{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Larval\" and tissue_curation = \"Liver\"", "rows": [[171, "DRR075399", "DRX069313", "DRS075494", "DRP004473", "PRJDB5226", "Effects of local gut tumor on whole organismal gene expressions in zebrafish", "DRP004473", "Other", "How tumors affects whole organismal physiology remains largely unknown. To address this we established the novel gut tumor model in zebrafish Danio rerio. This model develops tumor at an early stage of juvenile development when zebrafish larvae are small <4mm enabling us to perform whole organismal RNA seq experiments. Control or tumor bearing zebrafish were dissected into the three parts under microscope: the liver the gut/gut tumor and others. Tissues from >10 individuals were pooled and RNA extracted. Analyses on these RNA seq samples identified a set of host genes affected by the gut tumor contributing to discovering novel tumor organ interactions and their mediators in zebrafish.", null, null, "The liver of control fish 7dpf", "Control liver", "SAMD00065413", null, "sample name:3 control liver 150701 Hiseq3A l3 019|tissue type:Liver", null, null, null, null, null, null, null, null, "Illumina HiSeq 2500 sequencing of SAMD00065413", "DRX069313", "Control liver", "1", "Agilent SureSelect Strand Specific RNA Prep Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "360Application ReadForward1", "DRP004473", "Illumina HiSeq 2500 sequencing of SAMD00065413", null, null, null, 951579036.0, 26432751.0, "DRR075399", "0:36", "A:231570583;C:228182815;G:227223430;T:264569214;N:32994", 36, null, null, null, 231570583, 228182815, 227223430, 264569214, 32994, "DRX069313", "DRS075494", "DRA005199", "ATR|The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", "The Thomas N. Sato BioMEC-X Laboratories, Advanced Telecommunications Research Institute International", 1, 0.8903, null, 0.08667, null, 0.7236, null, 0.51557, null, 36, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2018-09-19", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8104, "ERR2455366", "ERX2474426", "ERS2327331", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 4", "SAMEA104725948", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725948|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 4|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:overfeeding|organism part:liver|sample name:E MTAB 6636:Sample 4|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 4 s", "Sample 4 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:overfeeding", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "OF-4_H7MWNALXX_L6_1.fq.gz", "fastq", 4961276550.0, 33075177.0, "E MTAB 6636:Sample 4", "0:150 1:0", "A:1349413168;C:1135314970;G:1137935563;T:1338034716;N:578133", 150, 0, null, null, 1349413168, 1135314970, 1137935563, 1338034716, 578133, "ERX2474426", "ERS2327331", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.90787, null, 0.11999, null, 0.66123, null, 0.49072, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8105, "ERR2455365", "ERX2474425", "ERS2327330", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 3", "SAMEA104725947", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725947|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:fructose|organism part:liver|sample name:E MTAB 6636:Sample 3|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 3 s", "Sample 3 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:fructose", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "Fru-3_H7MWNALXX_L5_1.fq.gz", "fastq", 5858273250.0, 39055155.0, "E MTAB 6636:Sample 3", "0:150 1:0", "A:1580150663;C:1353221682;G:1355865524;T:1568428138;N:607243", 150, 0, null, null, 1580150663, 1353221682, 1355865524, 1568428138, 607243, "ERX2474425", "ERS2327330", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.91505, null, 0.11036, null, 0.65985, null, 0.48443, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8106, "ERR2455364", "ERX2474424", "ERS2327329", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 2", "SAMEA104725946", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725946|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 2|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:cholesterol|organism part:liver|sample name:E MTAB 6636:Sample 2|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 2 s", "Sample 2 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:cholesterol", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "Cho-2_H7MWNALXX_L5_1.fq.gz", "fastq", 5636304900.0, 37575366.0, "E MTAB 6636:Sample 2", "0:150 1:0", "A:1526862069;C:1295343770;G:1298751994;T:1514766898;N:580169", 150, 0, null, null, 1526862069, 1295343770, 1298751994, 1514766898, 580169, "ERX2474424", "ERS2327329", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.91032, null, 0.11644, null, 0.66649, null, 0.47766, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [8107, "ERR2455363", "ERX2474423", "ERS2327328", "ERP107743", "PRJEB25789", "RNA seq of zebrafish larvae fed with different diets", "E-MTAB-6636", "Transcriptome Analysis", "We aim to establish NAFLD model of Zebrafish. Zebrafish larvae fed with high cholesterol diet high fructose diet and overfeed diet to induce liver steatosis. RNA seq was employed to analyze the effects of different diets on NAFLD development.", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 03 29", null, "Protocols: Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Sample 1", "SAMEA104725945", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College", "ENA FIRST PUBLIC:2018 12 01T17:02:09Z|ENA LAST UPDATE:2018 03 29T12:32:24Z|External Id:SAMEA104725945|INSDC center name:Institute of Medicinal Biotechnology Chinese Academy of Medical Sciences and Peking Union Medical College|INSDC first public:2018 12 01T17:02:09Z|INSDC last update:2018 03 29T12:32:24Z|INSDC status:public|Submitter Id:E MTAB 6636:Sample 1|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|diet:control|organism part:liver|sample name:E MTAB 6636:Sample 1|scientific name:Danio rerio", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "E MTAB 6636:Sample 1 s", "Sample 1 s", "RNA seq of zebrafish larvae fed with different diets", "Total RNAs were extracted from liver tissues of zebrafish larvae. A total amount of 1.5\u03bcg RNA per sample was used as input material for the RNA sample preparations. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB. Sequencing libraries were generated using NEBNext\u00ae UltraTM RNA Library Prep Kit for Illumina\u00ae NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample.", "Experimental Factor: diet:control", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "ERP107743", "Illumina HiSeq 4000 sequencing; RNA seq of zebrafish larvae fed with different diets", "ENA FIRST PUBLIC:2018 12 01|ENA LAST UPDATE:2018 11 16", "ND-1_H7MWNALXX_L5_1.fq.gz", "fastq", 5197165350.0, 34647769.0, "E MTAB 6636:Sample 1", "0:150 1:0", "A:1430911816;C:1174811274;G:1175616551;T:1415284019;N:541690", 150, 0, null, null, 1430911816, 1174811274, 1175616551, 1415284019, 541690, "ERX2474423", "ERS2327328", "ERA1259907", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", "Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College|European Nucleotide Archive", 1, 0.89838, null, 0.13883, null, 0.66129, null, 0.48467, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2018-03-29", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28955, "SRR26862014", "SRX22556964", "SRS19565505", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "atf4a / ;atf4b / ;sec31anju221 7dpf liver rep3", "GSM7905882", null, "source name:liver|tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "atf4a / ;atf4b / ;sec31anju221 7dpf liver rep3", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905882", "GSM7905882: atf4a / ;atf4b / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq", "GSM7905882 r1", "GSM7905882", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "atf4a_atf4b_sec31a_7dpf_liver_3_R1.fastq.gz atf4a_atf4b_sec31a_7dpf_liver_3_R2.fastq.gz", "fastq fastq", 5909169300.0, 19697231.0, "GSM7905882 r1", "0:150 1:150", "A:1814217313;C:1062889607;G:1281434828;T:1750535462;N:92090", 150, 150, null, null, 1814217313, 1062889607, 1281434828, 1750535462, 92090, "SRX22556964", "SRS19565505", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.76999, 