, 1033991995, 885977441, 878907105, 1046356459, 105950, "SRX24452435", "SRS21206086", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "WT 1", null, "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", null, null, null, null, null, null, null, null, "WT 1", "1", "1", "liver", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "SRP505663", null, null, "WT-1", "fastq", 3756883050.0, 25045887.0, "WT 1.gz", "0:150", "A:1005244721;C:868304979;G:865360007;T:1017811504;N:161839", 150, null, null, null, 1005244721, 868304979, 865360007, 1017811504, 161839, "SRX24452434", "SRS21206085", "SRA1858809", "Chinese Academy of Sciences (CAS)|The Institute of Hydrobiology", "Chinese Academy of Sciences (CAS)", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:40480975", null, "Liver PHx 11dpi", "GSM8403320", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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", null, null, null, null, null, null, null, null, null, null, null, "SRX25365557", "SRS22031297", "SRA1926595", "Regeneration and Stress Biology, IRIBHM, ULB", "Regeneration and Stress Biology, IRIBHM, ULB", 1, 0.92123, null, 0.07848, null, 0.87767, null, 0.63307, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 11dpi", "GSM8403320", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07901, null, 0.87805, null, 0.61529, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 11dpi", "GSM8403320", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07848, null, 0.87815, null, 0.62057, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 11dpi", "GSM8403320", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07821, null, 0.87941, null, 0.63528, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 4dpi", "GSM8403319", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07861, null, 0.82518, null, 0.61746, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 4dpi", "GSM8403319", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07975, null, 0.82599, null, 0.6186, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 4dpi", "GSM8403319", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07865, null, 0.82605, null, 0.61088, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver PHx 4dpi", "GSM8403319", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07894, null, 0.82509, null, 0.60912, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 9dppa", "GSM8403318", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.05435, null, 0.86983, null, 0.62046, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 9dppa", "GSM8403318", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.05332, null, 0.87, null, 0.61803, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 9dppa", "GSM8403318", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.0541, null, 0.87046, null, 0.61388, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 9dppa", "GSM8403318", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.05422, null, 0.86949, null, 0.6266, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07482, null, 0.81925, null, 0.57693, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07497, null, 0.81763, null, 0.58245, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07544, null, 0.81675, null, 0.57597, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07513, null, 0.81546, null, 0.58099, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07524, null, 0.81479, null, 0.57882, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07246, null, 0.81696, null, 0.50066, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07402, null, 0.82035, null, 0.58114, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 1dppa", "GSM8403317", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07454, null, 0.8199, null, 0.57856, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07832, null, 0.83207, null, 0.59038, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.08084, null, 0.83181, null, 0.58855, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07874, null, 0.83321, null, 0.5933, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07899, null, 0.83246, null, 0.59733, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07869, null, 0.83274, null, 0.59327, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07865, null, 0.83435, null, 0.60287, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07706, null, 0.83311, null, 0.58482, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control2", "GSM8403315", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07908, null, 0.83368, null, 0.59597, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07462, null, 0.81168, null, 0.58593, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07425, null, 0.81251, null, 0.56065, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07425, null, 0.81085, null, 0.58414, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07514, null, 0.80862, null, 0.57745, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07612, null, 0.80862, null, 0.5708, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07597, null, 0.80937, null, 0.5877, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07665, null, 0.80876, null, 0.57512, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver MTZ 0dppa", "GSM8403316", null, "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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.07653, null, 0.80803, null, 0.57631, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09448, null, 0.83725, null, 0.60089, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.0931, null, 0.83621, null, 0.60089, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09293, null, 0.83605, null, 0.59853, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09437, null, 0.83611, null, 0.58915, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09581, null, 0.83591, null, 0.59709, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09528, null, 0.8352, null, 0.60535, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09426, null, 0.83867, null, 0.53757, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:40480975", null, "Liver Control1", "GSM8403314", null, "source name:Liver|tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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 \u2018mkgtf\u2019 command of Cell Ranger options: \u2018\u2014attribute = gene biotype:lincRNA \u2013attribute = 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 \u2018count\u2019 command of the Cell Ranger software v.7.1.0 provided by 10x Genomics with the option \u201c\u2013include introns\u201d 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", null, "Zebrafish were euthanized in 500 mg/l solution of tricaine MS 222 Sigma Aldrich E10521. The entire liver was dissected out of the body using Dumont #5 forceps Fine Science Tools 11295 10. All steps for making the single cell suspension were performed with tubes and