{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Multi-stage\" and tissue_curation_coarse = \"Liver and Biliary System\"", "rows": [[43800, "SRR6144829", "SRX3256925", "SRS2570606", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "highARA f1 18", "GSM2805942", null, "source name:Liver|treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "highARA f1 18", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805942", "GSM2805942: highARA f1 18; Danio rerio; RNA Seq", "GSM2805942", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805942", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "highARA_f1_18.fastq", "fastq", 1088646952.0, 14324302.0, "GSM2805942 r1", "0:76 1:0", "A:270293793;C:252407731;G:251253668;T:314684999;N:6761", 76, 0, null, null, 270293793, 252407731, 251253668, 314684999, 6761, "SRX3256925", "SRS2570606", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95672, null, 0.0591, null, 0.79892, null, 0.58182, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43801, "SRR6144828", "SRX3256924", "SRS2570605", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "highARA f1 17", "GSM2805941", null, "source name:Liver|treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "highARA f1 17", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805941", "GSM2805941: highARA f1 17; Danio rerio; RNA Seq", "GSM2805941", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805941", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "highARA_f1_17.fastq", "fastq", 898551040.0, 11823040.0, "GSM2805941 r1", "0:76 1:0", "A:225401261;C:202636545;G:213047141;T:257460487;N:5606", 76, 0, null, null, 225401261, 202636545, 213047141, 257460487, 5606, "SRX3256924", "SRS2570605", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95289, null, 0.06582, null, 0.80164, null, 0.52895, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43802, "SRR6144827", "SRX3256923", "SRS2570604", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "highARA f1 16", "GSM2805940", null, "source name:Liver|treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "highARA f1 16", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805940", "GSM2805940: highARA f1 16; Danio rerio; RNA Seq", "GSM2805940", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805940", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "highARA_f1_16.fastq", "fastq", 953328572.0, 12543797.0, "GSM2805940 r1", "0:76 1:0", "A:237595330;C:217850567;G:224754832;T:273121934;N:5909", 76, 0, null, null, 237595330, 217850567, 224754832, 273121934, 5909, "SRX3256923", "SRS2570604", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.9564, null, 0.06004, null, 0.80172, null, 0.5658, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43803, "SRR6144826", "SRX3256922", "SRS2570603", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "highARA f1 15", "GSM2805939", null, "source name:Liver|treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "highARA f1 15", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805939", "GSM2805939: highARA f1 15; Danio rerio; RNA Seq", "GSM2805939", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805939", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "highARA_f1_15.fastq", "fastq", 954837476.0, 12563651.0, "GSM2805939 r1", "0:76 1:0", "A:237890439;C:218085647;G:225249786;T:273605669;N:5935", 76, 0, null, null, 237890439, 218085647, 225249786, 273605669, 5935, "SRX3256922", "SRS2570603", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95915, null, 0.06033, null, 0.8117, null, 0.57095, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43804, "SRR6144825", "SRX3256921", "SRS2570602", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "highARA f1 14", "GSM2805938", null, "source name:Liver|treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "highARA f1 14", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805938", "GSM2805938: highARA f1 14; Danio rerio; RNA Seq", "GSM2805938", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805938", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "highARA_f1_14.fastq", "fastq", 787682316.0, 10364241.0, "GSM2805938 r1", "0:76 1:0", "A:196480808;C:183785954;G:180965195;T:226445352;N:5007", 76, 0, null, null, 196480808, 183785954, 180965195, 226445352, 5007, "SRX3256921", "SRS2570602", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.96296, null, 0.05685, null, 0.81034, null, 0.58128, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43805, "SRR6144824", "SRX3256920", "SRS2570601", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "highARA f1 13", "GSM2805937", null, "source name:Liver|treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "highARA f1 13", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805937", "GSM2805937: highARA f1 13; Danio rerio; RNA Seq", "GSM2805937", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805937", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "highARA_f1_13.fastq", "fastq", 853624704.0, 11231904.0, "GSM2805937 r1", "0:76 1:0", "A:213210073;C:199107544;G:194108374;T:247193339;N:5374", 76, 0, null, null, 213210073, 199107544, 194108374, 247193339, 5374, "SRX3256920", "SRS2570601", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.9605, null, 0.05904, null, 0.8116, null, 0.56344, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43806, "SRR6144823", "SRX3256919", "SRS2570600", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "high ARA f0 18", "GSM2805936", null, "source name:Liver|treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "high ARA f0 18", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805936", "GSM2805936: high ARA f0 18; Danio rerio; RNA Seq", "GSM2805936", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805936", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "high_ARA_f0_18.fastq", "fastq", 781430404.0, 10281979.0, "GSM2805936 r1", "0:76 1:0", "A:191777180;C:181597581;G:184398697;T:223652010;N:4936", 76, 0, null, null, 191777180, 181597581, 184398697, 223652010, 4936, "SRX3256919", "SRS2570600", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95634, null, 0.05563, null, 0.81357, null, 0.57936, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43807, "SRR6144822", "SRX3256918", "SRS2570599", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "high ARA f0 17", "GSM2805935", null, "source name:Liver|treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "high ARA f0 17", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805935", "GSM2805935: high ARA f0 17; Danio rerio; RNA Seq", "GSM2805935", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805935", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "high_ARA_f0_17.fastq", "fastq", 1076538480.0, 14164980.0, "GSM2805935 r1", "0:76 1:0", "A:267896308;C:250279459;G:249384066;T:308971864;N:6783", 76, 0, null, null, 267896308, 250279459, 249384066, 308971864, 6783, "SRX3256918", "SRS2570599", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95576, null, 0.06056, null, 0.80373, null, 0.58226, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43808, "SRR6144821", "SRX3256917", "SRS2570598", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "high ARA f0 16", "GSM2805934", null, "source name:Liver|treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "high ARA f0 16", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805934", "GSM2805934: high ARA f0 16; Danio rerio; RNA Seq", "GSM2805934", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805934", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "high_ARA_f0_16.fastq", "fastq", 560125168.0, 7370068.0, "GSM2805934 r1", "0:76 1:0", "A:140094475;C:127885755;G:132590506;T:159550831;N:3601", 76, 0, null, null, 140094475, 127885755, 132590506, 159550831, 3601, "SRX3256917", "SRS2570598", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95641, null, 0.05996, null, 0.79736, null, 0.56491, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43809, "SRR6144820", "SRX3256916", "SRS2570597", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "high ARA f0 15", "GSM2805933", null, "source name:Liver|treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "high ARA f0 15", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805933", "GSM2805933: high ARA f0 15; Danio rerio; RNA Seq", "GSM2805933", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805933", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "high_ARA_f0_15.fastq", "fastq", 778651920.0, 10245420.0, "GSM2805933 r1", "0:76 1:0", "A:195675470;C:179574003;G:179834060;T:223563596;N:4791", 76, 0, null, null, 195675470, 179574003, 179834060, 223563596, 4791, "SRX3256916", "SRS2570597", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95574, null, 0.06125, null, 0.79744, null, 0.57178, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43810, "SRR6144819", "SRX3256915", "SRS2570596", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "high ARA f0 14", "GSM2805932", null, "source name:Liver|treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "high ARA f0 14", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805932", "GSM2805932: high ARA f0 14; Danio rerio; RNA Seq", "GSM2805932", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805932", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "high_ARA_f0_14.fastq", "fastq", 549851412.0, 7234887.0, "GSM2805932 r1", "0:76 1:0", "A:137151511;C:127528775;G:127338564;T:157829141;N:3421", 76, 0, null, null, 137151511, 127528775, 127338564, 157829141, 3421, "SRX3256915", "SRS2570596", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.96072, null, 0.06057, null, 0.80631, null, 0.57653, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43811, "SRR6144818", "SRX3256914", "SRS2570595", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "high ARA f0 13", "GSM2805931", null, "source name:Liver|treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "high ARA f0 13", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:High arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805931", "GSM2805931: high ARA f0 13; Danio rerio; RNA Seq", "GSM2805931", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805931", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "high_ARA_f0_13.fastq", "fastq", 575303888.0, 7569788.0, "GSM2805931 r1", "0:76 1:0", "A:144137425;C:131780222;G:135118510;T:164264223;N:3508", 76, 0, null, null, 144137425, 131780222, 135118510, 164264223, 3508, "SRX3256914", "SRS2570595", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.9563, null, 0.06221, null, 0.79482, null, 0.56822, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43812, "SRR6144817", "SRX3256913", "SRS2570594", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f1 9", "GSM2805930", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "cont f1 9", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805930", "GSM2805930: cont f1 9; Danio rerio; RNA Seq", "GSM2805930", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805930", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f1_9.fastq", "fastq", 479925560.0, 6314810.0, "GSM2805930 r1", "0:76 1:0", "A:120584089;C:110910147;G:109043764;T:139384590;N:2970", 76, 0, null, null, 120584089, 110910147, 109043764, 139384590, 2970, "SRX3256913", "SRS2570594", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95894, null, 0.0587, null, 0.80194, null, 0.58919, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43813, "SRR6144816", "SRX3256912", "SRS2570593", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f1 8", "GSM2805929", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "cont f1 8", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805929", "GSM2805929: cont f1 8; Danio rerio; RNA Seq", "GSM2805929", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805929", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f1_8.fastq", "fastq", 543204376.0, 7147426.0, "GSM2805929 r1", "0:76 1:0", "A:135958052;C:125790201;G:124341108;T:157111751;N:3264", 76, 0, null, null, 135958052, 125790201, 124341108, 157111751, 3264, "SRX3256912", "SRS2570593", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95884, null, 0.05786, null, 0.80377, null, 0.56612, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43814, "SRR6144815", "SRX3256911", "SRS2570592", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f1 7", "GSM2805928", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "cont f1 7", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805928", "GSM2805928: cont f1 7; Danio rerio; RNA Seq", "GSM2805928", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805928", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f1_7.fastq", "fastq", 500427852.0, 6584577.0, "GSM2805928 r1", "0:76 1:0", "A:125279026;C:115128319;G:115884895;T:144132459;N:3153", 76, 0, null, null, 125279026, 115128319, 115884895, 144132459, 3153, "SRX3256911", "SRS2570592", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.9594, null, 0.05715, null, 0.80913, null, 0.58347, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43815, "SRR6144814", "SRX3256910", "SRS2570590", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f1 12", "GSM2805927", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "cont f1 12", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805927", "GSM2805927: cont f1 12; Danio rerio; RNA Seq", "GSM2805927", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805927", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f1_12.fastq", "fastq", 647351432.0, 8517782.0, "GSM2805927 r1", "0:76 1:0", "A:161818508;C:150504197;G:147413569;T:187611056;N:4102", 76, 0, null, null, 161818508, 150504197, 147413569, 187611056, 