0.77426, 0.42801, 0.42392, 0.8016, 0.80275, 0.54736, 0.56955, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28956, "SRR26862015", "SRX22556963", "SRS19565504", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "atf4a / ;atf4b / ;sec31anju221 7dpf liver rep2", "GSM7905881", null, "source name:liver|tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "atf4a / ;atf4b / ;sec31anju221 7dpf liver rep2", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905881", "GSM7905881: atf4a / ;atf4b / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq", "GSM7905881 r1", "GSM7905881", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "atf4a_atf4b_sec31a_7dpf_liver_2_R2.fastq.gz atf4a_atf4b_sec31a_7dpf_liver_2_R1.fastq.gz", "fastq fastq", 5909169300.0, 19697231.0, "GSM7905881 r1", "0:150 1:150", "A:1814304871;C:1062851267;G:1281344920;T:1750575670;N:92572", 150, 150, null, null, 1814304871, 1062851267, 1281344920, 1750575670, 92572, "SRX22556963", "SRS19565504", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.77, 0.77338, 0.42787, 0.42319, 0.80137, 0.80314, 0.56997, 0.57195, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28957, "SRR26862016", "SRX22556962", "SRS19565503", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "atf4a / ;atf4b / ;sec31anju221 7dpf liver rep1", "GSM7905880", null, "source name:liver|tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "atf4a / ;atf4b / ;sec31anju221 7dpf liver rep1", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:atf4a / ;atf4b / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905880", "GSM7905880: atf4a / ;atf4b / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq", "GSM7905880 r1", "GSM7905880", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "atf4a_atf4b_sec31a_7dpf_liver_1_R1.fastq.gz atf4a_atf4b_sec31a_7dpf_liver_1_R2.fastq.gz", "fastq fastq", 5909169600.0, 19697232.0, "GSM7905880 r1", "0:150 1:150", "A:1814273460;C:1062781687;G:1281372048;T:1750650699;N:91706", 150, 150, null, null, 1814273460, 1062781687, 1281372048, 1750650699, 91706, "SRX22556962", "SRS19565503", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.76973, 0.77461, 0.42583, 0.42416, 0.80154, 0.80501, 0.56619, 0.57103, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28958, "SRR26862017", "SRX22556961", "SRS19565502", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "atf6 / ;sec31anju221 7dpf liver rep3", "GSM7905879", null, "source name:liver|tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "atf6 / ;sec31anju221 7dpf liver rep3", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905879", "GSM7905879: atf6 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq", "GSM7905879 r1", "GSM7905879", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "atf6_sec31a_7dpf_liver_3_R1.fastq.gz atf6_sec31a_7dpf_liver_3_R2.fastq.gz", "fastq fastq", 5861267700.0, 19537559.0, "GSM7905879 r1", "0:150 1:150", "A:1784341701;C:1072473445;G:1285100764;T:1719260200;N:91590", 150, 150, null, null, 1784341701, 1072473445, 1285100764, 1719260200, 91590, "SRX22556961", "SRS19565502", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.75325, 0.76151, 0.45725, 0.45689, 0.78798, 0.78922, 0.56218, 0.56438, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28959, "SRR26862018", "SRX22556960", "SRS19565501", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "atf6 / ;sec31anju221 7dpf liver rep2", "GSM7905878", null, "source name:liver|tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "atf6 / ;sec31anju221 7dpf liver rep2", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905878", "GSM7905878: atf6 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq", "GSM7905878 r1", "GSM7905878", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "atf6_sec31a_7dpf_liver_2_R1.fastq.gz atf6_sec31a_7dpf_liver_2_R2.fastq.gz", "fastq fastq", 5861267700.0, 19537559.0, "GSM7905878 r1", "0:150 1:150", "A:1784326758;C:1072428588;G:1285145147;T:1719275142;N:92065", 150, 150, null, null, 1784326758, 1072428588, 1285145147, 1719275142, 92065, "SRX22556960", "SRS19565501", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.75399, 0.76366, 0.46023, 0.46101, 0.79153, 0.79243, 0.56082, 0.56109, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28960, "SRR26862019", "SRX22556959", "SRS19565500", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "atf6 / ;sec31anju221 7dpf liver rep1", "GSM7905877", null, "source name:liver|tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "atf6 / ;sec31anju221 7dpf liver rep1", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:atf6 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905877", "GSM7905877: atf6 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq", "GSM7905877 r1", "GSM7905877", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "atf6_sec31a_7dpf_liver_1_R1.fastq.gz atf6_sec31a_7dpf_liver_1_R2.fastq.gz", "fastq fastq", 5861267700.0, 19537559.0, "GSM7905877 r1", "0:150 1:150", "A:1784239507;C:1072424839;G:1285216751;T:1719294746;N:91857", 150, 150, null, null, 1784239507, 1072424839, 1285216751, 1719294746, 91857, "SRX22556959", "SRS19565500", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.75279, 0.76268, 0.45792, 0.46002, 0.79251, 0.79482, 0.55778, 0.55965, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28961, "SRR26862020", "SRX22556958", "SRS19565499", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "srebf2 / ;sec31anju221 7dpf liver rep3", "GSM7905876", null, "source name:liver|tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "srebf2 / ;sec31anju221 7dpf liver rep3", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905876", "GSM7905876: srebf2 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq", "GSM7905876 r1", "GSM7905876", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "srebf2_sec31a_7dpf_liver_3_R2.fastq.gz srebf2_sec31a_7dpf_liver_3_R1.fastq.gz", "fastq fastq", 5510352000.0, 18367840.0, "GSM7905876 r1", "0:150 1:150", "A:1627756472;C:1023474678;G:1300851324;T:1558184587;N:84939", 150, 150, null, null, 1627756472, 1023474678, 1300851324, 1558184587, 84939, "SRX22556958", "SRS19565499", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.80994, 0.82412, 0.13867, 0.1397, 0.84264, 0.84228, 0.58499, 0.58509, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28962, "SRR26862021", "SRX22556957", "SRS19565498", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "srebf2 / ;sec31anju221 7dpf liver rep2", "GSM7905875", null, "source name:liver|tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "srebf2 / ;sec31anju221 7dpf liver rep2", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905875", "GSM7905875: srebf2 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq", "GSM7905875 r1", "GSM7905875", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "srebf2_sec31a_7dpf_liver_2_R1.fastq.gz srebf2_sec31a_7dpf_liver_2_R2.fastq.gz", "fastq fastq", 5510352000.0, 18367840.0, "GSM7905875 r1", "0:150 1:150", "A:1627771682;C:1023494582;G:1300898781;T:1558101507;N:85448", 150, 150, null, null, 1627771682, 1023494582, 1300898781, 1558101507, 85448, "SRX22556957", "SRS19565498", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.81036, 0.82384, 0.14055, 0.13973, 0.84151, 0.84145, 0.58974, 0.57294, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28963, "SRR26862022", "SRX22556956", "SRS19565497", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "srebf2 / ;sec31anju221 7dpf liver rep1", "GSM7905874", null, "source name:liver|tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "srebf2 / ;sec31anju221 7dpf liver rep1", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:srebf2 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905874", "GSM7905874: srebf2 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq", "GSM7905874 r1", "GSM7905874", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "srebf2_sec31a_7dpf_liver_1_R1.fastq.gz srebf2_sec31a_7dpf_liver_1_R2.fastq.gz", "fastq fastq", 5510352300.0, 18367841.0, "GSM7905874 r1", "0:150 1:150", "A:1627704384;C:1023445689;G:1301022904;T:1558092507;N:86816", 150, 150, null, null, 1627704384, 1023445689, 1301022904, 1558092507, 86816, "SRX22556956", "SRS19565497", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.81137, 0.82447, 0.13931, 0.13977, 0.84104, 0.84129, 0.58031, 