pipette tips coated with 1% BSA in PBS prior to the sample preparation. Briefly the liver was dissociated into single cells by incubation it in TrypLE Thermo Fisher 12563029 at 37\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer\u2019s instructions to yield 7 000 cells. Subsequently the cells were carefully mixed with reverse transcription mix before loading the cells on the 10x Genomics Chromium system Single Cell 3\u2019 v3. post the gel 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer\u2019s protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "tissue:Liver|transgene:Tgfabp10a:CellCousin|treatment:Control \u2013 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\u00b0C in a benchtop shaker set at 1000 rpm for 15 min. Following dissociation TrypLE was inactivated with goat serum. To remove undissociated chunks and debris the solution was passed through a 40 \u03bcm cell strainer Miltenyi Biotec 130 041 407. Cells were pelleted by centrifugation at 500 g for 5 min at 4\u00b0C with soft stop setting. The supernatant was carefully discarded and the pellet re suspended in 500 \u03bcl of PBS. To remove dead cells Calcein violet Thermo Fisher C34858 or Draq7 Thermo Fisher D15105 was added at a final concentration of 1 \u00b5M and 3 \u00b5M respectively and the cell suspension was incubated at room temperature for 20 min. The single cell preparation was sorted using appropriate gates including excitation with UV 405 nm or a 633 nm laser for identifying live cells with Calcein+ or Draq7 respectively. FACS was performed using a 100 \u00b5m nozzle and a minimum of 15 000 live cells per condition were collected into BSA coated tubes containing 1% BSA in PBS. Sorting time did not exceed 15 min. For single cell RNA sequencing using the 10x Genomics platform the cell suspension was adjusted with PBS to a density of 300 cells/\u00b5l and diluted with nuclease free water according to the manufacturer's instructions to yield 7 000 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\u2014involving fragmentation dA tailing adapter ligation and indexing PCR\u2014was performed based on the manufacturer's protocol. post quantification the libraries were sequenced on an Illumina NextSeq 550 machine.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP520597", null, "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, null, 0.09343, null, 0.83704, null, 0.59688, null, 120, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, null, null, null, "a6 R 1", null, "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", null, null, null, null, null, null, null, null, "Zebrafish hepatocytes treated with hexagingerol and RSL3", "a6 R 1", "a6 R 1", "Zebrafish hepatocytes treated with hexagingerol and RSL3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1737087421, 1412742895, 1434786235, 1727525167, 500862, "SRX27770376", "SRS24149655", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "a6 3", null, "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", null, null, null, null, null, null, null, null, "Zebrafish hepatocytes treated with hexagingerol", "a6 3", "a6 3", "Zebrafish hepatocytes treated with hexagingerol", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1967054238, 1576589056, 1603457184, 1957568817, 568963, "SRX27770375", "SRS24149654", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "a6 2", null, "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", null, null, null, null, null, null, null, null, "Zebrafish hepatocytes treated with hexagingerol", "a6 2", "a6 2", "Zebrafish hepatocytes treated with hexagingerol", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1774737720, 1423197995, 1445462269, 1767813232, 514544, "SRX27770374", "SRS24149653", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "a6 1", null, "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", null, null, null, null, null, null, null, null, "Zebrafish hepatocytes treated with hexagingerol", "a6 1", "a6 1", "Zebrafish hepatocytes treated with hexagingerol", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1872149169, 1498908791, 1521034783, 1862905844, 540583, "SRX27770373", "SRS24149652", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "R 3", null, "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", null, null, null, null, null, null, null, null, "Zebrafish hepatocytes treated with RSL3", "R 3", "R 3", "Zebrafish hepatocytes treated with RSL3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1902580151, 1560207132, 1591149353, 1888209871, 563807, "SRX27770372", "SRS24149651", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "R 2", null, "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", null, null, null, null, null, null, null, null, "Zebrafish hepatocytes treated with RSL3", "R 2", "R 2", "Zebrafish hepatocytes treated with RSL3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1853419911, 1519952383, 1546410472, 1841314407, 908119, "SRX27770371", "SRS24149650", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "R 1", null, "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", null, null, null, null, null, null, null, null, "Zebrafish hepatocytes treated with RSL3", "R 1", "R 1", "Zebrafish hepatocytes treated with RSL3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1893971807, 1546715304, 1570984307, 1883580575, 556211, "SRX27770370", "SRS24149649", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "a0 3", null, "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", null, null, null, null, null, null, null, null, "Untreated zebrafish hepatocytes", "a0 3", "a0 3", "Untreated zebrafish hepatocytes", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1948593052, 1578581045, 1609493554, 1938462155, 567718, "SRX27770369", "SRS24149648", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "a6 R 3", null, "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", null, null, null, null, null, null, null, null, "Zebrafish hepatocytes treated with hexagingerol and RSL3", "a6 R 3", "a6 R 3", "Zebrafish hepatocytes treated with hexagingerol and RSL3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1964563996, 1585337517, 1611230029, 1954816245, 570473, "SRX27770368", "SRS24149647", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "a6 R 2", null, "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", null, null, null, null, null, null, null, null, "Zebrafish hepatocytes treated with hexagingerol and RSL3", "a6 R 2", "a6 R 2", "Zebrafish hepatocytes treated with hexagingerol and RSL3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 1876556721, 1516219722, 1543095947, 1863186684, 548842, "SRX27770367", "SRS24149646", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "a0 2", null, "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", null, null, null, null, null, null, null, null, "Untreated zebrafish hepatocytes", "a0 2", "a0 