4102, "SRX3256910", "SRS2570590", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.96063, null, 0.05637, null, 0.80904, null, 0.58451, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43816, "SRR6144813", "SRX3256909", "SRS2570591", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f1 11", "GSM2805926", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "cont f1 11", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805926", "GSM2805926: cont f1 11; Danio rerio; RNA Seq", "GSM2805926", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805926", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f1_11.fastq", "fastq", 471737548.0, 6207073.0, "GSM2805926 r1", "0:76 1:0", "A:118808226;C:109075505;G:106918917;T:136931918;N:2982", 76, 0, null, null, 118808226, 109075505, 106918917, 136931918, 2982, "SRX3256909", "SRS2570591", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95702, null, 0.0594, null, 0.80986, null, 0.59868, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43817, "SRR6144812", "SRX3256908", "SRS2570589", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f1 10", "GSM2805925", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "cont f1 10", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F1 generation|tissue:liver", "GSM2805925", "GSM2805925: cont f1 10; Danio rerio; RNA Seq", "GSM2805925", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805925", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f1_10.fastq", "fastq", 776618844.0, 10218669.0, "GSM2805925 r1", "0:76 1:0", "A:193082171;C:180711159;G:178758833;T:224061840;N:4841", 76, 0, null, null, 193082171, 180711159, 178758833, 224061840, 4841, "SRX3256908", "SRS2570589", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95782, null, 0.05431, null, 0.81099, null, 0.57832, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43818, "SRR6144811", "SRX3256907", "SRS2570588", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f0 9", "GSM2805924", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "cont f0 9", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805924", "GSM2805924: cont f0 9; Danio rerio; RNA Seq", "GSM2805924", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805924", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f0_9.fastq", "fastq", 522365860.0, 6873235.0, "GSM2805924 r1", "0:76 1:0", "A:130662760;C:120492192;G:121699714;T:149508005;N:3189", 76, 0, null, null, 130662760, 120492192, 121699714, 149508005, 3189, "SRX3256907", "SRS2570588", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.9564, null, 0.06305, null, 0.79401, null, 0.57429, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43819, "SRR6144810", "SRX3256906", "SRS2570587", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f0 8", "GSM2805923", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "cont f0 8", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805923", "GSM2805923: cont f0 8; Danio rerio; RNA Seq", "GSM2805923", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805923", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f0_8.fastq", "fastq", 1438158260.0, 18923135.0, "GSM2805923 r1", "0:76 1:0", "A:357624758;C:333468469;G:335365931;T:411690130;N:8972", 76, 0, null, null, 357624758, 333468469, 335365931, 411690130, 8972, "SRX3256906", "SRS2570587", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95644, null, 0.05493, null, 0.81227, null, 0.59257, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43820, "SRR6144809", "SRX3256905", "SRS2570586", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f0 7", "GSM2805922", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "cont f0 7", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805922", "GSM2805922: cont f0 7; Danio rerio; RNA Seq", "GSM2805922", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805922", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f0_7.fastq", "fastq", 878647552.0, 11561152.0, "GSM2805922 r1", "0:76 1:0", "A:221367823;C:203138998;G:201853119;T:252282011;N:5601", 76, 0, null, null, 221367823, 203138998, 201853119, 252282011, 5601, "SRX3256905", "SRS2570586", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95792, null, 0.05884, null, 0.79458, null, 0.5762, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43821, "SRR6144808", "SRX3256904", "SRS2570585", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f0 12", "GSM2805921", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "cont f0 12", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805921", "GSM2805921: cont f0 12; Danio rerio; RNA Seq", "GSM2805921", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805921", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f0_12.fastq", "fastq", 542012392.0, 7131742.0, "GSM2805921 r1", "0:76 1:0", "A:134357730;C:124792481;G:127323726;T:155535065;N:3390", 76, 0, null, null, 134357730, 124792481, 127323726, 155535065, 3390, "SRX3256904", "SRS2570585", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95754, null, 0.05745, null, 0.80545, null, 0.59141, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43822, "SRR6144807", "SRX3256903", "SRS2570583", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f0 11", "GSM2805920", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "cont f0 11", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805920", "GSM2805920: cont f0 11; Danio rerio; RNA Seq", "GSM2805920", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805920", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f0_11.fastq", "fastq", 926339832.0, 12188682.0, "GSM2805920 r1", "0:76 1:0", "A:233732913;C:211948482;G:213356818;T:267295879;N:5740", 76, 0, null, null, 233732913, 211948482, 213356818, 267295879, 5740, "SRX3256903", "SRS2570583", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95749, null, 0.06087, null, 0.79977, null, 0.56991, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [43823, "SRR6144806", "SRX3256902", "SRS2570584", "SRP119524", "PRJNA413523", "Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish Danio rerio progeny", "GSE104692", "Transcriptome Analysis", "Disproportionate high intake of n 6 polyunsaturated fatty acids PUFAs in the diet is considered as a major human health concern. The present study examines changes in the hepatic gene expression pattern of adult male zebrafish progeny associated with high levels of the n 6 PUFA arachidonic acid ARA in the parental diet. The parental generation F0 was fed a diet which was either low control or high in ARA high ARA. Progenies of both groups F1 were given the control diet. No differences in body weight were found between the diet groups within adult stages of either F0 or F1 generation. Few differentially expressed genes were observed between the two dietary groups in the F0 in contrast to the F1 generation. Nonetheless  several links were found between the previous metabolic analysis of the parental fish and the gene expression analysis in their adult progeny. Main gene expression differences in the progeny were observed related to lipid and retinoid metabolism by PPAR/RXR playing a central role in mediating changes to lipid and long chain fatty acid metabolism. The enrichment of genes involved in \u00df oxidation observed in the progeny  corresponded to the increase in peroxisomal \u00df oxidative degradation of long chain fatty acids in the parental fish metabolomics data. Similar links between the F0 and F1 generation were identified for the methionine cycle and transsulfuration pathway in the high ARA group. In addition  estrogen signalling was found to be affected by parental high dietary ARA levels  where gene expression was opposite directed in F1 compared to F0. This study shows that the dietary n 3/n 6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effect is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. Overall design: In the present study  we fed parental zebrafish either a diet low in arachidonic acid ARA control diet or a diet high in ARA  whereas offspring from both dietary groups were fed the control diet until maturity. We demonstrate that parental high dietary ARA levels can impact transcriptomic patterns in mature offspring. 6 fish from each group and each generation were sampled and sequenced  in total 24 fish was analyzed", null, "pubmed:30070994;pubmed:31398226", null, "cont f0 10", "GSM2805919", null, "source name:Liver|treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "cont f0 10", "Sequence quality was assessed using FastQC v0.11.5  finding high quality Phred scores almost universally above 30 and close to zero adapter contamination on the raw reads Libraries were mapped to the GRCz10 Genome Reference Consortium Zebrafish Build 10 assembly based on both RefSeq GCF 000002035.5 GRCz10 and Ensembl using the default parameters of HISAT2 Kim D et al.  Nat Methods. 2015 Apr;124:357 60 resulting in an average of 76.29% of reads unambiguously assigned to RefSeq genes and 82.22% of reads unambiguously assigned to Ensembl genes. Read counts per gene were quantified using featureCounts Liao Y et al. Bioinformatics. 2014 Apr 01;307:923 30 and pre filtered to exclude combined mean read counts smaller than 10. Differential gene expression were estimated using DESeq2 for both the RefSeq mapped genes and the Ensembl mapped genes. The overlapping differntially expressed genes were used in the downstream analysis. Genome build: GCF 000002035.5 GRCz10 Supplementary files format and content: The two processed datafiles are available as txt files. The include the gene count matrix based on two mapping strategies  either against the zebrafish genome available in refseq database counts ensembl.txt or the refseq database counts refseq.txt", "Liver", "For the parental fish F0 the experimental diets high or low arachinoic acid were given twice a day from 27 DPF until sampling at 154 156 DPF . F1 generation  both progeny of High ARA group and Low ARA group was fed the control feed low arachidonic acid and sampled at 140 142 DPF", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "F0 embryos were collected randomly and larvae were fed with Gemma micro\u00ae Skretting as a start feed from 5 dpf DPF and Artemia nauplii Silver Star Artemia from 7 DPF until 26 DPF. Fish were kept in 10 gender mixed tanks containing 60 fish each until 44 DPF and therepost reduced to 20 fish each per diet group. All fish were kept under steadily monitored standard conditions with 28 \u00b1 1\u00b0C  14 h light   10 h dark period  conductivity of 500 \u00b5S and pH 7.5 in tanks in a reverse osmosis water treatment system Aquatic Habitats recirculation system. F0 generation was mated at 97 DPF.", "treatment:Low arachidonic acid group|generation:F0 generation|tissue:liver", "GSM2805919", "GSM2805919: cont f0 10; Danio rerio; RNA Seq", "GSM2805919", null, "1", "Livers were briefly rinsed in 1x PBS  snap frozen with liquid nitrogen and stored at  80\u00b0C for transcriptome analysis RNA sequencing. Total RNA was extracted using QIAzol Lysis Reagent Qiagen and RNA samples were DNase treated with the DNA freeTM DNA Removal Kit Ambion in order to avoid remaining genomic DNA. RNA quantity was verified using NanoDrop\u00ae ND 1000 Spectrophotometer NanoDrop Technologies  USA. RNA integrity RIN was determined using an Agilent 2100 Bioanalyser RNA 6000 Nano LabChip kit  Agilent Technologies  USA. RIN values from the 12 extracted RNA samples were on average 9.06 \u00b1 0.39 The Norwegian Sequencing Centre CEES performed RNA sequencing RNA seq and library preparation using TruSeqTM Stranded mRNA Library Prep Kit Illumina", "GEO Accession:GSM2805919", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP119524", null, null, "cont_f0_10.fastq", "fastq", 740733696.0, 9746496.0, "GSM2805919 r1", "0:76 1:0", "A:187100850;C:170350514;G:169864627;T:213413168;N:4537", 76, 0, null, null, 187100850, 170350514, 169864627, 213413168, 4537, "SRX3256902", "SRS2570584", "SRA617763", "GEO", "Feed Safety, National Institute of nutrition and seafood research (NIFES)", 1, 0.95793, null, 0.06739, null, 0.7976, null, 0.54473, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2017-10-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [52228, "SRR13912633", "SRX10292190", "SRS8427105", "SRP195753", "PRJNA541476", "Transcriptomic profiling of zebrafish livers with nAtf6 overexpression at collected at 78 hpf and 120 hpf", "GSE130800", "Transcriptome Analysis", "Activting transcription factor 6 Atf6 is one of three main mediators of the Unfolded Protein Response and it gets cleaved cleaved in the Golgi and its N terminal consisting of the bZip domain translocates into the nucleus to generate a transcriptional response nAtf6. This study carries out RNAseq on an established transgenic overexpression of nAtf6 in zebrafish hepatocytes  tgfabp10:nAtf6 cherry; cmlc2:GFP C allele.  Samples were collected at 78 hpf and 120 hpf to detect gene expression changes at early and late time points post nAtf6 is overexpressed. Overall design: We used two  transgenic lines: Tgfabp10a: CAAX EGFP to use as a marker of the liver for dissction and tgfabp10:nAtf6 cherry; cmlc2:GFP C allele to overexpress nAtf6 specifically in hepatocytes.This experiment was conducted by natural spawnings between tg:fabp10:nAtf6 cherry; cmlc2:GFP C  and tgfabp10a:CAAX EGFP . Using GFP to guide microdissscion of 20 25 livers at 78 hpf and 120 hpf . Total RNA isolated using TRIZOL and treated by DNAse I.  