0.57864, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28964, "SRR26862023", "SRX22556955", "SRS19565496", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "srebf1 / ;sec31anju221 7dpf liver rep3", "GSM7905873", null, "source name:liver|tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "srebf1 / ;sec31anju221 7dpf liver rep3", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905873", "GSM7905873: srebf1 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq", "GSM7905873 r1", "GSM7905873", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "srebf1_sec31a_7dpf_liver_3_R1.fastq.gz srebf1_sec31a_7dpf_liver_3_R2.fastq.gz", "fastq fastq", 6400097700.0, 21333659.0, "GSM7905873 r1", "0:150 1:150", "A:1899190871;C:1190525037;G:1467138729;T:1843142069;N:100994", 150, 150, null, null, 1899190871, 1190525037, 1467138729, 1843142069, 100994, "SRX22556955", "SRS19565496", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.81425, 0.82461, 0.21108, 0.21197, 0.82221, 0.82323, 0.56957, 0.594, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28965, "SRR26862024", "SRX22556954", "SRS19565495", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "srebf1 / ;sec31anju221 7dpf liver rep2", "GSM7905872", null, "source name:liver|tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "srebf1 / ;sec31anju221 7dpf liver rep2", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905872", "GSM7905872: srebf1 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq", "GSM7905872 r1", "GSM7905872", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "srebf1_sec31a_7dpf_liver_2_R1.fastq.gz srebf1_sec31a_7dpf_liver_2_R2.fastq.gz", "fastq fastq", 6400098000.0, 21333660.0, "GSM7905872 r1", "0:150 1:150", "A:1898994954;C:1190735681;G:1467311615;T:1842955236;N:100514", 150, 150, null, null, 1898994954, 1190735681, 1467311615, 1842955236, 100514, "SRX22556954", "SRS19565495", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.81439, 0.82458, 0.20976, 0.20983, 0.82252, 0.82278, 0.57027, 0.58785, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28966, "SRR26862025", "SRX22556953", "SRS19565494", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "srebf1 / ;sec31anju221 7dpf liver rep1", "GSM7905871", null, "source name:liver|tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "srebf1 / ;sec31anju221 7dpf liver rep1", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:srebf1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905871", "GSM7905871: srebf1 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq", "GSM7905871 r1", "GSM7905871", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "srebf1_sec31a_7dpf_liver_1_R1.fastq.gz srebf1_sec31a_7dpf_liver_1_R2.fastq.gz", "fastq fastq", 6400098000.0, 21333660.0, "GSM7905871 r1", "0:150 1:150", "A:1899112598;C:1190526850;G:1467278074;T:1843080128;N:100350", 150, 150, null, null, 1899112598, 1190526850, 1467278074, 1843080128, 100350, "SRX22556953", "SRS19565494", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.81419, 0.82464, 0.20997, 0.21061, 0.82317, 0.82296, 0.57794, 0.57323, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28967, "SRR26862026", "SRX22556952", "SRS19565493", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "xbp1 / ;sec31anju221 7dpf liver rep3", "GSM7905870", null, "source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "xbp1 / ;sec31anju221 7dpf liver rep3", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905870", "GSM7905870: xbp1 / ;sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq", "GSM7905870 r1", "GSM7905870", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "xbp1_sec31a_7dpf_liver_3_R1.fastq.gz xbp1_sec31a_7dpf_liver_3_R2.fastq.gz", "fastq fastq", 6187152600.0, 20623842.0, "GSM7905870 r1", "0:150 1:150", "A:1877363692;C:1115080777;G:1381299595;T:1812977195;N:431341", 150, 150, null, null, 1877363692, 1115080777, 1381299595, 1812977195, 431341, "SRX22556952", "SRS19565493", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.76954, 0.76951, 0.43867, 0.43143, 0.77993, 0.78291, 0.54133, 0.5381, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28968, "SRR26862027", "SRX22556951", "SRS19565492", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "xbp1 / ;sec31anju221 7dpf liver rep2", "GSM7905869", null, "source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "xbp1 / ;sec31anju221 7dpf liver rep2", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905869", "GSM7905869: xbp1 / ;sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq", "GSM7905869 r1", "GSM7905869", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "xbp1_sec31a_7dpf_liver_2_R1.fastq.gz xbp1_sec31a_7dpf_liver_2_R2.fastq.gz", "fastq fastq", 6187152600.0, 20623842.0, "GSM7905869 r1", "0:150 1:150", "A:1877413505;C:1115113811;G:1381185230;T:1813009192;N:430862", 150, 150, null, null, 1877413505, 1115113811, 1381185230, 1813009192, 430862, "SRX22556951", "SRS19565492", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.77052, 0.77186, 0.4375, 0.43158, 0.77857, 0.78376, 0.54778, 0.54495, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28969, "SRR26862028", "SRX22556950", "SRS19565491", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "xbp1 / ;sec31anju221 7dpf liver rep1", "GSM7905868", null, "source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "xbp1 / ;sec31anju221 7dpf liver rep1", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905868", "GSM7905868: xbp1 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq", "GSM7905868 r1", "GSM7905868", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "xbp1_sec31a_7dpf_liver_1_R1.fastq.gz xbp1_sec31a_7dpf_liver_1_R2.fastq.gz", "fastq fastq", 6187152900.0, 20623843.0, "GSM7905868 r1", "0:150 1:150", "A:1877304250;C:1115136591;G:1381366555;T:1812912124;N:433380", 150, 150, null, null, 1877304250, 1115136591, 1381366555, 1812912124, 433380, "SRX22556950", "SRS19565491", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.77014, 0.76961, 0.43869, 0.43265, 0.77863, 0.78293, 0.54465, 0.54127, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28970, "SRR26862029", "SRX22556949", "SRS19565490", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "sec31anju221 7dpf liver rep3", "GSM7905867", null, "source name:liver|tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "sec31anju221 7dpf liver rep3", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905867", "GSM7905867: sec31anju221 7dpf liver rep3; Danio rerio; RNA Seq", "GSM7905867 r1", "GSM7905867", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "sec31a_7dpf_liver_3_R1.fastq.gz sec31a_7dpf_liver_3_R2.fastq.gz", "fastq fastq", 7290483000.0, 24301610.0, "GSM7905867 r1", "0:150 1:150", "A:2201443580;C:1310250352;G:1667114316;T:2111120776;N:553976", 150, 150, null, null, 2201443580, 1310250352, 1667114316, 2111120776, 553976, "SRX22556949", "SRS19565490", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.80458, 0.80677, 0.27528, 0.27217, 0.8228, 0.82507, 0.58018, 0.57745, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28971, "SRR26862030", "SRX22556948", "SRS19565489", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "sec31anju221 7dpf liver rep2", "GSM7905866", null, "source name:liver|tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "sec31anju221 7dpf liver rep2", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905866", "GSM7905866: sec31anju221 7dpf liver rep2; Danio rerio; RNA Seq", "GSM7905866 r1", "GSM7905866", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "sec31a_7dpf_liver_2_R1.fastq.gz sec31a_7dpf_liver_2_R2.fastq.gz", "fastq fastq", 7290483300.0, 24301611.0, "GSM7905866 r1", "0:150 1:150", "A:2201546187;C:1310316929;G:1666786006;T:2111279666;N:554512", 150, 150, null, null, 2201546187, 1310316929, 1666786006, 2111279666, 554512, "SRX22556948", "SRS19565489", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.80528, 0.80845, 0.27376, 0.27196, 0.82286, 0.82451, 0.58075, 0.57876, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28972, "SRR26862031", "SRX22556947", "SRS19565488", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "sec31anju221 7dpf liver rep1", "GSM7905865", null, "source name:liver|tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "sec31anju221 7dpf liver rep1", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:sec31anju221|treatment:Digested with 2.5percent