2", "Untreated zebrafish hepatocytes", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 2041975942, 1667033398, 1714016742, 2022303021, 594751, "SRX27770366", "SRS24149645", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, null, null, null, "a0 1", null, "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", null, null, null, null, null, null, null, null, "Untreated zebrafish hepatocytes", "a0 1", "a0 1", "Untreated zebrafish hepatocytes", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP565693", null, null, "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, null, null, 2126497578, 1711136637, 1741192106, 2115729594, 616995, "SRX27770365", "SRS24149644", "SRA2082274", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "mRNA from HBx+HCP transgenic line", "GSM850201", null, "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 \u00b0C.", "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", null, "GEO Accession:GSM850201", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "500Application ReadForward1", "SRP009863", null, null, "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, null, null, null, null, null, null, null, null, "SRX112005", "SRS282726", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.71816, null, 0.05681, null, 0.91727, null, 0.25279, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "mRNA from HCP transgenic line", "GSM850200", null, "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 \u00b0C.", "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", null, "GEO Accession:GSM850200", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "500Application ReadForward1", "SRP009863", null, null, "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, null, null, null, null, null, null, null, null, "SRX112004", "SRS282725", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.70132, null, 0.05286, null, 0.94422, null, 0.26785, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "mRNA from HBx transgenic line", "GSM850199", null, "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 \u00b0C.", "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", null, "GEO Accession:GSM850199", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "500Application ReadForward1", "SRP009863", null, null, "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, null, null, null, null, null, null, null, null, "SRX112003", "SRS282724", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.70675, null, 0.04174, null, 0.94146, null, 0.22954, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "mRNA from AB strain", "GSM850198", null, "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 \u00b0C.", "phenotype:n1|strain:AB|tissue:liver", "GSM850198", "GSM850198: mRNA from AB strain; Danio rerio; RNA Seq", "GSM850198 1", "GSM850198: mRNA from AB strain", "1", null, "GEO Accession:GSM850198", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "500Application ReadForward1", "SRP009863", null, null, "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, null, null, null, null, null, null, null, null, "SRX112002", "SRS282723", "SRA048698", "GEO", "Institute of Cellular and Organismic Biology, Academia Sinica", 1, 0.73072, null, 0.04843, null, 0.95574, null, 0.21796, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "6T2", "GSM1297515", null, "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.", null, "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", null, "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", null, "SRP034710", null, null, "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, null, null, null, null, null, null, null, null, "SRX398517", "SRS518969", "SRA122333", "GEO", "National University of Singapore", 1, 0.03756, null, 0.0064, null, 0.99931, null, 0.92063, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "6T1", "GSM1297514", null, "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.", null, "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", null, "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", null, "SRP034710", null, null, "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, null, null, null, null, null, null, null, null, "SRX398516", "SRS518968", "SRA122333", "GEO", "National University of Singapore", 1, 0.0542, null, 0.00664, null, 0.99876, null, 0.95184, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "6M2", "GSM1297513", null, "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.", null, "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", null, "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", null, "SRP034710", null, null, "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, null, null, null, null, null, null, null, null, "SRX398515", "SRS518967", "SRA122333", "GEO", "National University of Singapore", 1, 0.28369, null, 0.05854, null, 0.97611, null, 0.92541, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "pubmed:24633177", null, "6M1", "GSM1297512", null, "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.", null, "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", null, "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", null, "SRP034710", null, null, "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, null, null, null, null, null, null, null, null, "SRX398514", "SRS518966", "SRA122333", "GEO", "National University of Singapore", 1, 0.28477, null, 0.05061, null, 0.9735, null, 0.86701, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:26574018", null, "Female Liver Replicate 3 sRNAseq", "GSM1376637", null, "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 Friedl\u00e4nder 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 m r 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\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "SRP041544", null, null, "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, null, null, null, 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, null, 0.0017, null, 0.99691, null, 0.56539, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:26574018", null, "Female Liver Replicate 2 sRNAseq", "GSM1376636", null, "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 Friedl\u00e4nder 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 m r 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\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "SRP041544", null, null, "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, null, null, null, 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, null, 0.00112, null, 0.9964, null, 0.61558, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:26574018", null, "Female Liver Replicate 1 sRNAseq", "GSM1376635", null, "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 Friedl\u00e4nder 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 m r 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\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "SRP041544", null, null, "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, null, null, null, 