Libraries were prepared using RiboZero for 120 hpf samples or polyA selection for 78 hpf samples. Samples from 2 clutches collected at 78 hpf and 3 clutches  at 120 hpf. Samples were sequenced on NextSeq550 Illumina", "parent bioproject:PRJNA541472", null, null, "78 hpf liver from transgenics overexpressing nAtf6   Clutch 2", "GSM5145709", null, "tissue:Liver|genotype:Tgfabp10a:CAAX EGFP; Tgfabp10:nAtf6 mcherry; cmlc2:EGFP C|pool:20", "78 hpf liver from transgenics overexpressing nAtf6   Clutch 2", "Illumina Casava  software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Alignment by HISTA2 with default parameters  only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of  ensemble gene annotation with HTseq  in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V4.0.2 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes", "Liver", "At approximately 78 hpf/3 dpf   3 PM  and at 120 hpf/  5  dpf  9 AM   plates were treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA and  were first sorted for green liver positive as all fish needed to have marked livers to proceed. Next  green liver positive fish were spilt between siblings without xxx hearts larvae that don't express nAtf6   Sample name  Sibs and with green hearts larvae that express nAtf6  Sample name : Natf6. These fish were dissected in 3% methyl cellulose.", "20 livers were microdissected and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026. RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc.RNA was quantified by Qubit flurometer.Thermo Scientific The 120 hpf samples were DNAseI treated for 30 minutes at 37\u00b0C followed by RNA purification RapidOut DNA Removal Kit\u2013Thermo Fisher Scientific.", "This experiment was conducted by natural spawnings between tg:fabp10:nAtf6 cherry; cmlc2:GFP C   and tgfabp10a:CAAX EGFP  . Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in embryo medium Zebrafish Information Network. Plates were cleaned daily to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:CAAX EGFP; Tgfabp10:nAtf6 mcherry; cmlc2:EGFP C|pool:20|rna qbit concentrationng/ul:10", "GSM5145709", "GSM5145709: LIV nAtf6 2; Danio rerio; RNA Seq", "GSM5145709", null, "1", "TRIzol/Choloform RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM5145709", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP195753", null, null, "Liv_SIBS_2_S1_read1.fastq.gz Liv_SIBS_2_S1_read2.fastq.gz", "fastq fastq", 2358265150.0, 8259166.0, "GSM5145709 r1", "0:142.48 1:143.06", "A:628232000;C:556398561;G:558335926;T:614539765;N:758898", 142, 143, null, null, 628232000, 556398561, 558335926, 614539765, 758898, "SRX10292190", "SRS8427105", "SRA883585", "GEO", "Biology, New York University Abu Dhabi", 2, 0.79869, 0.80429, 0.04449, 0.04602, 0.75422, 0.76355, 0.569, 0.56414, 142, 142, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United Arab Emirates", "2021-03-09", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [52229, "SRR13912632", "SRX10292189", "SRS8427104", "SRP195753", "PRJNA541476", "Transcriptomic profiling of zebrafish livers with nAtf6 overexpression at collected at 78 hpf and 120 hpf", "GSE130800", "Transcriptome Analysis", "Activting transcription factor 6 Atf6 is one of three main mediators of the Unfolded Protein Response and it gets cleaved cleaved in the Golgi and its N terminal consisting of the bZip domain translocates into the nucleus to generate a transcriptional response nAtf6. This study carries out RNAseq on an established transgenic overexpression of nAtf6 in zebrafish hepatocytes  tgfabp10:nAtf6 cherry; cmlc2:GFP C allele.  Samples were collected at 78 hpf and 120 hpf to detect gene expression changes at early and late time points post nAtf6 is overexpressed. Overall design: We used two  transgenic lines: Tgfabp10a: CAAX EGFP to use as a marker of the liver for dissction and tgfabp10:nAtf6 cherry; cmlc2:GFP C allele to overexpress nAtf6 specifically in hepatocytes.This experiment was conducted by natural spawnings between tg:fabp10:nAtf6 cherry; cmlc2:GFP C  and tgfabp10a:CAAX EGFP . Using GFP to guide microdissscion of 20 25 livers at 78 hpf and 120 hpf . Total RNA isolated using TRIZOL and treated by DNAse I.  Libraries were prepared using RiboZero for 120 hpf samples or polyA selection for 78 hpf samples. Samples from 2 clutches collected at 78 hpf and 3 clutches  at 120 hpf. Samples were sequenced on NextSeq550 Illumina", "parent bioproject:PRJNA541472", null, null, "78 hpf liver from transgenics overexpressing nAtf6   Clutch 1", "GSM5145708", null, "tissue:Liver|genotype:Tgfabp10a:CAAX EGFP; Tgfabp10:nAtf6 mcherry; cmlc2:EGFP C|pool:20", "78 hpf liver from transgenics overexpressing nAtf6   Clutch 1", "Illumina Casava  software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Alignment by HISTA2 with default parameters  only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of  ensemble gene annotation with HTseq  in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V4.0.2 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes", "Liver", "At approximately 78 hpf/3 dpf   3 PM  and at 120 hpf/  5  dpf  9 AM   plates were treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA and  were first sorted for green liver positive as all fish needed to have marked livers to proceed. Next  green liver positive fish were spilt between siblings without xxx hearts larvae that don't express nAtf6   Sample name  Sibs and with green hearts larvae that express nAtf6  Sample name : Natf6. These fish were dissected in 3% methyl cellulose.", "20 livers were microdissected and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026. RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc.RNA was quantified by Qubit flurometer.Thermo Scientific The 120 hpf samples were DNAseI treated for 30 minutes at 37\u00b0C followed by RNA purification RapidOut DNA Removal Kit\u2013Thermo Fisher Scientific.", "This experiment was conducted by natural spawnings between tg:fabp10:nAtf6 cherry; cmlc2:GFP C   and tgfabp10a:CAAX EGFP  . Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in embryo medium Zebrafish Information Network. Plates were cleaned daily to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:CAAX EGFP; Tgfabp10:nAtf6 mcherry; cmlc2:EGFP C|pool:20|rna qbit concentrationng/ul:11", "GSM5145708", "GSM5145708: LIV nAtf6 1; Danio rerio; RNA Seq", "GSM5145708", null, "1", "TRIzol/Choloform RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM5145708", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP195753", null, null, "Liv_SIBS_1_S2_read1.fastq.gz Liv_SIBS_1_S2_read2.fastq.gz", "fastq fastq", 2343584780.0, 8171101.0, "GSM5145708 r1", "0:143.19 1:143.63", "A:614229890;C:561589004;G:564419718;T:602659222;N:686946", 143, 143, null, null, 614229890, 561589004, 564419718, 602659222, 686946, "SRX10292189", "SRS8427104", "SRA883585", "GEO", "Biology, New York University Abu Dhabi", 2, 0.93582, 0.94016, 0.04928, 0.04942, 0.76315, 0.7707, 0.55576, 0.5626, 151, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United Arab Emirates", "2021-03-09", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [52230, "SRR13912631", "SRX10292188", "SRS8427103", "SRP195753", "PRJNA541476", "Transcriptomic profiling of zebrafish livers with nAtf6 overexpression at collected at 78 hpf and 120 hpf", "GSE130800", "Transcriptome Analysis", "Activting transcription factor 6 Atf6 is one of three main mediators of the Unfolded Protein Response and it gets cleaved cleaved in the Golgi and its N terminal consisting of the bZip domain translocates into the nucleus to generate a transcriptional response nAtf6. This study carries out RNAseq on an established transgenic overexpression of nAtf6 in zebrafish hepatocytes  tgfabp10:nAtf6 cherry; cmlc2:GFP C allele.  Samples were collected at 78 hpf and 120 hpf to detect gene expression changes at early and late time points post nAtf6 is overexpressed. Overall design: We used two  transgenic lines: Tgfabp10a: CAAX EGFP to use as a marker of the liver for dissction and tgfabp10:nAtf6 cherry; cmlc2:GFP C allele to overexpress nAtf6 specifically in hepatocytes.This experiment was conducted by natural spawnings between tg:fabp10:nAtf6 cherry; cmlc2:GFP C  and tgfabp10a:CAAX EGFP . Using GFP to guide microdissscion of 20 25 livers at 78 hpf and 120 hpf . Total RNA isolated using TRIZOL and treated by DNAse I.  Libraries were prepared using RiboZero for 120 hpf samples or polyA selection for 78 hpf samples. Samples from 2 clutches collected at 78 hpf and 3 clutches  at 120 hpf. Samples were sequenced on NextSeq550 Illumina", "parent bioproject:PRJNA541472", null, null, "78 hpf liver from sibling of transgenics overexpressing nAtf6   Clutch 2", "GSM5145707", null, "tissue:dissected liver|genotype:Tgfabp10a:CAAX EGFP; Tgfabp10:nAtf6 mcherry; cmlc2:EGFP C|pool:20", "78 hpf liver from sibling of transgenics overexpressing nAtf6   Clutch 2", "Illumina Casava  software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Alignment by HISTA2 with default parameters  only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of  ensemble gene annotation with HTseq  in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V4.0.2 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes", "dissected liver", "At approximately 78 hpf/3 dpf   3 PM  and at 120 hpf/  5  dpf  9 AM   plates were treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA and  were first sorted for green liver positive as all fish needed to have marked livers to proceed. Next  green liver positive fish were spilt between siblings without xxx hearts larvae that don't express nAtf6   Sample name  Sibs and with green hearts larvae that express nAtf6  Sample name : Natf6. These fish were dissected in 3% methyl cellulose.", "20 livers were microdissected and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026. RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc.RNA was quantified by Qubit flurometer.Thermo Scientific The 120 hpf samples were DNAseI treated for 30 minutes at 37\u00b0C followed by RNA purification RapidOut DNA Removal Kit\u2013Thermo Fisher Scientific.", "This experiment was conducted by natural spawnings between tg:fabp10:nAtf6 cherry; cmlc2:GFP C   and tgfabp10a:CAAX EGFP  . Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in embryo medium Zebrafish Information Network. Plates were cleaned daily to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:CAAX EGFP; Tgfabp10:nAtf6 mcherry; cmlc2:EGFP C|pool:20|rna qbit concentrationng/ul:11", "GSM5145707", "GSM5145707: LIV Sibs 2; Danio rerio; RNA Seq", "GSM5145707", null, "1", "TRIzol/Choloform RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM5145707", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP195753", null, null, "Liv_Natf6_3_S3_read1.fastq.gz Liv_Natf6_3_S3_read2.fastq.gz", "fastq fastq", 2379459060.0, 8325143.0, "GSM5145707 r1", "0:142.70 1:143.12", "A:618663373;C:577354955;G:577612285;T:605323263;N:505184", 142, 143, null, null, 618663373, 577354955, 577612285, 605323263, 505184, "SRX10292188", "SRS8427103", "SRA883585", "GEO", "Biology, New York University Abu Dhabi", 2, 0.93847, 0.94341, 0.04874, 0.04907, 0.77289, 0.7796, 0.55045, 0.55975, 150, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "bulk", "unknown", "unknown", null, "United Arab Emirates", "2021-03-09", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55196, "SRR10153191", "SRX6878621", "SRS5414403", "SRP222786", "PRJNA573063", "Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137784", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "NoHCC [Single cell]", "GSM4087821", null, "tissue:Liver|transgenic line:Tgfabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC", "NoHCC [Single cell]", "10x Genomics\u2019 Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp  FASTQ files. Custom transgenic genomic reference was built with \u2018cellranger mkref\u2019  but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with \u2018cellranger mkgtf\u2019 for gene biotypes matching \u2018protein coding\u2019  \u2018lincRNA\u2019 and \u2018antisense\u2019 tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with \u2018cellranger count\u2019 pipeline with their respective transgenic genome build with parameter \u2018  expect cells=3000\u2019 In attempt to recover those perhaps lower quality GEM partitions  the raw gene barcode matrices from \u2018cellranger count\u2019 located in \u2018outs/raw gene bc matrices\u2019 was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al.  2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells  while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al.  2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al.  2008. Cells with extremely low UMI counts  extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally  cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells suspected of being low quality were removed from downstream analysis. Genome build: GRCz11 Supplementary files format and content: MTX", "Liver", "Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank\u2019s Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with 3\u2019 chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC", "GSM4087821", "GSM4087821: NoHCC [Single cell]; Danio rerio; RNA Seq", "GSM4087821", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with three prime chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "GEO Accession:GSM4087821", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP222786", null, null, "15547X4_S11_L007_R2_001.fastq.gz 15547X4_S11_L007_R1_001.fastq.gz", "fastq fastq", 16861988178.0, 133825303.0, "GSM4087821 r1", "0:26 1:100", "A:4788108995;C:3905645218;G:3694064311;T:4468647482;N:5522172", 26, 100, null, null, 4788108995, 3905645218, 3694064311, 4468647482, 5522172, "SRX6878621", "SRS5414403", "SRA965504", "GEO", "Pathology, University of California, San Francisco", 2, 0.00236, 0.93017, 0.0008, 0.04645, 0.99626, 0.89043, 0.52233, 0.64352, 26, 100, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55197, "SRR10153190", "SRX6878620", "SRS5414402", "SRP222786", "PRJNA573063", "Single cell transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137784", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of three 6mpf liver samples from three different transgenic lines with/without xxx hydroxytamoxifen TAM treatment.