trypsin", "GSM7905865", "GSM7905865: sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq", "GSM7905865 r1", "GSM7905865", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "sec31a_7dpf_liver_1_R2.fastq.gz sec31a_7dpf_liver_1_R1.fastq.gz", "fastq fastq", 7290483300.0, 24301611.0, "GSM7905865 r1", "0:150 1:150", "A:2201492232;C:1310255361;G:1666931918;T:2111261791;N:541998", 150, 150, null, null, 2201492232, 1310255361, 1666931918, 2111261791, 541998, "SRX22556947", "SRS19565488", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.80672, 0.80946, 0.27449, 0.27121, 0.82026, 0.82238, 0.58542, 0.58114, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28973, "SRR26862032", "SRX22556946", "SRS19565487", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "WT 7dpf liver rep3", "GSM7905864", null, "source name:liver|tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "WT 7dpf liver rep3", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin", "GSM7905864", "GSM7905864: WT 7dpf liver rep3; Danio rerio; RNA Seq", "GSM7905864 r1", "GSM7905864", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "ctrl_7dpf_liver_3_R1.fastq.gz ctrl_7dpf_liver_3_R2.fastq.gz", "fastq fastq", 6492651600.0, 21642172.0, "GSM7905864 r1", "0:150 1:150", "A:1911454132;C:1210565181;G:1559325152;T:1810846037;N:461098", 150, 150, null, null, 1911454132, 1210565181, 1559325152, 1810846037, 461098, "SRX22556946", "SRS19565487", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.83482, 0.84576, 0.18949, 0.18912, 0.84853, 0.84914, 0.67518, 0.67721, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28974, "SRR26862033", "SRX22556945", "SRS19565486", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "WT 7dpf liver rep2", "GSM7905863", null, "source name:liver|tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "WT 7dpf liver rep2", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin", "GSM7905863", "GSM7905863: WT 7dpf liver rep2; Danio rerio; RNA Seq", "GSM7905863 r1", "GSM7905863", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "ctrl_7dpf_liver_2_R1.fastq.gz ctrl_7dpf_liver_2_R2.fastq.gz", "fastq fastq", 6492651600.0, 21642172.0, "GSM7905863 r1", "0:150 1:150", "A:1911298884;C:1210698281;G:1559339763;T:1810859879;N:454793", 150, 150, null, null, 1911298884, 1210698281, 1559339763, 1810859879, 454793, "SRX22556945", "SRS19565486", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.83478, 0.84217, 0.19106, 0.18909, 0.84642, 0.84717, 0.67888, 0.67654, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [28975, "SRR26862034", "SRX22556944", "SRS19565485", "SRP472550", "PRJNA1041773", "Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing", "GSE248098", "Transcriptome Analysis", "We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext\u00ae Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform.", null, "pubmed:39139065", null, "WT 7dpf liver rep1", "GSM7905862", null, "source name:liver|tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing", "WT 7dpf liver rep1", "Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample", "liver", null, "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "tissue:liver|genotype:wild type|treatment:Digested with 2.5percent trypsin", "GSM7905862", "GSM7905862: WT 7dpf liver rep1; Danio rerio; RNA Seq", "GSM7905862 r1", "GSM7905862", "1", "At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP472550", null, null, "ctrl_7dpf_liver_1_R1.fastq.gz ctrl_7dpf_liver_1_R2.fastq.gz", "fastq fastq", 6492651600.0, 21642172.0, "GSM7905862 r1", "0:150 1:150", "A:1911338464;C:1210670533;G:1559401753;T:1810786876;N:453974", 150, 150, null, null, 1911338464, 1210670533, 1559401753, 1810786876, 453974, "SRX22556944", "SRS19565485", "SRA1753371", "Xin Lou Lab, Medical School, Nanjing University", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.83368, 0.84388, 0.18806, 0.18877, 0.84713, 0.84932, 0.67925, 0.67975, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "China", "2023-11-17", "Larval", "Larval", "Liver", "Liver and Biliary System"], [29816, "SRR27496346", "SRX23167489", "SRS20117077", "SRP483191", "PRJNA1063616", "Protection from starvation induced liver atrophy.", "GSE252997", "Transcriptome Analysis", "Starvation causes the accumulation of lipid droplets in the liver a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover cavefish are resistant to liver atrophy during starvation providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish surface fish and cavefish we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall our study identifies a conserved druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment no exogenous food was added. At 6 dpf the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.", null, "pubmed:38467419", null, "Liver 6dpf DMSO rep1", "GSM8012203", null, "source name:Liver|tissue:Liver|genotype:AB|treatment:DMSO|geo loc name:missing|collection date:missing", "Liver 6dpf DMSO rep1", "Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome and counted using FeatureCounts. For normalization differential gene expression analysis and GO analysis iDEP version 0.951 was utilized with default parameters. For differential gene expression a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.", "Liver", "Lipofermata or DMSO treatment for 48 hours", "For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture\u2019s instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.", "Zebrafish larvae at 6 dpf.", "tissue:Liver|genotype:AB|treatment:DMSO", "GSM8012203", "GSM8012203: Liver 6dpf DMSO rep1; Danio rerio; RNA Seq", "GSM8012203 r1", "GSM8012203", "1", "For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483191", null, "loader:fastq load.py", "DMSO_1_R1.fastq.gz DMSO_1_R2.fastq.gz", "fastq fastq", 3947938488.0, 13072644.0, "GSM8012203 r1", "0:151 1:151", "A:1068152483;C:899059502;G:921482728;T:1059209932;N:33843", 151, 151, null, null, 1068152483, 899059502, 921482728, 1059209932, 33843, "SRX23167489", "SRS20117077", "SRA1784007", "Regeneration and Stress Biology, IRIBHM, ULB", "Regeneration and Stress Biology, IRIBHM, ULB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Belgium", "2024-01-11", "Larval", "Larval", "Liver", "Liver and Biliary System"], [29817, "SRR27496347", "SRX23167488", "SRS20117076", "SRP483191", "PRJNA1063616", "Protection from starvation induced liver atrophy.", "GSE252997", "Transcriptome Analysis", "Starvation causes the accumulation of lipid droplets in the liver a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover cavefish are resistant to liver atrophy during starvation providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish surface fish and cavefish we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall our study identifies a conserved druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment no exogenous food was added. At 6 dpf the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.", null, "pubmed:38467419", null, "Liver 6dpf Lipofermata rep2", "GSM8012206", null, "source name:Liver|tissue:Liver|genotype:AB|treatment:Lipofermata|geo loc name:missing|collection date:missing", "Liver 6dpf Lipofermata rep2", "Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome and counted using FeatureCounts. For normalization differential gene expression analysis and GO analysis iDEP version 0.951 was utilized with default parameters. For differential gene expression a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.", "Liver", "Lipofermata or DMSO treatment for 48 hours", "For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture\u2019s instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.", "Zebrafish larvae at 6 dpf.", "tissue:Liver|genotype:AB|treatment:Lipofermata", "GSM8012206", "GSM8012206: Liver 6dpf Lipofermata rep2; Danio rerio; RNA Seq", "GSM8012206 r1", "GSM8012206", "1", "For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483191", null, "loader:fastq load.py", "Lipofermata_2_R1.fastq.gz Lipofermata_2_R2.fastq.gz", "fastq fastq", 3365739868.0, 11144834.0, "GSM8012206 r1", "0:151 1:151", "A:904693218;C:775639535;G:792394997;T:892981123;N:30995", 151, 151, null, null, 904693218, 775639535, 792394997, 892981123, 30995, "SRX23167488", "SRS20117076", "SRA1784007", "Regeneration and Stress Biology, IRIBHM, ULB", "Regeneration and Stress