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, null, 0.001, null, 0.99709, null, 0.55264, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:26574018", null, "Male Liver Replicate 3 sRNAseq", "GSM1376634", null, "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 Friedl\u00e4nder 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 m r 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\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "SRP041544", null, null, "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, null, null, null, 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, null, 0.00026, null, 0.99791, null, 0.69537, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:26574018", null, "Male Liver Replicate 2 sRNAseq", "GSM1376633", null, "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 Friedl\u00e4nder 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 m r 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\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "SRP041544", null, null, "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, null, null, null, 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, null, 0.00067, null, 0.99679, null, 0.72807, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:26574018", null, "Male Liver Replicate 1 sRNAseq", "GSM1376632", null, "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 Friedl\u00e4nder 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 m r 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\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "SRP041544", null, null, "MZL007_CAGATC_L007_R1.fastq.gz", "fastq", 976402599.0, 19145149.0, "GSM1376632 r1", null, null, null, null, null, null, null, null, null, null, null, "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, null, 0.00035, null, 0.99742, null, 0.69292, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "ZF RNA sequence", "ZF RNA sequence", "wt1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP009841", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "ZF RNA sequence", "ZF RNA sequence", "wt1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP009841", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "ZF RNA sequence", "ZF RNA sequence", "wt1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP009841", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "ZF RNA sequence", "ZF RNA sequence", "wt1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP009841", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "ZF RNA sequence", "ZF RNA sequence", "wt1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP009841", null, null, "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, null, null, 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", null, "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.", null, null, "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", null, null, null, null, null, null, null, null, null, null, "ZF RNA sequence", "ZF RNA sequence", "wt1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2000Application ReadForward11Application ReadReverse101", "SRP009841", null, null, "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, null, null, 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", null, "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 2\u00b5M 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.", null, "pubmed:31827597", null, "NormM", "GSM2465777", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", null, "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", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", "GEO Accession:GSM2465777", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP097636", null, null, "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, null, null, null, null, null, null, null, null, "SRX2511744", "SRS1935437", "SRA530985", "GEO", "The Biomedical Center", 1, 0.28369, null, 0.05854, null, 0.97605, null, 0.92502, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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 2\u00b5M 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.", null, "pubmed:31827597", null, "Norm", "GSM2465776", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", null, "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", null, "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\u2032 RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer\u2019s protocol and 10\u201323 million reads were generated from each sample", "GEO Accession:GSM2465776", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP097636", null, null, "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, null, null, null, null, null, null, null, null, "SRX2511743", "SRS1935436", "SRA530985", "GEO", "The Biomedical Center", 1, 0.28477, null, 0.05056, null, 0.97348, null, 0.86678, null, 30, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:29391432", null, "CL68", "GSM2679611", null, "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\u2019s 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 29\u00baC 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 17\u03b1 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 70\u00baC 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.", null, "agent:5.8 nM 2 ethylhexyl phthalate", "GSM2679611", "GSM2679611: CL68; Danio rerio; RNA Seq", "GSM2679611", null, "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", null, "SRP110156", null, null, "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, null, null, null, 16875146, 13379903, 16312762, 18482630, 2813, "SRX2947031", "SRS2306327", "SRA579533", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:29391432", null, "CL67", "GSM2679610", null, "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\u2019s 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 29\u00baC 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 17\u03b1 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 70\u00baC 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.", null, "agent:5.8 nM 2 ethylhexyl phthalate", "GSM2679610", "GSM2679610: CL67; Danio rerio; RNA Seq", "GSM2679610", null, "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", null, "SRP110156", null, null, "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, null, null, null, 25604873, 20781116, 24203084, 27358188, 4257, "SRX2947030", "SRS2306326", "SRA579533", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:29391432", null, "CL66", "GSM2679609", null, "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\u2019s 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 29\u00baC 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 17\u03b1 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 70\u00baC 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.", null, "agent:0.65 