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "HCCCreLox [Single cell]", "GSM4087820", null, "tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "HCCCreLox [Single cell]", "10x Genomics\u2019 Cell Ranger software v2.2.0 executed primary data analysis for each sample. Pipeline 'cellranger mkfastq' generated R1 26 bp and R2 100 bp  FASTQ files. Custom transgenic genomic reference was built with \u2018cellranger mkref\u2019  but shared the common Danio rerio genome reference build GRCz11 with annotations from Ensembl release 94. The Ensembl gene annotations were filtered with \u2018cellranger mkgtf\u2019 for gene biotypes matching \u2018protein coding\u2019  \u2018lincRNA\u2019 and \u2018antisense\u2019 tags. All samples had additional transgenic sequence/annotations added. Each sample was processed with \u2018cellranger count\u2019 pipeline with their respective transgenic genome build with parameter \u2018  expect cells=3000\u2019 In attempt to recover those perhaps lower quality GEM partitions  the raw gene barcode matrices from \u2018cellranger count\u2019 located in \u2018outs/raw gene bc matrices\u2019 was processed with the EmptyDrops algorithm R package DropletUtils v1.2.2 to discriminate cells from background GEM partitions at a false discovery rate FDR of 1% Lun ATL et al.  2019. GEM partitions with 500 UMI counts or less were considered to be devoid of viable cells  while those with at least 10 000 UMI counts were automatically considered to be cells. Cell based QC metrics were calculated with R package scater v1.10.1 using the calculateQCMetrics function McCarthy DJ et al.  2017. Principal component analysis PCA on the cell based QC metrics combined with a multivariate outlier method flagged cells with outlying values in QC metrics as suspect P. Filzmoser et al.  2008. Cells with extremely low UMI counts  extremely low gene counts or extremely high percentage of expression attributed to mitochondrial genes were also flagged as low quality. Extremeness in any of these three measures was determined by 3 median absolute deviations from the median with the scater::isOutlier function applied to each sample individually. Additionally  cells were required to have greater than 800 UMIs and less than 20% of total expression attributed to mitochondrial transcripts. Those cells suspected of being low quality were removed from downstream analysis. Genome build: GRCz11 Supplementary files format and content: MTX", "Liver", "Larvae for Samples 2 and 3 were treated with 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank\u2019s Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with 3\u2019 chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:6 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "GSM4087820", "GSM4087820: HCCCreLox [Single cell]; Danio rerio; RNA Seq", "GSM4087820", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The remaining half of each liver was dissociated into single cell suspensions and prepared for single tube single cell RNA sequencing scRNA seq based on the 10X Genomics platform. Dissected liver tissue was immersed in 5% Fetal Bovine Serum FBS in Hank's Buffered Saline Solution HBSS without xxx red  with calcium and magnesium and chopped finely. The cells were were homogenized in 1 mL of 0.25% trypsin + EDTA for 5 minutes at room temperature and re suspended in 1 mL of 5%FBS+5mM EDTA in HBSS Free solution. Cells were then filtered through a 40 micron membrane filter  and the filtrate was centrifuged at 1200 RPM  4\uf0b0C for 5 minutes. The cell pellet was then re suspended in phosphate buffered saline with 0.04% bovine serum albumin.  The cell suspension was then filtered again through 40 micron cell strainers to obtain a liver single cell suspension. Viability and cell count were assessed on Countess I Thermo Scientific.  The Chromium Single Cell Gene Expression Solution with three prime chemistry  version 2 PN 120237 was used to barcode individual cells with 16 bp 10x Barcode and to tag cell specific transcript molecules with 10 bp Unique Molecular Identifier UMI according to the manufactures instruction.  Equilibrium to targeted cell recovery of 6 000 cells along with 10x Gel Beads and reverse transcription reagents were loaded to Chromium Single Cell A Chip PN 120236 to form Gel Bead In EMulsions GEMs  the micro droplets.  Within individual GEMs  cDNA generated from captured and barcoded mRNA was synthesized by reverse transcription at the setting of 53\u00b0C for 45 min followed by 85\u00b0C for 5 min.  Subsequent A tailing  end repair  adaptor ligation and sample indexing was performed in bulk according to the manufacturer's instructions. Multiple libraries were then normalized and sequenced on NovaSeq 6000 with 2x150 PE mode. Single cell three prime RNA Sequencing", "GEO Accession:GSM4087820", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP222786", null, null, "15547X2_S9_L006_R1_001.fastq.gz 15547X2_S9_L006_R2_001.fastq.gz", "fastq fastq", 16758654318.0, 133005193.0, "GSM4087820 r1", "0:26 1:100", "A:4758015356;C:3904784528;G:3787834220;T:4302283542;N:5736672", 26, 100, null, null, 4758015356, 3904784528, 3787834220, 4302283542, 5736672, "SRX6878620", "SRS5414402", "SRA965504", "GEO", "Pathology, University of California, San Francisco", 2, 0.00291, 0.94432, 0.00084, 0.04281, 0.99539, 0.88203, 0.48041, 0.60684, 26, 100, "T", "B", "sc-like readlen", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55210, "SRR10153634", "SRX6879049", "SRS5414797", "SRP222804", "PRJNA573071", "Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137787", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish  compared to wildtype/nonHCC siblings.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "609", "GSM4087869", null, "tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC", "609", "The Zebrafish GRCz11 FASTA  and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.\u00a0 Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.\u00a0 Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.\u00a0 Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.", "Liver", "Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer\u2019s protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina\u2019s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC", "GSM4087869", "GSM4087869: 609; Danio rerio; RNA Seq", "GSM4087869", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "GEO Accession:GSM4087869", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP222804", null, null, "16048X9_190607_A00421_0071_BHL22MDSXX_S20_L004_R1_001.fastq.gz 16048X9_190607_A00421_0071_BHL22MDSXX_S20_L004_R2_001.fastq.gz", "fastq fastq", 9109094026.0, 30162563.0, "GSM4087869 r1", "0:151 1:151", "A:2407747194;C:2151727590;G:2238603631;T:2310854013;N:161598", 151, 151, null, null, 2407747194, 2151727590, 2238603631, 2310854013, 161598, "SRX6879049", "SRS5414797", "SRA965568", "GEO", "Pathology, University of California, San Francisco", 2, 0.95438, 0.95659, 0.04172, 0.04068, 0.80267, 0.80308, 0.56788, 0.56779, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55211, "SRR10153633", "SRX6879048", "SRS5414796", "SRP222804", "PRJNA573071", "Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137787", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish  compared to wildtype/nonHCC siblings.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "624", "GSM4087868", null, "tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "624", "The Zebrafish GRCz11 FASTA  and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.\u00a0 Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.\u00a0 Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.\u00a0 Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.", "Liver", "Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer\u2019s protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina\u2019s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "GSM4087868", "GSM4087868: 624; Danio rerio; RNA Seq", "GSM4087868", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "GEO Accession:GSM4087868", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP222804", null, null, "16048X8_190607_A00421_0071_BHL22MDSXX_S19_L004_R1_001.fastq.gz 16048X8_190607_A00421_0071_BHL22MDSXX_S19_L004_R2_001.fastq.gz", "fastq fastq", 9818272170.0, 32510835.0, "GSM4087868 r1", "0:151 1:151", "A:2609919214;C:2318388621;G:2406490919;T:2483290917;N:182499", 151, 151, null, null, 2609919214, 2318388621, 2406490919, 2483290917, 182499, "SRX6879048", "SRS5414796", "SRA965568", "GEO", "Pathology, University of California, San Francisco", 2, 0.95073, 0.95151, 0.04785, 0.0469, 0.80919, 0.81055, 0.54958, 0.55772, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55213, "SRR10153631", "SRX6879046", "SRS5414794", "SRP222804", "PRJNA573071", "Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137787", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish  compared to wildtype/nonHCC siblings.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "625", "GSM4087866", null, "tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC", "625", "The Zebrafish GRCz11 FASTA  and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.\u00a0 Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.\u00a0 Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.\u00a0 Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.", "Liver", "Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer\u2019s protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina\u2019s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf HCC", "GSM4087866", "GSM4087866: 625; Danio rerio; RNA Seq", "GSM4087866", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "GEO Accession:GSM4087866", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP222804", null, null, "16048X6_190607_A00421_0071_BHL22MDSXX_S17_L004_R2_001.fastq.gz 16048X6_190607_A00421_0071_BHL22MDSXX_S17_L004_R1_001.fastq.gz", "fastq fastq", 9650060284.0, 31953842.0, "GSM4087866 r1", "0:151 1:151", "A:2558021442;C:2277296580;G:2371770140;T:2442792643;N:179479", 151, 151, null, null, 2558021442, 2277296580, 2371770140, 2442792643, 179479, "SRX6879046", "SRS5414794", "SRA965568", "GEO", "Pathology, University of California, San Francisco", 2, 0.95395, 0.95537, 0.0475, 0.04582, 0.79947, 0.80046, 0.53471, 0.54384, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55214, "SRR10153630", "SRX6879045", "SRS5414793", "SRP222804", "PRJNA573071", "Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137787", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish  compared to wildtype/nonHCC siblings.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "623", "GSM4087865", null, "tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "623", "The Zebrafish GRCz11 FASTA  and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.\u00a0 Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.\u00a0 Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.\u00a0 Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.", "Liver", "Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer\u2019s protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina\u2019s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "GSM4087865", "GSM4087865: 623; Danio rerio; RNA Seq", "GSM4087865", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "GEO Accession:GSM4087865", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP222804", null, null, "16048X5_190607_A00421_0071_BHL22MDSXX_S16_L004_R2_001.fastq.gz 16048X5_190607_A00421_0071_BHL22MDSXX_S16_L004_R1_001.fastq.gz", "fastq fastq", 11046705188.0, 36578494.0, "GSM4087865 r1", "0:151 1:151", "A:2912202858;C:2634649411;G:2724125067;T:2775523373;N:204479", 151, 151, null, null, 2912202858, 2634649411, 2724125067, 2775523373, 204479, "SRX6879045", "SRS5414793", "SRA965568", "GEO", "Pathology, University of California, San Francisco", 2, 0.95836, 0.95975, 0.04299, 0.04253, 0.79433, 0.795, 0.55057, 0.55465, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55217, "SRR10153627", "SRX6879042", "SRS5414790", "SRP222804", "PRJNA573071", "Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137787", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish  compared to wildtype/nonHCC siblings.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "605", "GSM4087862", null, "tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "605", "The Zebrafish GRCz11 FASTA  and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.\u00a0 Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.\u00a0 Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.