Biology, IRIBHM, ULB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Belgium", "2024-01-11", "Larval", "Larval", "Liver", "Liver and Biliary System"], [29818, "SRR27496348", "SRX23167487", "SRS20117075", "SRP483191", "PRJNA1063616", "Protection from starvation induced liver atrophy.", "GSE252997", "Transcriptome Analysis", "Starvation causes the accumulation of lipid droplets in the liver a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover cavefish are resistant to liver atrophy during starvation providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish surface fish and cavefish we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall our study identifies a conserved druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment no exogenous food was added. At 6 dpf the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.", null, "pubmed:38467419", null, "Liver 6dpf Lipofermata rep1", "GSM8012205", null, "source name:Liver|tissue:Liver|genotype:AB|treatment:Lipofermata|geo loc name:missing|collection date:missing", "Liver 6dpf Lipofermata rep1", "Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome and counted using FeatureCounts. For normalization differential gene expression analysis and GO analysis iDEP version 0.951 was utilized with default parameters. For differential gene expression a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.", "Liver", "Lipofermata or DMSO treatment for 48 hours", "For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture\u2019s instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.", "Zebrafish larvae at 6 dpf.", "tissue:Liver|genotype:AB|treatment:Lipofermata", "GSM8012205", "GSM8012205: Liver 6dpf Lipofermata rep1; Danio rerio; RNA Seq", "GSM8012205 r1", "GSM8012205", "1", "For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483191", null, "loader:fastq load.py", "Lipofermata_1_R1.fastq.gz Lipofermata_1_R2.fastq.gz", "fastq fastq", 3645146040.0, 12070020.0, "GSM8012205 r1", "0:151 1:151", "A:981366033;C:836975744;G:858564002;T:968208667;N:31594", 151, 151, null, null, 981366033, 836975744, 858564002, 968208667, 31594, "SRX23167487", "SRS20117075", "SRA1784007", "Regeneration and Stress Biology, IRIBHM, ULB", "Regeneration and Stress Biology, IRIBHM, ULB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Belgium", "2024-01-11", "Larval", "Larval", "Liver", "Liver and Biliary System"], [29819, "SRR27496349", "SRX23167486", "SRS20117074", "SRP483191", "PRJNA1063616", "Protection from starvation induced liver atrophy.", "GSE252997", "Transcriptome Analysis", "Starvation causes the accumulation of lipid droplets in the liver a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover cavefish are resistant to liver atrophy during starvation providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish surface fish and cavefish we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall our study identifies a conserved druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment no exogenous food was added. At 6 dpf the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.", null, "pubmed:38467419", null, "Liver 6dpf DMSO rep2", "GSM8012204", null, "source name:Liver|tissue:Liver|genotype:AB|treatment:DMSO|geo loc name:missing|collection date:missing", "Liver 6dpf DMSO rep2", "Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome and counted using FeatureCounts. For normalization differential gene expression analysis and GO analysis iDEP version 0.951 was utilized with default parameters. For differential gene expression a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.", "Liver", "Lipofermata or DMSO treatment for 48 hours", "For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture\u2019s instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.", "Zebrafish larvae at 6 dpf.", "tissue:Liver|genotype:AB|treatment:DMSO", "GSM8012204", "GSM8012204: Liver 6dpf DMSO rep2; Danio rerio; RNA Seq", "GSM8012204 r1", "GSM8012204", "1", "For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. 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"breed:AB|dev stage:7 dpf|collection date:2021 12 22|geo loc name:China: Wuhan|sex:not determined|tissue:liver|replicate:replicate=control biolobical replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "c1", "c1", "normal RNA seq of Danio rerio", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP488393", null, null, "control1_1.fq.gz control1_2.fq.gz", "fastq fastq", 13024707900.0, 43415693.0, "control1 1.fq.gz", "0:150 1:150", "A:3266649802;C:3212798200;G:3383472165;T:3161753039;N:34694", 150, 150, null, null, 3266649802, 3212798200, 3383472165, 3161753039, 34694, "SRX23547057", "SRS20394834", "SRA1798310", "Wuhan University|School of Basic Medical Sciences", "Wuhan University", 2, 0.93586, 0.9333, 0.02078, 0.02096, 0.77197, 0.77729, 0.53822, 0.52512, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-02-06", "Larval", "Larval", "Liver", "Liver and Biliary System"], [33210, "SRR29868290", "SRX25365557", "SRS22031297", "SRP520597", "PRJNA1136957", "Cholangiocytes contribute to hepatocyte regeneration post partial liver injury in larval zebrafish", "GSE272484", "Transcriptome Analysis", "Liver possesses robust regenerative ability characterized by flexibility in the cellular source of regeneration based on the extent of the injury. post partial hepatectomy or minor injuries hepatocytes the primary liver cells undergo self duplication to replenish the liver mass. In contrast when the damage is extensive or hepatocyte proliferation is impaired cholangiocytes contribute to hepatocyte recovery. This current paradigm of regenerative flexibility in the liver has been established for animals with little or no growth. However the regenerative mechanisms during periods of growth in young animals remain unexplored. Here we establish two new partial liver injury protocols in the zebrafish model of rapid growth during late larval stage and observe emergence of de novo hepatocytes in the presence of spared hepatocytes. Using single cell RNA sequencing and lineage tracing we identify cholangiocytes as the source of de novo hepatocytes. Our study offers a new perspective on the current paradigm of liver regenerating by proposing cholangiocyte to hepatocyte transdifferentiation as the default mechanism of hepatocyte recovery in late larval stage zebrafish. Overall design: We conducted single cell RNA Sequencing using the 10x platform of larval zebrafish liver. This was performed in the basal state Control1 Control2 post partial ablation MTZ 0dppa MTZ 1dppa and MTZ 9dppa and post partial hepatectomy PHx 4dpi and PHx 11dpi. The two control samples were not treated with 4 OHT and were also not injured. The control samples are from 13 dpf zebrafish raised under normal rearing condition. For all experiments Tgfabp10a:CellCousin line was used.", 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"], [35821, "SRR33048251", "SRX28313562", "SRS24652529", "SRP577496", "PRJNA1248508", "Transcriptome sequencing of hepatocytes with or without xxx during liver development in zebrafish", "PRJNA1248508", "Other", "The hepatocytes and non hepatocytes within the livers of 3dpf 7 dpf and adult transgenic Tgfabp10:GFP zebrafish were utilized for experimentation. Upon cessation of opercular movements animals were euthanized via immersion in ice cold water for ten minutes. In this transgenic line hepatocytes in the liver express GFP. Subsequently liver tissues were subjected to enzymatic digestion using 1 mg Collagenase IV dissolved in 1 ml L 15 medium incubated at room temperature for 20 minutes. Liver tissues were then transferred to Leibovitz L 15 medium with an osmolarity of 300 mOsm and pH adjusted to 7.35. Hepatocytes and non hepatocytes were isolated through gentle trituration. The chamber was mounted onto the stage of an Olympus inverted microscope equipped with fluorescence capabilities perfused with fresh L 15 medium for 5 minutes to rinse off debris. Calibrate flow cytometer Moflo XDP Beckman ensuring that the instrument settings such as voltage thresholds and compensation matrices are properly configured for GFP detection. Use beads calibrated for green fluorescent protein to adjust the photomultiplier tube voltages and other parameters. Prepare sterile sorting tubes filled with a suitable buffer to