nM Ethinylestradiol EE2", "GSM2679609", "GSM2679609: CL66; Danio rerio; RNA Seq", "GSM2679609", null, "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", null, "SRP110156", null, null, "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, null, null, null, 20840478, 16298564, 19354919, 23058169, 3514, "SRX2947029", "SRS2306325", "SRA579533", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:29391432", null, "CL65", "GSM2679608", null, "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\u2019s 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 29\u00baC 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 17\u03b1 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 70\u00baC 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.", null, "agent:0.65 nM Ethinylestradiol EE2", "GSM2679608", "GSM2679608: CL65; Danio rerio; RNA Seq", "GSM2679608", null, "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", null, "SRP110156", null, null, "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, null, null, null, 19262431, 15422889, 18345920, 21623880, 3324, "SRX2947028", "SRS2306324", "SRA579533", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:29391432", null, "CL64", "GSM2679607", null, "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\u2019s 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 29\u00baC 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 17\u03b1 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 70\u00baC 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.", null, "agent:Control", "GSM2679607", "GSM2679607: CL64; Danio rerio; RNA Seq", "GSM2679607", null, "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", null, "SRP110156", null, null, "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, null, null, null, 21427784, 17542697, 20002613, 22964734, 3584, "SRX2947027", "SRS2306322", "SRA579533", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:29391432", null, "CL63", "GSM2679606", null, "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\u2019s 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 29\u00baC 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 17\u03b1 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 70\u00baC 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.", null, "agent:Control", "GSM2679606", "GSM2679606: CL63; Danio rerio; RNA Seq", "GSM2679606", null, "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", null, "SRP110156", null, null, "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, null, null, null, 25465262, 20166931, 24797943, 28984279, 4499, "SRX2947026", "SRS2306323", "SRA579533", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:30563618", null, "CL62", "GSM2679636", null, "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\u2019s 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 29\u00baC 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 17\u03b2 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 70\u00baC 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.", null, "agent:100 nM Nonylphenol NP|Sex:Male", "GSM2679636", "GSM2679636: CL62; Danio rerio; RNA Seq", "GSM2679636", null, "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", null, "SRP110158", null, null, "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, null, null, null, 31987859, 24358295, 32088563, 34053478, 5477, "SRX2947056", "SRS2306352", "SRA579535", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-06-22", "Undetermined", "Undetermined", "Liver", "Liver and Biliary System"]], "truncated": false, "filtered_table_rows_count": 289, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "Undetermined", "p1": "Liver and Biliary System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 277, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_strategy=miRNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 221, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 68, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "cDNA", "label": "cDNA", "count": 240, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_selection=cDNA", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_selection=Oligo-dT", "selected": false}, {"value": "size fractionation", "label": "size fractionation", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_selection=size+fractionation", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_selection=PolyA", "selected": false}, {"value": "RT-PCR", "label": "RT-PCR", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_selection=RT-PCR", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 154, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 135, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 267, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.platform=BGISEQ", "selected": false}, {"value": "ABI_SOLID", "label": "ABI_SOLID", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&experiment.platform=ABI_SOLID", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 166, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&devstage_curation_coarse=Undetermined", "selected": false}, {"value": "Larval", "label": "Larval", "count": 88, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&devstage_curation_coarse=Larval", "selected": false}, {"value": "Adult", "label": "Adult", "count": 25, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&devstage_curation_coarse=Adult", "selected": false}, {"value": "Embryo", "label": "Embryo", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&devstage_curation_coarse=Embryo", "selected": false}, {"value": "Multi-stage", "label": "Multi-stage", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&devstage_curation_coarse=Multi-stage", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 289, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation_coarse=Liver+and+Biliary+System", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "Liver and Biliary System", "label": "Liver and Biliary System", "count": 289, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "Liver", "label": "Liver", "count": 289, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&tissue_curation=Liver", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System", "results": [{"value": "unknown", "label": "unknown", "count": 213, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&technology=unknown", "selected": false}, {"value": "10x", "label": "10x", "count": 72, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&technology=10x", "selected": false}, {"value": "microwellseq", "label": "microwellseq", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&technology=microwellseq", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "42539", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation_coarse=Liver+and+Biliary+System&_next=42539", "private": false, "allow_execute_sql": true, "query_ms": 124.489480000193}