\u00a0 Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.", "Liver", "Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer\u2019s protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina\u2019s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "GSM4087862", "GSM4087862: 605; Danio rerio; RNA Seq", "GSM4087862", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "GEO Accession:GSM4087862", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP222804", null, null, "16048X2_190607_A00421_0071_BHL22MDSXX_S2_L004_R1_001.fastq.gz 16048X2_190607_A00421_0071_BHL22MDSXX_S2_L004_R2_001.fastq.gz", "fastq fastq", 9642566456.0, 31929028.0, "GSM4087862 r1", "0:151 1:151", "A:2562227409;C:2265732155;G:2354688485;T:2459736870;N:181537", 151, 151, null, null, 2562227409, 2265732155, 2354688485, 2459736870, 181537, "SRX6879042", "SRS5414790", "SRA965568", "GEO", "Pathology, University of California, San Francisco", 2, 0.9525, 0.95448, 0.0459, 0.04564, 0.78173, 0.78317, 0.54755, 0.54727, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [55218, "SRR10153626", "SRX6879041", "SRS5414789", "SRP222804", "PRJNA573071", "Bulk transcriptomic analysis of two models of zebrafish beta catenin driven HCC", "GSE137787", "Transcriptome Analysis", "Up to 41% of hepatocellular carcinomas HCCs result from activating mutations in the CTNNB1 gene encoding \u00df catenin. \u00df catenin has dual cellular functions as a component of the Wnt signaling pathway and adherens junctions. HCC associated CTNNB1 mutations stabilize the \u00df catenin protein  leading to nuclear and/or cytoplasmic localization of \u00df catenin and downstream activation of Wnt target genes. In patient HCC samples  \u00df catenin nuclear and cytoplasmic localization are typically patchy  even among HCC with highly active CTNNB1 mutations. The functional and clinical relevance of this heterogeneity in \u00df catenin activation are not well understood. To define mechanisms of \u00df catenin driven HCC initiation  we generated a Cre lox system that enabled switching on activated \u00df catenin in 1 a small number of hepatocytes in early development; or 2 the majority of hepatocytes in later development or maturity. We discovered that switching on activated \u00df catenin in a subset of larval hepatocytes was sufficient to drive HCC initiation. To determine the role of Wnt/\u00df catenin signaling heterogeneity later in hepatocarcinogenesis  we performed RNA seq analysis of zebrafish \u00df catenin driven HCC. Ingenuity Pathway Analysis of differentially expressed genes in the Cre lox HCC model revealed that \u201cCancer\u201d and \u201cLiver Tumor\u201d categories were significantly altered  indicating transcriptional similarities with human HCC and other vertebrate HCC models. At the single cell level  2.9% to 15.2% of hepatocytes from zebrafish \u00df catenin driven HCC expressed two or more of the Wnt target genes axin2  mtor  glula  myca  and wif1  indicating focal activation of Wnt signaling in established tumors. Thus  heterogeneous \u00df catenin activation drives HCC initiation and persists throughout hepatocarcinogenesis. Overall design: Examination of HCC and nonHCC liver samples from two different models of zebrafish  compared to wildtype/nonHCC siblings.", "parent bioproject:PRJNA573068", "pubmed:31575545", null, "604", "GSM4087861", null, "tissue:Liver|transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "604", "The Zebrafish GRCz11 FASTA  and GTF files were downloaded from Ensembl release 94. The reference database was created using STAR version 2.6.1b with splice junctions optimized for 125 base pair reads.\u00a0 Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.\u00a0 Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.\u00a0 Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.22.2. Genome build: GRCz11 Supplementary files format and content: Raw gene expression quantification with featureCounts v1.6.3 was collated into a tab delimited matrix where each column denotes a sample and each row corresponds to a gene.", "Liver", "Larvae were treated with either 0.1% ethanol or 10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer\u2019s protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina\u2019s NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "Fish were raised following IACUC approved protocols in insititutional zebrafish facility.", "transgenic line:Tgfabp10a CreERT2;fabp10a flox beta catenin|age:11 mpf at larval stg:10micromolar 4 hydroxytamoxifen from 3 dpf to 6 dpf", "GSM4087861", "GSM4087861: 604; Danio rerio; RNA Seq", "GSM4087861", null, "1", "Zebrafish were euthanized by rapid chilling and their livers were dissected. Half of each liver was submitted for histologic evaluation to confirm the diagnosis HCC or no HCC. The other half of each dissected liver was flash frozen on dry ice and stored in  80\uf0b0C prior to RNA extraction. RNA was isolated using TriReagent Cat# R2050 1 50  Zymo Research and Direct Zol RNA Mini prep kit Cat# R2050  Zymo Research including DNase treatment following manufacturer's protocols. Samples were eluted in RNase /DNase free water. Sample quality control  library preparation  sequencing and alignments were performed by the Huntsman Cancer Institute HCI High Throughput Genomics and Bioinformatic Analysis Shared Resource. Paired read  150 base pair sequencing was performed using Illumina's NovaSeq instrument. Three or four pooled libraries were run on each lane of the flow cell. Illumina TruSeq Stranded mRNA Library Prep RIN 8 10", "GEO Accession:GSM4087861", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP222804", null, null, "16048X1_190607_A00421_0071_BHL22MDSXX_S3_L004_R1_001.fastq.gz 16048X1_190607_A00421_0071_BHL22MDSXX_S3_L004_R2_001.fastq.gz", "fastq fastq", 12056607986.0, 39922543.0, "GSM4087861 r1", "0:151 1:151", "A:3165745037;C:2870251386;G:2976751806;T:3043633552;N:226205", 151, 151, null, null, 3165745037, 2870251386, 2976751806, 3043633552, 226205, "SRX6879041", "SRS5414789", "SRA965568", "GEO", "Pathology, University of California, San Francisco", 2, 0.95408, 0.95527, 0.04826, 0.04735, 0.79366, 0.79425, 0.52338, 0.53718, 151, 151, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2019-09-20", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59319, "SRR11856744", "SRX8406857", "SRS6719220", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf liver exposed to 350 mM Ethanol   clutch 7", "GSM4572124", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20", "5 dpf liver exposed to 350 mM Ethanol   clutch 7", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:23.8", "GSM4572124", "GSM4572124: LIV 2ETOH 7; Danio rerio; RNA Seq", "GSM4572124", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572124", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_2ETOH_7_S23_read2.fastq.gz LIV_2ETOH_7_S23_read1.fastq.gz", "fastq fastq", 6357898307.0, 22104243.0, "GSM4572124 r1", "0:143.74 1:143.89", "A:1712090294;C:1465925369;G:1489380825;T:1689427333;N:1074486", 143, 143, null, null, 1712090294, 1465925369, 1489380825, 1689427333, 1074486, "SRX8406857", "SRS6719220", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.69131, 0.71792, 0.04808, 0.0499, 0.82477, 0.83082, 0.47278, 0.49809, 150, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59320, "SRR11856743", "SRX8406856", "SRS6719219", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf liver exposed to 175mM Ethanol   clutch 7", "GSM4572123", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20", "5 dpf liver exposed to 175mM  Ethanol   clutch 7", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:15.7", "GSM4572123", "GSM4572123: LIV 1ETOH 7; Danio rerio; RNA Seq", "GSM4572123", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572123", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_1ETOH_7_S22_read2.fastq.gz LIV_1ETOH_7_S22_read1.fastq.gz", "fastq fastq", 4305184103.0, 15015974.0, "GSM4572123 r1", "0:143.31 1:143.40", "A:1153593916;C:998854522;G:1012290687;T:1139809167;N:635811", 143, 143, null, null, 1153593916, 998854522, 1012290687, 1139809167, 635811, "SRX8406856", "SRS6719219", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.9174, 0.9191, 0.06548, 0.06503, 0.8143, 0.82148, 0.54687, 0.54095, 151, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59321, "SRR11856756", "SRX8406855", "SRS6719218", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf Untreated liver   clutch 7", "GSM4572122", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20", "5 dpf Untreated liver   clutch 7", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:14.4", "GSM4572122", "GSM4572122: LIV UT 7; Danio rerio; RNA Seq", "GSM4572122", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572122", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_UT_7_S21_read2.fastq.gz LIV_UT_7_S21_read1.fastq.gz", "fastq fastq", 4730299683.0, 16394224.0, "GSM4572122 r1", "0:144.23 1:144.30", "A:1269896715;C:1097260368;G:1106021062;T:1256450979;N:670559", 144, 144, null, null, 1269896715, 1097260368, 1106021062, 1256450979, 670559, "SRX8406855", "SRS6719218", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.92607, 0.92755, 0.06001, 0.05999, 0.81613, 0.82187, 0.55335, 0.53614, 151, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59322, "SRR11856755", "SRX8406854", "SRS6719217", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf liver exposed to 350 mM Ethanol   clutch 5", "GSM4572121", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:35", "5 dpf liver exposed to 350 mM Ethanol   clutch 5", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:35|rna qbit concentrationng/ul:32.6", "GSM4572121", "GSM4572121: LIV 2ETOH 5; Danio rerio; RNA Seq", "GSM4572121", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572121", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_2ETOH_5_S20_read2.fastq.gz LIV_2ETOH_5_S20_read1.fastq.gz", "fastq fastq", 5199368627.0, 17618880.0, "GSM4572121 r1", "0:147.54 1:147.56", "A:1399517489;C:1172048358;G:1240786042;T:1386342191;N:674547", 147, 147, null, null, 1399517489, 1172048358, 1240786042, 1386342191, 674547, "SRX8406854", "SRS6719217", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.91793, 0.91561, 0.14142, 0.13588, 0.80941, 0.81889, 0.47417, 0.50399, 151, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59323, "SRR11856754", "SRX8406853", "SRS6719216", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf liver exposed to 175mM Ethanol   clutch 5", "GSM4572120", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:35", "5 dpf liver exposed to 175mM  Ethanol   clutch 5", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:35|rna qbit concentrationng/ul:34.8", "GSM4572120", "GSM4572120: LIV 1ETOH 5; Danio rerio; RNA Seq", "GSM4572120", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572120", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_1ETOH_5_S19_read2.fastq.gz LIV_1ETOH_5_S19_read1.fastq.gz", "fastq fastq", 4664825517.0, 15773614.0, "GSM4572120 r1", "0:147.85 1:147.89", "A:1254524905;C:1075035904;G:1088910190;T:1245664535;N:689983", 147, 147, null, null, 1254524905, 1075035904, 1088910190, 1245664535, 689983, "SRX8406853", "SRS6719216", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.94346, 0.94595, 0.05958, 0.05908, 0.82183, 0.83053, 0.53444, 0.52504, 151, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59324, "SRR11856753", "SRX8406852", "SRS6719215", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf Untreated liver   clutch 5", "GSM4572119", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:35", "5 dpf Untreated liver   clutch 5", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:35|rna qbit concentrationng/ul:31.2", "GSM4572119", "GSM4572119: LIV UT 5; Danio rerio; RNA Seq", "GSM4572119", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572119", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_UT_5_S18_read2.fastq.gz LIV_UT_5_S18_read1.fastq.gz", "fastq fastq", 5809354899.0, 19717109.0, "GSM4572119 r1", "0:147.29 1:147.35", "A:1543780226;C:1359647607;G:1375859882;T:1529075527;N:991657", 147, 147, null, null, 1543780226, 1359647607, 1375859882, 1529075527, 991657, "SRX8406852", "SRS6719215", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.94774, 0.95056, 0.05145, 0.05139, 0.82079, 0.82735, 0.52842, 0.53743, 151, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59325, "SRR11856752", "SRX8406851", "SRS6719214", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf liver exposed to 350 mM Ethanol   clutch 4", "GSM4572118", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:25", "5 dpf liver exposed to 350 mM Ethanol   clutch 4", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:25|rna qbit concentrationng/ul:30", "GSM4572118", "GSM4572118: LIV 2ETOH 4; Danio rerio; RNA Seq", "GSM4572118", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572118", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_2ETOH_4_S17_read2.fastq.gz LIV_2ETOH_4_S17_read1.fastq.gz", "fastq fastq", 8917001757.0, 31312885.0, "GSM4572118 r1", "0:142.34 1:142.43", "A:2376946463;C:2080235380;G:2109059237;T:2349386126;N:1374551", 142, 142, null, null, 2376946463, 2080235380, 2109059237, 2349386126, 1374551, "SRX8406851", "SRS6719214", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.9451, 0.9474, 0.05499, 0.05486, 0.81201, 0.81671, 0.51433, 0.49899, 151, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59326, "SRR11856751", "SRX8406850", "SRS6719213", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf liver exposed to 175mM Ethanol   clutch 4", "GSM4572117", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:25", "5 dpf liver exposed to 175mM  Ethanol   clutch 4", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:25|rna qbit concentrationng/ul:25", "GSM4572117", "GSM4572117: LIV 1ETOH 4; Danio rerio; RNA Seq", "GSM4572117", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_1ETOH_4_S16_read2.fastq.gz LIV_1ETOH_4_S16_read1.fastq.gz", "fastq fastq", 4433846645.0, 15018858.0, "GSM4572117 r1", "0:147.60 1:147.62", "A:1172428411;C:1023473648;G:1076620756;T:1160707870;N:615960", 147, 147, null, null, 1172428411, 1023473648, 1076620756, 1160707870, 615960, "SRX8406850", "SRS6719213", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.94202, 0.94639, 0.05176, 0.05178, 0.8314, 0.83907, 0.52355, 0.51763, 143, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59327, "SRR11856750", "SRX8406849", "SRS6719212", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf Untreated liver   clutch 4", "GSM4572116", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:25", "5 dpf Untreated liver   clutch 4", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:25|rna qbit concentrationng/ul:17.58", "GSM4572116", "GSM4572116: LIV UT 4; Danio rerio; RNA Seq", "GSM4572116", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_UT_4_S15_read2.fastq.gz LIV_UT_4_S15_read1.fastq.gz", "fastq fastq", 6974105009.0, 23629447.0, "GSM4572116 r1", "0:147.55 1:147.59", "A:1890464005;C:1566267612;G:1641684624;T:1874721633;N:967135", 147, 147, null, null, 1890464005, 1566267612, 1641684624, 1874721633, 967135, "SRX8406849", "SRS6719212", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.92362, 0.92292, 0.13719, 0.13717, 0.81152, 0.82231, 0.55749, 0.56875, 147, 147, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59328, "SRR11856749", "SRX8406848", "SRS6719211", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf liver exposed to 175mM Ethanol   clutch 2", "GSM4572115", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20", "5 dpf liver exposed to 175mM  Ethanol   clutch 2", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:18.1", "GSM4572115", "GSM4572115: LIV 1ETOH 2; Danio rerio; RNA Seq", "GSM4572115", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_1ETOH_2_S13_read2.fastq.gz LIV_1ETOH_2_S13_read1.fastq.gz", "fastq fastq", 6052855736.0, 21232534.0, "GSM4572115 r1", "0:142.48 1:142.60", "A:1597569726;C:1423191233;G:1450513142;T:1580519025;N:1062610", 142, 142, null, null, 1597569726, 1423191233, 1450513142, 1580519025, 1062610, "SRX8406848", "SRS6719211", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.94966, 0.95254, 0.04637, 0.04576, 0.82256, 0.82826, 0.50683, 0.51378, 151, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59330, "SRR11856747", "SRX8406846", "SRS6719209", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf liver exposed to 350 mM Ethanol   clutch 1", "GSM4572113", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20", "5 dpf liver exposed to 350 mM Ethanol   clutch 1", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:16.4", "GSM4572113", "GSM4572113: LIV 2ETOH 1; Danio rerio; RNA Seq", "GSM4572113", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_2ETOH_1_S11_read2.fastq.gz LIV_2ETOH_1_S11_read1.fastq.gz", "fastq fastq", 5019400938.0, 17774097.0, "GSM4572113 r1", "0:141.13 1:141.27", "A:1309017001;C:1200452411;G:1214953253;T:1294219330;N:758943", 141, 141, null, null, 1309017001, 1200452411, 1214953253, 1294219330, 758943, "SRX8406846", "SRS6719209", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.95628, 0.95923, 0.05361, 0.05331, 0.80417, 0.81117, 0.45274, 0.46681, 131, 131, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59331, "SRR11856746", "SRX8406845", "SRS6719208", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf liver exposed to 175 mM Ethanol   clutch 1", "GSM4572112", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20", "5 dpf liver exposed to 175 mM  Ethanol   clutch 1", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "Larvae were anesthetized with tricane and 20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:9.34", "GSM4572112", "GSM4572112: LIV 1ETOH 1; Danio rerio; RNA Seq", "GSM4572112", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_1ETOH_1_S10_read2.fastq.gz LIV_1ETOH_1_S10_read1.fastq.gz", "fastq fastq", 5347733862.0, 18832427.0, "GSM4572112 r1", "0:141.93 1:142.03", "A:1419840934;C:1254883122;G:1270564370;T:1401639043;N:806393", 141, 142, null, null, 1419840934, 1254883122, 1270564370, 1401639043, 806393, "SRX8406845", "SRS6719208", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.96009, 0.96098, 0.06164, 0.06104, 0.81785, 0.82451, 0.51603, 0.52553, 151, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [59332, "SRR11856745", "SRX8406844", "SRS6719207", "SRP264975", "PRJNA635397", "Transcriptomic profiling of the liver from zebrafish larvae exposed to 175 mM and 350 mM ethanol for xxx hours collected at xxx hpf", "GSE151291", "Transcriptome Analysis", "Exposure to ethanol causes liver injury and activates stress response pathways. Here we compared gene expression in the zebrafish larval liver between larvae that were untreated and those exposed to 175 mM and 350 mM ethanol from xxx 120 hpf. Overall design: We utlized transgenic zebrafish larvae that express a fluorescent protein in the endoplasmic reticulum tgfabp10a: ER tdTomato specifically in hepatocytes as this is used to guide the microdisssection of larval livers. This experiment was conducted by natural spawnings between tg:fabp10:ER tdTomato and WT ABNYU and larvae were exposed from 96 hpf 120 hpf ttwo xxx   175 and 350 mM ethanol. We collected livers from 20 35 larvae for each condition and these were pooled for total RNA extraction using TRIZOL and library preparation using polyA selection as per manufacturer's instructions.  Samples were obtained from 5 separate clutches.  Samples were sequenced on NextSeq550 Illumina.", null, null, null, "5 dpf Untreated liver   clutch 1", "GSM4572111", null, "tissue:Liver|genotype:Tgfabp10a:ER tdTomato|pool:20", "5 dpf Untreated liver   clutch 1", "Illumina Casava1.8 software used for basecalling. The raw reads were quality assessed using FastQC  v0.11.5. The raw reads were then quality trimmed using Trimmomatic trimmomatic adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36 Alignments of trimmed reads were performed using tophat2  v2.1.0  with the parameters \u201c\u2013no novel junctions\u201d and \u201c\u2013G\u201d Accepted bam files were used for counting gene read numbers with HTSeq   a 10  s no Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor Genome build: GRCz10 Supplementary files format and content: .txt Reads count of genes", "Liver", "At  96 hpf  4 days post the embryos were collected  plates were treated with 1% and 2% Ethanol  Sigma Aldrich for 24 hour exposure with untreated as control. At 5 dpf  9 am the ethanol was washed out 3X  and treated with 500 uM tricaine Ethyl 3  aminobenzoate methanesulfonate  Sigma Aldrich  USA. Larvae were sorted for red liver positive and these fish were dissected in 3% methyl cellulose.", "20 35  livers were microdissected for each condition and immediately placed into 500 uL of TRIzol Thermo Fisher  15596026.RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc. RNA was quantified by Qubit flurometer.", "Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection  embryos were divided into 30 mL plates  60 embryos per plate in egg water at 28C in 10:14 light / dark cycle. Plates were cleaned to remove unfertilized or dead embryos.", "genotype:Tgfabp10a:ER tdTomato|pool:20|rna qbit concentrationng/ul:12.5", "GSM4572111", "GSM4572111: LIV UT 1; Danio rerio; RNA Seq", "GSM4572111", null, "1", "20 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions. RNA seq libraries treated with polyA were prepared by Mehar", "GEO Accession:GSM4572111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP264975", null, null, "LIV_UT_1_S9_read2.fastq.gz LIV_UT_1_S9_read1.fastq.gz", "fastq fastq", 4223733224.0, 14914881.0, "GSM4572111 r1", "0:141.51 1:141.68", "A:1130300439;C:980426283;G:997735889;T:1114572233;N:698380", 141, 141, null, null, 1130300439, 980426283, 997735889, 1114572233, 698380, "SRX8406844", "SRS6719207", "SRA1080364", "GEO", "Biology, New York University Abu Dhabi", 2, 0.9553, 0.95751, 0.06169, 0.06146, 0.80943, 0.81923, 0.51998, 0.50994, 151, 150, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Arab Emirates", "2020-05-27", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64402, "SRR14693488", "SRX11031603", "SRS9102420", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "10Replicate 1: Zebrafish was exposed to 20 ug/L cadmium water.", "L 20ul 1", "20ug Cd 1", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:10|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 20ug 1", "L 20ug 1", "Replicate 1: Zebrafish was exposed to 20 ug/L cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-20-1_1.fq.gz L-20-1_2.fq.gz", "fastq fastq", 9474023100.0, 31580077.0, "L 20 1 1.fq.gz", "0:150 1:150", "A:2507398715;C:2252082443;G:2227638071;T:2486773496;N:130375", 150, 150, null, null, 2507398715, 2252082443, 2227638071, 2486773496, 130375, "SRX11031603", "SRS9102420", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.93542, 0.93585, 0.01814, 0.0179, 0.8546, 0.85695, 0.19856, 0.19808, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64403, "SRR14693489", "SRX11031602", "SRS9102419", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "9Replicate 3: Zebrafish was exposed to 10 ug/L cadmium water.", "L 10ul 3", "10ug Cd 3", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 10ug 3", "L 10ug 3", "Replicate 3: Zebrafish was exposed to 10 ug/L cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-10-3_1.fq.gz L-10-3_2.fq.gz", "fastq fastq", 9151789800.0, 30505966.0, "L 10 3 1.fq.gz", "0:150 1:150", "A:2426773789;C:2174734982;G:2145008987;T:2405145887;N:126155", 150, 150, null, null, 2426773789, 2174734982, 2145008987, 2405145887, 126155, "SRX11031602", "SRS9102419", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.92781, 0.92778, 0.02775, 0.02769, 0.83339, 0.83782, 0.32765, 0.3323, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64404, "SRR14693490", "SRX11031601", "SRS9102417", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "8Replicate 2: Zebrafish was exposed to 10 ug/L cadmium water.", "L 10ul 2", "10ug Cd 2", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 10ug 2", "L 10ug 2", "Replicate 2: Zebrafish was exposed to 10 ug/L cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-10-2_1.fq.gz L-10-2_2.fq.gz", "fastq fastq", 9227241600.0, 30757472.0, "L 10 2 1.fq.gz", "0:150 1:150", "A:2446195454;C:2194133974;G:2162408521;T:2424376012;N:127639", 150, 150, null, null, 2446195454, 2194133974, 2162408521, 2424376012, 127639, "SRX11031601", "SRS9102417", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.93861, 0.93883, 0.02665, 0.02699, 0.82964, 0.83266, 0.34166, 0.34402, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64405, "SRR14693491", "SRX11031600", "SRS9102418", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "7Replicate 1: Zebrafish was exposed to 10 ug/L cadmium water.", "L 10ul 1", "10ug Cd 1", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 10ug 1", "L 10ug 1", "Replicate 1: Zebrafish was exposed to 10 ug/L cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-10-1_1.fq.gz L-10-1_2.fq.gz", "fastq fastq", 9953955000.0, 33179850.0, "L 10 1 1.fq.gz", "0:150 1:150", "A:2634231234;C:2372235006;G:2336820401;T:2610532208;N:136151", 150, 150, null, null, 2634231234, 2372235006, 2336820401, 2610532208, 136151, "SRX11031600", "SRS9102418", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.93022, 0.93036, 0.02647, 0.02638, 0.82528, 0.82893, 0.35069, 0.34799, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64406, "SRR14693492", "SRX11031599", "SRS9102416", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "6Replicate 3: Zebrafish was exposed to 5 ug/L cadmium water.", "L 5ul 3", "5ug Cd 3", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 5ug 3", "L 5ug 3", "Replicate 3: Zebrafish was exposed to 5 ug/L cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-5-3_1.fq.gz L-5-3_2.fq.gz", "fastq fastq", 10510383300.0, 35034611.0, "L 5 3 1.fq.gz", "0:150 1:150", "A:2780249486;C:2506463997;G:2468678073;T:2754845377;N:146367", 150, 150, null, null, 2780249486, 2506463997, 2468678073, 2754845377, 146367, "SRX11031599", "SRS9102416", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.93599, 0.93675, 0.02788, 0.028, 0.82826, 0.83134, 0.3691, 0.36755, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64407, "SRR14693493", "SRX11031598", "SRS9102415", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "5Replicate 2: Zebrafish was exposed to 5 ug/L cadmium water.", "L 5ul 2", "5ug Cd 2", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 5ug 2", "L 5ug 2", "Replicate 2: Zebrafish was exposed to 5 ug/L cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-5-2_1.fq.gz L-5-2_2.fq.gz", "fastq fastq", 9663058500.0, 32210195.0, "L 5 2 1.fq.gz", "0:150 1:150", "A:2566225232;C:2292358860;G:2261409980;T:2542931680;N:132748", 150, 150, null, null, 2566225232, 2292358860, 2261409980, 2542931680, 132748, "SRX11031598", "SRS9102415", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.9279, 0.92716, 0.03066, 0.03036, 0.84064, 0.84469, 0.29604, 0.29012, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64408, "SRR14693494", "SRX11031597", "SRS9102414", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "4Replicate 1: Zebrafish was exposed to 5 ug/L cadmium water.", "L 5ul 1", "5ug Cd 1", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 5ug 1", "L 5ug 1", "Replicate 1: Zebrafish was exposed to 5 ug/L cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-5-1_1.fq.gz L-5-1_2.fq.gz", "fastq fastq", 9511116000.0, 31703720.0, "L 5 1 1.fq.gz", "0:150 1:150", "A:2522646698;C:2260594111;G:2228650384;T:2499094495;N:130312", 150, 150, null, null, 2522646698, 2260594111, 2228650384, 2499094495, 130312, "SRX11031597", "SRS9102414", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.92788, 0.92717, 0.02999, 0.03034, 0.83126, 0.8351, 0.33408, 0.32916, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64409, "SRR14693495", "SRX11031596", "SRS9102413", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "3Replicate 3: Zebrafish was exposed to non cadmium water.", "L 0ul 3", "Control 3", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 