collect sorted cells. Pre chill if necessary. Use an argon laser typically at 488 nm for GFP excitation. Set appropriate filters to detect GFP emission usually centred around 530 nm. Discriminate intact cells from cell fragments based on size and internal complexity. Balance purity and yield by adjusting sort speed and stringency of gating parameters. Follow strict cleaning protocols post sorting to avoid contamination. Isolated cells were collected utilizing flow cytometry enabling precise sorting of GFP positive hepatocytes from GFP negative non hepatocytes. Approximately 400 hepatocytes and non hepatocytes were harvested from around 12 zebrafish with 3 replicates per sample. The careful isolation procedures and subsequent sorting by flow cytometry facilitated acquisition of pure populations of hepatocytes and non hepatocytes ensuring gene expression profiles and reliable downstream analyses of cellular composition.", null, null, null, "D7 GFP", "The hepatocytes within the liver of 7 dpf transgenic Tgfabp10:GFP zebrafish", null, "strain:not applicable|isolate:not applicable|breed:hepatocytes|cultivar:transgenic Tgfabp10:GFP zebrafish|ecotype:not applicable|age:not collected|dev stage:7 dpf date:2019 06 19|geo loc name:China: Sichuan|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D7 GFP", "ED19155408", "ED19155408", "library preparations were sequenced on an Illumina Novaseq platform and 150bp paired end reads were generated", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP577496", null, null, "D7_GFP_R1.fq.gz D7_GFP_R2.fq.gz", "fastq fastq", 7981076700.0, 26603589.0, "D7 GFP R1.fq.gz", "0:150 1:150", "A:2179536437;C:1804626545;G:1832481252;T:2164370673;N:61793", 150, 150, null, null, 2179536437, 1804626545, 1832481252, 2164370673, 61793, "SRX28313562", "SRS24652529", "SRA2109063", "Chengdu Medical College|School of Basic Medicine", "Chengdu Medical College", 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", "2025-04-09", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35822, "SRR33048252", "SRX28313561", "SRS24652526", "SRP577496", "PRJNA1248508", "Transcriptome sequencing of hepatocytes with or without xxx during liver development in zebrafish", "PRJNA1248508", "Other", "The hepatocytes and non hepatocytes within the livers of 3dpf 7 dpf and adult transgenic Tgfabp10:GFP zebrafish were utilized for experimentation. Upon cessation of opercular movements animals were euthanized via immersion in ice cold water for ten minutes. In this transgenic line hepatocytes in the liver express GFP. Subsequently liver tissues were subjected to enzymatic digestion using 1 mg Collagenase IV dissolved in 1 ml L 15 medium incubated at room temperature for 20 minutes. Liver tissues were then transferred to Leibovitz L 15 medium with an osmolarity of 300 mOsm and pH adjusted to 7.35. Hepatocytes and non hepatocytes were isolated through gentle trituration. The chamber was mounted onto the stage of an Olympus inverted microscope equipped with fluorescence capabilities perfused with fresh L 15 medium for 5 minutes to rinse off debris. Calibrate flow cytometer Moflo XDP Beckman ensuring that the instrument settings such as voltage thresholds and compensation matrices are properly configured for GFP detection. Use beads calibrated for green fluorescent protein to adjust the photomultiplier tube voltages and other parameters. Prepare sterile sorting tubes filled with a suitable buffer to collect sorted cells. Pre chill if necessary. Use an argon laser typically at 488 nm for GFP excitation. Set appropriate filters to detect GFP emission usually centred around 530 nm. Discriminate intact cells from cell fragments based on size and internal complexity. Balance purity and yield by adjusting sort speed and stringency of gating parameters. Follow strict cleaning protocols post sorting to avoid contamination. Isolated cells were collected utilizing flow cytometry enabling precise sorting of GFP positive hepatocytes from GFP negative non hepatocytes. Approximately 400 hepatocytes and non hepatocytes were harvested from around 12 zebrafish with 3 replicates per sample. The careful isolation procedures and subsequent sorting by flow cytometry facilitated acquisition of pure populations of hepatocytes and non hepatocytes ensuring gene expression profiles and reliable downstream analyses of cellular composition.", null, null, null, "D3 GFP", "The hepatocytes within the liver of 3dpf transgenic Tgfabp10:GFP zebrafish", null, "strain:not applicable|isolate:not applicable|breed:hepatocytes|cultivar:transgenic Tgfabp10:GFP zebrafish|ecotype:not applicable|age:not collected|dev stage:3 dpf date:2019 06 19|geo loc name:China: Sichuan|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D3 GFP", "ED19155403", "ED19155403", "library preparations were sequenced on an Illumina Novaseq platform and 150bp paired end reads were generated", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP577496", null, null, "D3_GFP_R1.fq.gz D3_GFP_R2.fq.gz", "fastq fastq", 5675477100.0, 18918257.0, "D3 GFP R1.fq.gz", "0:150 1:150", "A:1686172751;C:1174770916;G:1187685676;T:1626795743;N:52014", 150, 150, null, null, 1686172751, 1174770916, 1187685676, 1626795743, 52014, "SRX28313561", "SRS24652526", "SRA2109063", "Chengdu Medical College|School of Basic Medicine", "Chengdu Medical College", 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", "2025-04-09", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35823, "SRR33048253", "SRX28313560", "SRS24652527", "SRP577496", "PRJNA1248508", "Transcriptome sequencing of hepatocytes with or without xxx during liver development in zebrafish", "PRJNA1248508", "Other", "The hepatocytes and non hepatocytes within the livers of 3dpf 7 dpf and adult transgenic Tgfabp10:GFP zebrafish were utilized for experimentation. Upon cessation of opercular movements animals were euthanized via immersion in ice cold water for ten minutes. In this transgenic line hepatocytes in the liver express GFP. Subsequently liver tissues were subjected to enzymatic digestion using 1 mg Collagenase IV dissolved in 1 ml L 15 medium incubated at room temperature for 20 minutes. Liver tissues were then transferred to Leibovitz L 15 medium with an osmolarity of 300 mOsm and pH adjusted to 7.35. Hepatocytes and non hepatocytes were isolated through gentle trituration. The chamber was mounted onto the stage of an Olympus inverted microscope equipped with fluorescence capabilities perfused with fresh L 15 medium for 5 minutes to rinse off debris. Calibrate flow cytometer Moflo XDP Beckman ensuring that the instrument settings such as voltage thresholds and compensation matrices are properly configured for GFP detection. Use beads calibrated for green fluorescent protein to adjust the photomultiplier tube voltages and other parameters. Prepare sterile sorting tubes filled with a suitable buffer to collect sorted cells. Pre chill if necessary. Use an argon laser typically at 488 nm for GFP excitation. Set appropriate filters to detect GFP emission usually centred around 530 nm. Discriminate intact cells from cell fragments based on size and internal complexity. Balance purity and yield by adjusting sort speed and stringency of gating parameters. Follow strict cleaning protocols post sorting to avoid contamination. Isolated cells were collected utilizing flow cytometry enabling precise sorting of GFP positive hepatocytes from GFP negative non hepatocytes. Approximately 400 hepatocytes and non hepatocytes were harvested from around 12 zebrafish with 3 replicates per sample. The careful isolation procedures and subsequent sorting by flow cytometry facilitated acquisition of pure populations of hepatocytes and non hepatocytes ensuring gene expression profiles and reliable downstream analyses of cellular composition.", null, null, null, "D3 Cont", "The non hepatocytes within the liver of 3dp transgenic Tgfabp10:GFP zebrafish", null, "strain:not applicable|isolate:not applicable|breed:non hepatocytes|cultivar:transgenic Tgfabp10:GFP zebrafish|ecotype:not applicable|age:not collected|dev stage:3 dpf date:2019 06 19|geo loc name:China: Sichuan|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "D3 Cont", "ED19155405", "ED19155405", "library preparations were sequenced on an Illumina Novaseq platform and 150bp paired