0ug 3", "L 0ug 3", "Replicate 3: Zebrafish was exposed to non cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-0-3_1.fq.gz L-0-3_2.fq.gz", "fastq fastq", 7654392600.0, 25514642.0, "L 0 3 1.fq.gz", "0:150 1:150", "A:2032769604;C:1821251953;G:1783264200;T:2016799319;N:307524", 150, 150, null, null, 2032769604, 1821251953, 1783264200, 2016799319, 307524, "SRX11031596", "SRS9102413", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.91721, 0.91751, 0.04656, 0.04603, 0.79565, 0.80117, 0.55344, 0.49994, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64410, "SRR14693496", "SRX11031595", "SRS9102412", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "12Replicate 3: Zebrafish was exposed to 20 ug/L cadmium water.", "L 20ul 3", "20ug Cd 3", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:12|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 20ug 3", "L 20ug 3", "Replicate 3: Zebrafish was exposed to 20 ug/L cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-20-3_1.fq.gz L-20-3_2.fq.gz", "fastq fastq", 11570116200.0, 38567054.0, "L 20 3 1.fq.gz", "0:150 1:150", "A:3068598229;C:2743734564;G:2712429005;T:3045193228;N:161174", 150, 150, null, null, 3068598229, 2743734564, 2712429005, 3045193228, 161174, "SRX11031595", "SRS9102412", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.94888, 0.94877, 0.01872, 0.0183, 0.84774, 0.85137, 0.20467, 0.21064, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64411, "SRR14693497", "SRX11031594", "SRS9102411", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "11Replicate 2: Zebrafish was exposed to 20 ug/L cadmium water.", "L 20ul 2", "20ug Cd 2", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:11|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 20ug 2", "L 20ug 2", "Replicate 2: Zebrafish was exposed to 20 ug/L cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-20-2_1.fq.gz L-20-2_2.fq.gz", "fastq fastq", 9841853700.0, 32806179.0, "L 20 2 1.fq.gz", "0:150 1:150", "A:2608034663;C:2337766225;G:2312575335;T:2583339974;N:137503", 150, 150, null, null, 2608034663, 2337766225, 2312575335, 2583339974, 137503, "SRX11031594", "SRS9102411", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.94246, 0.94248, 0.01874, 0.01896, 0.84666, 0.85054, 0.21152, 0.20874, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64412, "SRR14693498", "SRX11031593", "SRS9102410", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "2Replicate 2: Zebrafish was exposed to non cadmium water.", "L 0ul 2", "Control 2", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 0ug 2", "L 0ug 2", "Replicate 2: Zebrafish was exposed to non cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-0-2_1.fq.gz L-0-2_2.fq.gz", "fastq fastq", 7597792500.0, 25325975.0, "L 0 2 1.fq.gz", "0:150 1:150", "A:2013644367;C:1811649004;G:1773238271;T:1998958516;N:302342", 150, 150, null, null, 2013644367, 1811649004, 1773238271, 1998958516, 302342, "SRX11031593", "SRS9102410", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.92149, 0.92172, 0.04905, 0.04968, 0.78983, 0.79373, 0.54893, 0.54061, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [64413, "SRR14693499", "SRX11031592", "SRS9102409", "SRP322002", "PRJNA733995", "Transcriptome of zebrafish", "PRJNA733995", "Other", "Transcriptomic responses in the liver of zebrafish exposed to 0  5  10 and 20 ug/L", null, null, "1Replicate 1: Zebrafish was exposed to non cadmium water.", "L 0ul 1", "Control 1", null, "strain:AB line|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:62 days|dev stage:adult|sex:missing|tissue:Liver|treatment:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish to Cd change", "L 0ug 1", "L 0ug 1", "Replicate 1: Zebrafish was exposed to non cadmium water.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP322002", null, null, "L-0-1_1.fq.gz L-0-1_2.fq.gz", "fastq fastq", 7864294200.0, 26214314.0, "L 0 1 1.fq.gz", "0:150 1:150", "A:2079682755;C:1878602959;G:1839465846;T:2066231062;N:311578", 150, 150, null, null, 2079682755, 1878602959, 1839465846, 2066231062, 311578, "SRX11031592", "SRS9102409", "SRA1238751", "Zhejiang Ocean University|School of Marine Science and Technology", "Zhejiang Ocean University", 2, 0.92722, 0.92694, 0.04229, 0.04234, 0.80659, 0.80894, 0.55648, 0.56618, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-05-31", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71949, "SRR22143703", "SRX18123015", "SRS15624889", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "liver adult male dnvdra rep4", "GSM6705373", null, "tissue:liver dissected|cell type:liver dissected|genotype:fabp10a:dn vdra|time:4.5 mpf", "liver adult male dnvdra rep4", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "liver dissected", null, "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:liver dissected|genotype:fabp10a:dn vdra|time:4.5 mpf", "GSM6705373", "GSM6705373: liver adult male dnvdra rep4; Danio rerio; RNA Seq", "GSM6705373 r1", "GSM6705373", "1", "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "dnvdra_adult_rep4_R1.fastq.gz dnvdra_adult_rep4_R2.fastq.gz", "fastq fastq", 7306840200.0, 24356134.0, "GSM6705373 r1", "0:150 1:150", "A:1634647728;C:2022515119;G:2117265738;T:1531516499;N:895116", 150, 150, null, null, 1634647728, 2022515119, 2117265738, 1531516499, 895116, "SRX18123015", "SRS15624889", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.9391, 0.94285, 0.23119, 0.22942, 0.8271, 0.8322, 0.69581, 0.68762, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71950, "SRR22143704", "SRX18123014", "SRS15624888", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "liver adult male dnvdra rep3", "GSM6705372", null, "tissue:liver dissected|cell type:liver dissected|genotype:fabp10a:dn vdra|time:4.5 mpf", "liver adult male dnvdra rep3", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "liver dissected", null, "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:liver dissected|genotype:fabp10a:dn vdra|time:4.5 mpf", "GSM6705372", "GSM6705372: liver adult male dnvdra rep3; Danio rerio; RNA Seq", "GSM6705372 r1", "GSM6705372", "1", "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "dnvdra_adult_rep3_R1.fastq.gz dnvdra_adult_rep3_R2.fastq.gz", "fastq fastq", 9479471100.0, 31598237.0, "GSM6705372 r1", "0:150 1:150", "A:2405849550;C:2317260206;G:2431705693;T:2323757766;N:897885", 150, 150, null, null, 2405849550, 2317260206, 2431705693, 2323757766, 897885, "SRX18123014", "SRS15624888", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.93979, 0.94112, 0.24887, 0.24751, 0.81387, 0.81925, 0.64579, 0.66305, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71951, "SRR22143705", "SRX18123013", "SRS15624887", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "liver adult male dnvdra rep2", "GSM6705371", null, "tissue:liver dissected|cell type:liver dissected|genotype:fabp10a:dn vdra|time:4.5 mpf", "liver adult male dnvdra rep2", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "liver dissected", null, "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:liver dissected|genotype:fabp10a:dn vdra|time:4.5 mpf", "GSM6705371", "GSM6705371: liver adult male dnvdra rep2; Danio rerio; RNA Seq", "GSM6705371 r1", "GSM6705371", "1", "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "dnvdra_adult_rep2_R1.fastq.gz dnvdra_adult_rep2_R2.fastq.gz", "fastq fastq", 8869425900.0, 29564753.0, "GSM6705371 r1", "0:150 1:150", "A:2267704368;C:2156453672;G:2240562899;T:2203642179;N:1062782", 150, 150, null, null, 2267704368, 2156453672, 2240562899, 2203642179, 1062782, "SRX18123013", "SRS15624887", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.93845, 0.93921, 0.27865, 0.27576, 0.7853, 0.79162, 0.61608, 0.63768, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71952, "SRR22143706", "SRX18123012", "SRS15624886", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "liver adult male dnvdra rep1", "GSM6705370", null, "tissue:liver dissected|cell type:liver dissected|genotype:fabp10a:dn vdra|time:4.5 mpf", "liver adult male dnvdra rep1", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "liver dissected", null, "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:liver dissected|genotype:fabp10a:dn vdra|time:4.5 mpf", "GSM6705370", "GSM6705370: liver adult male dnvdra rep1; Danio rerio; RNA Seq", "GSM6705370 r1", "GSM6705370", "1", "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "dnvdra_adult_rep1_R1.fastq.gz dnvdra_adult_rep1_R2.fastq.gz", "fastq fastq", 8759752200.0, 29199174.0, "GSM6705370 r1", "0:150 1:150", "A:2264343597;C:2102066713;G:2185344986;T:2207175493;N:821411", 150, 150, null, null, 2264343597, 2102066713, 2185344986, 2207175493, 821411, "SRX18123012", "SRS15624886", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.93769, 0.93817, 0.24989, 0.24753, 0.81481, 0.8202, 0.63281, 0.63874, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71953, "SRR22143707", "SRX18123011", "SRS15624885", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "liver adult male wt rep4", "GSM6705369", null, "tissue:liver dissected|cell type:liver dissected|genotype:wt|time:4.5 mpf", "liver adult male wt rep4", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "liver dissected", null, "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:liver dissected|genotype:wt|time:4.5 mpf", "GSM6705369", "GSM6705369: liver adult male wt rep4; Danio rerio; RNA Seq", "GSM6705369 r1", "GSM6705369", "1", "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "wt_adult_rep4_R1.fastq.gz wt_adult_rep4_R2.fastq.gz", "fastq fastq", 7872584100.0, 26241947.0, "GSM6705369 r1", "0:150 1:150", "A:1865503313;C:2068473857;G:2151329739;T:1786324155;N:953036", 150, 150, null, null, 1865503313, 2068473857, 2151329739, 1786324155, 953036, "SRX18123011", "SRS15624885", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.9447, 0.94715, 0.22373, 0.22171, 0.79864, 0.80549, 0.65508, 0.66645, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71954, "SRR22143708", "SRX18123010", "SRS15624884", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "liver adult male wt rep3", "GSM6705368", null, "tissue:liver dissected|cell type:liver dissected|genotype:wt|time:4.5 mpf", "liver adult male wt rep3", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "liver dissected", null, "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:liver dissected|genotype:wt|time:4.5 mpf", "GSM6705368", "GSM6705368: liver adult male wt rep3; Danio rerio; RNA Seq", "GSM6705368 r1", "GSM6705368", "1", "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "wt_adult_rep3_R1.fastq.gz wt_adult_rep3_R2.fastq.gz", "fastq fastq", 9680029200.0, 32266764.0, "GSM6705368 r1", "0:150 1:150", "A:2443094631;C:2377026277;G:2498468205;T:2360520382;N:919705", 150, 150, null, null, 2443094631, 2377026277, 2498468205, 2360520382, 919705, "SRX18123010", "SRS15624884", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.94453, 0.9447, 0.23051, 0.22889, 0.8201, 0.82572, 0.64982, 0.66988, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71955, "SRR22143709", "SRX18123009", "SRS15624883", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "liver adult male wt rep2", "GSM6705367", null, "tissue:liver dissected|cell type:liver dissected|genotype:wt|time:4.5 mpf", "liver adult male wt rep2", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "liver dissected", null, "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:liver dissected|genotype:wt|time:4.5 mpf", "GSM6705367", "GSM6705367: liver adult male wt rep2; Danio rerio; RNA Seq", "GSM6705367 r1", "GSM6705367", "1", "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "wt_adult_rep2_R1.fastq.gz wt_adult_rep2_R2.fastq.gz", "fastq fastq", 8892641100.0, 29642137.0, "GSM6705367 r1", "0:150 1:150", "A:2163882206;C:2269881186;G:2365476524;T:2092339476;N:1061708", 150, 150, null, null, 2163882206, 2269881186, 2365476524, 2092339476, 1061708, "SRX18123009", "SRS15624883", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.94617, 0.94758, 0.23159, 0.22967, 0.81491, 0.8227, 0.65719, 0.658, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71956, "SRR22143710", "SRX18123008", "SRS15624882", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "liver adult male wt rep1", "GSM6705366", null, "tissue:liver dissected|cell type:liver dissected|genotype:wt|time:4.5 mpf", "liver adult male wt rep1", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "liver dissected", null, "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:liver dissected|genotype:wt|time:4.5 mpf", "GSM6705366", "GSM6705366: liver adult male wt rep1; Danio rerio; RNA Seq", "GSM6705366 r1", "GSM6705366", "1", "Adult livers were dissected following euthanasia  and RNA was extracted using TRIZOL reagent ThermoFisher Scientific. Libraries were constructed using the NEBNext Ultra II RNA Library Preparation Kit Illumina following DNase treatment and rRNA depletion using the QIAseq\u00ae FastSelectTM\u2212rRNA HMR kit Qiagen.