end reads were generated", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP577496", null, null, "D3_Cont_R1.fq.gz D3_Cont_R2.fq.gz", "fastq fastq", 6351962700.0, 21173209.0, "D3 Cont R1.fq.gz", "0:150 1:150", "A:1820293872;C:1368447220;G:1385705833;T:1777459731;N:56044", 150, 150, null, null, 1820293872, 1368447220, 1385705833, 1777459731, 56044, "SRX28313560", "SRS24652527", "SRA2109063", "Chengdu Medical College|School of Basic Medicine", "Chengdu Medical College", 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", "2025-04-09", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35953, "SRR33299171", "SRX28544214", "SRS24843394", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT pos 3", null, "strain:ppat|isolate:RNA wt pos 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt pos 3", "RNA wt pos 3", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT-pos-3_S10_R1_001.fastq.gz WT-pos-3_S10_R2_001.fastq.gz", "fastq fastq", 15038194818.0, 74446509.0, "WT pos 3 S10 R1 001.fastq.gz", "0:101 1:101", "A:4616878123;C:2865206674;G:2927449871;T:4628427327;N:232823", 101, 101, null, null, 4616878123, 2865206674, 2927449871, 4628427327, 232823, "SRX28544214", "SRS24843394", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35954, "SRR33299172", "SRX28544213", "SRS24843393", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT pos 2", null, "strain:ppat|isolate:RNA wt pos 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt pos 2", "RNA wt pos 2", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT-pos-2_S6_R1_001.fastq.gz WT-pos-2_S6_R2_001.fastq.gz", "fastq fastq", 12522438742.0, 61992271.0, "WT pos 2 S6 R1 001.fastq.gz", "0:101 1:101", "A:3774656054;C:2451528285;G:2501043573;T:3795016419;N:194411", 101, 101, null, null, 3774656054, 2451528285, 2501043573, 3795016419, 194411, "SRX28544213", "SRS24843393", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35955, "SRR33299173", "SRX28544212", "SRS24843392", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT pos 1", null, "strain:ppat|isolate:RNA wt pos 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt pos 1", "RNA wt pos 1", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT-pos-1_S2_R1_001.fastq.gz WT-pos-1_S2_R2_001.fastq.gz", "fastq fastq", 13192760794.0, 65310697.0, "WT pos 1 S2 R1 001.fastq.gz", "0:101 1:101", "A:4175600031;C:2392141464;G:2448567492;T:4176248719;N:203088", 101, 101, null, null, 4175600031, 2392141464, 2448567492, 4176248719, 203088, "SRX28544212", "SRS24843392", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35956, "SRR33299174", "SRX28544211", "SRS24843391", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT neg 3", null, "strain:ppat|isolate:RNA wt neg 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt neg 3", "RNA wt neg 3", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT-neg-3_S9_R1_001.fastq.gz WT-neg-3_S9_R2_001.fastq.gz", "fastq fastq", 14228466708.0, 70437954.0, "WT neg 3 S9 R1 001.fastq.gz", "0:101 1:101", "A:4251988096;C:2825656049;G:2882063617;T:4268538044;N:220902", 101, 101, null, null, 4251988096, 2825656049, 2882063617, 4268538044, 220902, "SRX28544211", "SRS24843391", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35957, "SRR33299176", "SRX28544209", "SRS24843389", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT neg 2", null, "strain:ppat|isolate:RNA wt neg 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt neg 2", "RNA wt neg 2", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT-neg-2_S5_R1_001.fastq.gz WT-neg-2_S5_R2_001.fastq.gz", "fastq fastq", 29197644388.0, 144542794.0, "WT neg 2 S5 R1 001.fastq.gz", "0:101 1:101", "A:8825536643;C:5697075068;G:5851684325;T:8822896313;N:452039", 101, 101, null, null, 8825536643, 5697075068, 5851684325, 8822896313, 452039, "SRX28544209", "SRS24843389", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35958, "SRR33299177", "SRX28544208", "SRS24843388", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "WT neg 1", null, "strain:ppat|isolate:RNA wt neg 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA wt neg 1", "RNA wt neg 1", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "WT-neg-1_S1_R1_001.fastq.gz WT-neg-1_S1_R2_001.fastq.gz", "fastq fastq", 24310317816.0, 120348108.0, "WT neg 1 S1 R1 001.fastq.gz", "0:101 1:101", "A:7529245228;C:4579294064;G:4681930604;T:7519470895;N:377025", 101, 101, null, null, 7529245228, 4579294064, 4681930604, 7519470895, 377025, "SRX28544208", "SRS24843388", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35959, "SRR33299178", "SRX28544207", "SRS24843387", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut pos 3", null, "strain:ppat|isolate:RNA mut pos 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut pos 3", "RNA mut pos 3", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mutant-pos-3_S12_R1_001.fastq.gz Mutant-pos-3_S12_R2_001.fastq.gz", "fastq fastq", 12331802050.0, 61048525.0, "Mutant pos 3 S12 R1 001.fastq.gz", "0:101 1:101", "A:3738975619;C:2387112788;G:2450941491;T:3754579907;N:192245", 101, 101, null, null, 3738975619, 2387112788, 2450941491, 3754579907, 192245, "SRX28544207", "SRS24843387", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35960, "SRR33299179", "SRX28544206", "SRS24843386", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut pos 2", null, "strain:ppat|isolate:RNA mut pos 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut pos 2", "RNA mut pos 2", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mutant-pos-2_S8_R1_001.fastq.gz Mutant-pos-2_S8_R2_001.fastq.gz", "fastq fastq", 14310451034.0, 70843817.0, "Mutant pos 2 S8 R1 001.fastq.gz", "0:101 1:101", "A:4323214668;C:2795555578;G:2854780783;T:4336680703;N:219302", 101, 101, null, null, 4323214668, 2795555578, 2854780783, 4336680703, 219302, "SRX28544206", "SRS24843386", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35961, "SRR33299180", "SRX28544205", "SRS24843385", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut pos 1", null, "strain:ppat|isolate:RNA mut pos 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut pos 1", "RNA mut pos 1", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mutant-pos-1_S4_R1_001.fastq.gz Mutant-pos-1_S4_R2_001.fastq.gz", "fastq fastq", 11742623802.0, 58131801.0, "Mutant pos 1 S4 R1 001.fastq.gz", "0:101 1:101", "A:3631609351;C:2213363935;G:2258388450;T:3639080712;N:181354", 101, 101, null, null, 3631609351, 2213363935, 2258388450, 3639080712, 181354, "SRX28544205", "SRS24843385", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35962, "SRR33299181", "SRX28544204", "SRS24843384", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut neg 3", null, "strain:ppat|isolate:RNA mut neg 3|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut neg 3", "RNA mut neg 3", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mutant-neg-3_S11_R1_001.fastq.gz Mutant-neg-3_S11_R2_001.fastq.gz", "fastq fastq", 24089537270.0, 119255135.0, "Mutant neg 3 S11 R1 001.fastq.gz", "0:101 1:101", "A:7187277815;C:4790199860;G:4897671441;T:7214028116;N:360038", 101, 101, null, null, 7187277815, 4790199860, 4897671441, 7214028116, 360038, "SRX28544204", "SRS24843384", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35963, "SRR33299182", "SRX28544203", "SRS24843383", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut neg 2", null, "strain:ppat|isolate:RNA mut neg 2|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut neg 2", "RNA mut neg 2", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mutant-neg-2_S7_R1_001.fastq.gz Mutant-neg-2_S7_R2_001.fastq.gz", "fastq fastq", 27776865470.0, 137509235.0, "Mutant neg 2 S7 R1 001.fastq.gz", "0:101 1:101", "A:8522694394;C:5302545250;G:5464259742;T:8486935677;N:430407", 101, 101, null, null, 8522694394, 5302545250, 5464259742, 8486935677, 430407, "SRX28544203", "SRS24843383", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [35964, "SRR33299183", "SRX28544202", "SRS24843382", "SRP580984", "PRJNA1255065", "A Novel Transgenic Reporter to Study Vertebrate Epigenetics", "PRJNA1255065", "Other", "Epigenetic reprogramming contributes to the generation of cellular diversity during vertebratedevelopment but the mechanisms directing this are still not well understood. Large scale genetic screens have been highly successful in identifying epigenetic regulatory genes in invertebrates such as worms and flies but similar large scale genetic screens to identify epigenetic regulators have not been carried out in vertebrates. Here we report a newly generated EpiTag zebrafish transgenic reporter line that permits easy cellular level visualization of epigenetic silencing or activation in living animals during development gametogenesis and regeneration. We use the EpiTag reporter to carry out an F3 ENU mutagenesis screen for epigenetic silencing or activating mutants identifying relevant vertebrate tissue specific epigenetic regulatory genes including a new epigenetic model for metabolic dysfunction associated fatty liver disease MAFLD. The EpiTag reporter line represents a powerful new tool for genetic and experimental analysis of tissue specific epigenetic gene regulation in vertebrates.", null, null, null, null, "Mut neg 1", null, "strain:ppat|isolate:RNA mut neg 1|age:6dpf|collection date:2024|geo loc name:USA|sex:unknown|tissue:liver & other|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of EpiTag Danio Rerio", "RNA mut neg 1", "RNA mut neg 1", "Zymo Seq RiboFree Total RNA Library Kit Zymo Research; R3000", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP580984", null, null, "Mutant-neg-1_S3_R1_001.fastq.gz Mutant-neg-1_S3_R2_001.fastq.gz", "fastq fastq", 12942402802.0, 64071301.0, "Mutant neg 1 S3 R1 001.fastq.gz", "0:101 1:101", "A:3952970077;C:2483104981;G:2560604982;T:3945521897;N:200865", 101, 101, null, null, 3952970077, 2483104981, 2560604982, 3945521897, 200865, "SRX28544202", "SRS24843382", "SRA2117853", "NIH|NICHD", "NIH", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2025-04-24", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36506, "SRR566696", "SRX185761", "SRS361914", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: liver tumor M+D+", "GSM1000561: M+D+ 2", "GSM1000561", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "M+D+ 2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor M+D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "GSM1000561", "GSM1000561: M+D+ 2; Danio rerio; RNA Seq", "GSM1000561 1", null, "1", null, "GEO Accession:GSM1000561", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M+D+_2_QV.qual M+D+_2.csfasta", "SOLiD_native SOLiD_native", 1493416960.0, 42669056.0, "GSM1000561 r1", "0:35", "0:377247910;1:348861020;2:522134600;3:237405266;.:7768164", 35, null, null, null, null, null, null, null, null, "SRX185761", "SRS361914", "SRA058618", "GEO", "National University of Singapore", 1, 0.06244, null, 0.00306, null, 0.99567, null, 0.34618, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36507, "SRR566695", "SRX185760", "SRS361913", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: liver tumor M+D+", "GSM1000560: M+D+ 1", "GSM1000560", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "M+D+ 1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "liver tumor M+D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:doxycycline", "GSM1000560", "GSM1000560: M+D+ 1; Danio rerio; RNA Seq", "GSM1000560 1", null, "1", null, "GEO Accession:GSM1000560", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, null, null, 1291539515.0, 36901129.0, "GSM1000560 r1", "0:35", "0:266006021;1:328523841;2:440474617;3:254266912;.:2268124", 35, null, null, null, null, null, null, null, null, "SRX185760", "SRS361913", "SRA058618", "GEO", "National University of Singapore", 1, 0.10629, null, 0.0044, null, 0.99239, null, 0.31953, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36508, "SRR566694", "SRX185759", "SRS361912", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver M D+", "GSM1000559: M D+ 2", "GSM1000559", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "M D+ 2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver M D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "GSM1000559", "GSM1000559: M D+ 2; Danio rerio; RNA Seq", "GSM1000559 1", null, "1", null, "GEO Accession:GSM1000559", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D+_2_QV.qual", "SOLiD_native", 1438423910.0, 41097826.0, "GSM1000559 r1", "0:35", "0:353104627;1:349496969;2:433338629;3:275089557;.:27394128", 35, null, null, null, null, null, null, null, null, "SRX185759", "SRS361912", "SRA058618", "GEO", "National University of Singapore", 1, 0.04748, null, 0.00442, null, 0.99425, null, 0.53794, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36509, "SRR566693", "SRX185758", "SRS361911", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver M D+", "GSM1000558: M D+ 1", "GSM1000558", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "M D+ 1", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver M D+", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:wildtype|tissue:liver|treatment:doxycycline", "GSM1000558", "GSM1000558: M D+ 1; Danio rerio; RNA Seq", "GSM1000558 1", null, "1", null, "GEO Accession:GSM1000558", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M-D+_1.csfasta", "SOLiD_native", 1284638285.0, 36703951.0, "GSM1000558 r1", "0:35", "0:328871758;1:317693850;2:402981931;3:233637468;.:1453278", 35, null, null, null, null, null, null, null, null, "SRX185758", "SRS361911", "SRA058618", "GEO", "National University of Singapore", 1, 0.10539, null, 0.00562, null, 0.99141, null, 0.37635, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"], [36510, "SRR566692", "SRX185757", "SRS361910", "SRP015680", "PRJNA174800", "Transcriptomic analyses of Myc induced zebrafish liver cancer", "GSE40745", "Transcriptome Analysis", "To study the characteristics and mechanisms of Myc induced zebrafish liver tumor next generation sequencing based SAGE analyses were used to examine the transcriptomes of tumor and control samples. The results indicated that ribosome proteins were overwhelmingly up regulated in the Myc induced liver tumors. Cross species analyses showed that the zebrafish Myc model correlated well with Myc transgenic mouse models for liver cancers. The Myc induced zebrafish liver tumors also possessed molecular signatures highly similar to human hepatocellular carcinoma HCC. Thus our zebrafish model demonstrated the conserved role of Myc in promoting hepatocarcinogenesis in all vertebrate species. Overall design: Transcriptome profiling of tumor samples M+D+ and control samples M D M+D M D+ were generated by deep sequencing each in duplicates using three prime RNA SAGE on the SOLiD system.", null, "pubmed:23038063", "source: control liver M+D ", "GSM1000557: M+D 2", "GSM1000557", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "M+D 2", "The SOLiD generated RNA Seq reads were 27 bp in length. An initial filtering process was performed to remove any non desirable contamination sequences. The reads were mapped to the zebrafish RefSeq mRNA database Release 39 allowing maxium mismatches using ABI pipeline BioScope v1.0.1. The expression levels of the mapped transcripts were normalized into transcript per million TPM to faciliate comparison among different samples. Genome build: RefSeq Release 39 Supplementary files format and content: The mapped transcripts were listed with GI and RefSeq ID together with expression levels in TPM.", "control liver M+D ", "Transgenic zebrafish and their wildtype siblings were treated starting from 21 dpf. Doxycycline treatment was conducted in 6 L tanks with around 25 adults and water was changed every other day.", "Total RNA was extracted using TRIzol Invitrogen. Library construction was conducted by Mission Biotech Taiwan following the standard ABI SOLiD protocol.", null, "genotype:Tgfabp10:TA; TRE:Myc; krt4:GFP|tissue:liver|treatment:n1", "GSM1000557", "GSM1000557: M+D 2; Danio rerio; RNA Seq", "GSM1000557 1", null, "1", null, "GEO Accession:GSM1000557", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD 3 Plus System", null, "SRP015680", null, null, "M+D-_2_QV.qual", "SOLiD_native", 1404966080.0, 40141888.0, "GSM1000557 r1", "0:35", "0:371691603;1:354481639;2:405221861;3:271978812;.:1592165", 35, null, null, null, null, null, null, null, null, "SRX185757", "SRS361910", "SRA058618", "GEO", "National University of Singapore", 1, 0.07869, null, 0.00455, null, 0.99253, null, 0.51508, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2012-09-10", "Larval", "Larval", "Liver", "Liver and Biliary System"]], "truncated": 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