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "wt_adult_rep1_R1.fastq.gz wt_adult_rep1_R2.fastq.gz", "fastq fastq", 9582971400.0, 31943238.0, "GSM6705366 r1", "0:150 1:150", "A:2419330244;C:2350798107;G:2466673851;T:2345262587;N:906611", 150, 150, null, null, 2419330244, 2350798107, 2466673851, 2345262587, 906611, "SRX18123008", "SRS15624882", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.93855, 0.94009, 0.2557, 0.25425, 0.80673, 0.81268, 0.62408, 0.64101, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "rrna_depletion", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71957, "SRR22143711", "SRX18123007", "SRS15624881", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf cavdra expt2 rep3", "GSM6705365", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf", "hepatocytes 96hpf cavdra expt2 rep3", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf", "GSM6705365", "GSM6705365: hepatocytes 96hpf cavdra expt2 rep3; Danio rerio; RNA Seq", "GSM6705365 r1", "GSM6705365", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP405931", null, null, "cavdra_expt2_rep3_R1.fastq.gz", "fastq", 6706002750.0, 44706685.0, "GSM6705365 r1", "0:150 1:0", "A:1750156238;C:1597023915;G:1614921548;T:1743765130;N:135919", 150, 0, null, null, 1750156238, 1597023915, 1614921548, 1743765130, 135919, "SRX18123007", "SRS15624881", null, null, "Goessling Lab, Brigham and Women's Hospital", 1, 0.88313, null, 0.04409, null, 0.87661, null, 0.55505, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71958, "SRR22143712", "SRX18123006", "SRS15624880", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf cavdra expt2 rep2", "GSM6705364", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf", "hepatocytes 96hpf cavdra expt2 rep2", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf", "GSM6705364", "GSM6705364: hepatocytes 96hpf cavdra expt2 rep2; Danio rerio; RNA Seq", "GSM6705364 r1", "GSM6705364", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP405931", null, null, "cavdra_expt2_rep2_R1.fastq.gz", "fastq", 7680154500.0, 51201030.0, "GSM6705364 r1", "0:150 1:0", "A:1982779701;C:1851808902;G:1881749764;T:1963662978;N:153155", 150, 0, null, null, 1982779701, 1851808902, 1881749764, 1963662978, 153155, "SRX18123006", "SRS15624880", null, null, "Goessling Lab, Brigham and Women's Hospital", 1, 0.8513, null, 0.05087, null, 0.8756, null, 0.58342, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71959, "SRR22143713", "SRX18123005", "SRS15624879", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf cavdra expt2 rep1", "GSM6705363", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf", "hepatocytes 96hpf cavdra expt2 rep1", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:fabp10a:ca vdra|time:96 hpf", "GSM6705363", "GSM6705363: hepatocytes 96hpf cavdra expt2 rep1; Danio rerio; RNA Seq", "GSM6705363 r1", "GSM6705363", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP405931", null, null, "cavdra_expt2_rep1_R1.fastq.gz", "fastq", 8901213300.0, 59341422.0, "GSM6705363 r1", "0:150 1:0", "A:2306334188;C:2127419797;G:2168880418;T:2298400416;N:178481", 150, 0, null, null, 2306334188, 2127419797, 2168880418, 2298400416, 178481, "SRX18123005", "SRS15624879", null, null, "Goessling Lab, Brigham and Women's Hospital", 1, 0.90473, null, 0.05586, null, 0.88347, null, 0.56493, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71960, "SRR22143714", "SRX18123004", "SRS15624878", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf wt expt2 rep4", "GSM6705362", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "hepatocytes 96hpf wt expt2 rep4", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "GSM6705362", "GSM6705362: hepatocytes 96hpf wt expt2 rep4; Danio rerio; RNA Seq", "GSM6705362 r1", "GSM6705362", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP405931", null, null, "wt_expt2_rep4_R1.fastq.gz", "fastq", 11932077600.0, 79547184.0, "GSM6705362 r1", "0:150 1:0", "A:3141493904;C:2835740238;G:2863257406;T:3091339595;N:246457", 150, 0, null, null, 3141493904, 2835740238, 2863257406, 3091339595, 246457, "SRX18123004", "SRS15624878", null, null, "Goessling Lab, Brigham and Women's Hospital", 1, 0.88366, null, 0.04537, null, 0.88185, null, 0.58207, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71961, "SRR22143715", "SRX18123003", "SRS15624877", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf wt expt2 rep3", "GSM6705361", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "hepatocytes 96hpf wt expt2 rep3", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "GSM6705361", "GSM6705361: hepatocytes 96hpf wt expt2 rep3; Danio rerio; RNA Seq", "GSM6705361 r1", "GSM6705361", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP405931", null, null, "wt_expt2_rep3_R1.fastq.gz", "fastq", 9232946100.0, 61552974.0, "GSM6705361 r1", "0:150 1:0", "A:2407612258;C:2198887087;G:2229947120;T:2396306352;N:193283", 150, 0, null, null, 2407612258, 2198887087, 2229947120, 2396306352, 193283, "SRX18123003", "SRS15624877", null, null, "Goessling Lab, Brigham and Women's Hospital", 1, 0.87181, null, 0.05876, null, 0.87864, null, 0.58855, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71962, "SRR22143716", "SRX18123002", "SRS15624876", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf wt expt2 rep2", "GSM6705360", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "hepatocytes 96hpf wt expt2 rep2", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "GSM6705360", "GSM6705360: hepatocytes 96hpf wt expt2 rep2; Danio rerio; RNA Seq", "GSM6705360 r1", "GSM6705360", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP405931", null, null, "wt_expt2_rep2_R1.fastq.gz", "fastq", 6185704050.0, 41238027.0, "GSM6705360 r1", "0:150 1:0", "A:1603435702;C:1515988796;G:1488677966;T:1577474793;N:126793", 150, 0, null, null, 1603435702, 1515988796, 1488677966, 1577474793, 126793, "SRX18123002", "SRS15624876", null, null, "Goessling Lab, Brigham and Women's Hospital", 1, 0.78101, null, 0.04338, null, 0.88266, null, 0.5608, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71963, "SRR22143717", "SRX18123001", "SRS15624875", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf wt expt2 rep1", "GSM6705359", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "hepatocytes 96hpf wt expt2 rep1", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "GSM6705359", "GSM6705359: hepatocytes 96hpf wt expt2 rep1; Danio rerio; RNA Seq", "GSM6705359 r1", "GSM6705359", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP405931", null, null, "wt_expt2_rep1_R1.fastq.gz", "fastq", 6197680950.0, 41317873.0, "GSM6705359 r1", "0:150 1:0", "A:1603637872;C:1495661601;G:1502876654;T:1595377016;N:127807", 150, 0, null, null, 1603637872, 1495661601, 1502876654, 1595377016, 127807, "SRX18123001", "SRS15624875", null, null, "Goessling Lab, Brigham and Women's Hospital", 1, 0.86333, null, 0.05099, null, 0.88919, null, 0.56132, null, 150, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71964, "SRR22143718", "SRX18123000", "SRS15624874", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf dnvdra expt1 rep4", "GSM6705358", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf", "hepatocytes 96hpf dnvdra expt1 rep4", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf", "GSM6705358", "GSM6705358: hepatocytes 96hpf dnvdra expt1 rep4; Danio rerio; RNA Seq", "GSM6705358 r1", "GSM6705358", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "dnvdra_expt1_rep4_R1.fastq.gz dnvdra_expt1_rep4_R2.fastq.gz", "fastq fastq", 18831415800.0, 62771386.0, "GSM6705358 r1", "0:150 1:150", "A:4640361931;C:4661552439;G:4707320281;T:4820985318;N:1195831", 150, 150, null, null, 4640361931, 4661552439, 4707320281, 4820985318, 1195831, "SRX18123000", "SRS15624874", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.94748, 0.94729, 0.03313, 0.03287, 0.79719, 0.79945, 0.47574, 0.47792, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71965, "SRR22143719", "SRX18122999", "SRS15624873", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf dnvdra expt1 rep3", "GSM6705357", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf", "hepatocytes 96hpf dnvdra expt1 rep3", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf", "GSM6705357", "GSM6705357: hepatocytes 96hpf dnvdra expt1 rep3; Danio rerio; RNA Seq", "GSM6705357 r1", "GSM6705357", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "dnvdra_expt1_rep3_R1.fastq.gz dnvdra_expt1_rep3_R2.fastq.gz", "fastq fastq", 16955597400.0, 56518658.0, "GSM6705357 r1", "0:150 1:150", "A:4191429329;C:4181155612;G:4191314524;T:4390631329;N:1066606", 150, 150, null, null, 4191429329, 4181155612, 4191314524, 4390631329, 1066606, "SRX18122999", "SRS15624873", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.94938, 0.94935, 0.0338, 0.03364, 0.79545, 0.79695, 0.48365, 0.48166, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71966, "SRR22143720", "SRX18122998", "SRS15624872", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf dnvdra expt1 rep2", "GSM6705356", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf", "hepatocytes 96hpf dnvdra expt1 rep2", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf", "GSM6705356", "GSM6705356: hepatocytes 96hpf dnvdra expt1 rep2; Danio rerio; RNA Seq", "GSM6705356 r1", "GSM6705356", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "dnvdra_expt1_rep2_R1.fastq.gz dnvdra_expt1_rep2_R2.fastq.gz", "fastq fastq", 17388104700.0, 57960349.0, "GSM6705356 r1", "0:150 1:150", "A:4247868125;C:4323132556;G:4325289881;T:4490744969;N:1069169", 150, 150, null, null, 4247868125, 4323132556, 4325289881, 4490744969, 1069169, "SRX18122998", "SRS15624872", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.94837, 0.94745, 0.03174, 0.03157, 0.79184, 0.79381, 0.47513, 0.47039, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71967, "SRR22143721", "SRX18122997", "SRS15624871", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf dnvdra expt1 rep1", "GSM6705355", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf", "hepatocytes 96hpf dnvdra expt1 rep1", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:fabp10a:dn vdra|time:96 hpf", "GSM6705355", "GSM6705355: hepatocytes 96hpf dnvdra expt1 rep1; Danio rerio; RNA Seq", "GSM6705355 r1", "GSM6705355", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "dnvdra_expt1_rep1_R1.fastq.gz dnvdra_expt1_rep1_R2.fastq.gz", "fastq fastq", 18386589600.0, 61288632.0, "GSM6705355 r1", "0:150 1:150", "A:4509534555;C:4473109680;G:4706080457;T:4696713250;N:1151658", 150, 150, null, null, 4509534555, 4473109680, 4706080457, 4696713250, 1151658, "SRX18122997", "SRS15624871", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.94402, 0.94369, 0.03471, 0.03448, 0.79478, 0.7964, 0.43544, 0.43575, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71968, "SRR22143722", "SRX18122996", "SRS15624870", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf wt expt1 rep4", "GSM6705354", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "hepatocytes 96hpf wt expt1 rep4", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "GSM6705354", "GSM6705354: hepatocytes 96hpf wt expt1 rep4; Danio rerio; RNA Seq", "GSM6705354 r1", "GSM6705354", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "wt_expt1_rep4_R1.fastq.gz wt_expt1_rep4_R2.fastq.gz", "fastq fastq", 14844320700.0, 49481069.0, "GSM6705354 r1", "0:150 1:150", "A:3676168506;C:3664928523;G:3671171564;T:3831144092;N:908015", 150, 150, null, null, 3676168506, 3664928523, 3671171564, 3831144092, 908015, "SRX18122996", "SRS15624870", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.94938, 0.94888, 0.02974, 0.02976, 0.80444, 0.80614, 0.47385, 0.42037, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71969, "SRR22143723", "SRX18122995", "SRS15624869", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf wt expt1 rep3", "GSM6705353", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "hepatocytes 96hpf wt expt1 rep3", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "GSM6705353", "GSM6705353: hepatocytes 96hpf wt expt1 rep3; Danio rerio; RNA Seq", "GSM6705353 r1", "GSM6705353", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "wt_expt1_rep3_R1.fastq.gz wt_expt1_rep3_R2.fastq.gz", "fastq fastq", 16613218800.0, 55377396.0, "GSM6705353 r1", "0:150 1:150", "A:4069624360;C:4165320060;G:4040198029;T:4337025346;N:1051005", 150, 150, null, null, 4069624360, 4165320060, 4040198029, 4337025346, 1051005, "SRX18122995", "SRS15624869", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.94839, 0.94783, 0.03158, 0.03154, 0.79703, 0.79859, 0.41789, 0.4109, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71970, "SRR22143724", "SRX18122994", "SRS15624868", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf wt expt1 rep2", "GSM6705352", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "hepatocytes 96hpf wt expt1 rep2", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "GSM6705352", "GSM6705352: hepatocytes 96hpf wt expt1 rep2; Danio rerio; RNA Seq", "GSM6705352 r1", "GSM6705352", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "wt_expt1_rep2_R1.fastq.gz wt_expt1_rep2_R2.fastq.gz", "fastq fastq", 15406857900.0, 51356193.0, "GSM6705352 r1", "0:150 1:150", "A:3790021506;C:3872684076;G:3750856541;T:3992308410;N:987367", 150, 150, null, null, 3790021506, 3872684076, 3750856541, 3992308410, 987367, "SRX18122994", "SRS15624868", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.94749, 0.94642, 0.02824, 0.02814, 0.80044, 0.80275, 0.41703, 0.46905, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [71971, "SRR22143725", "SRX18122993", "SRS15624867", "SRP405931", "PRJNA896973", "Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish", "GSE217120", "Transcriptome Analysis", "Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity  but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates  this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation  respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra  N = 4 wt  4 dn vdra. For fabp10a:ca vdra  N = 4 wt  3 ca vdra. For adult fabp10a:dn vdra  N = 4 wt  4 dn vdra.", null, "pubmed:38944835", null, "hepatocytes 96hpf wt expt1 rep1", "GSM6705351", null, "tissue:hepatocytes sorted|cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "hepatocytes 96hpf wt expt1 rep1", "FASTQ files were mapped to GRCz11 using STAR v2.5.3  and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids  gene names  and raw read counts or normalized read counts for each experiment", "hepatocytes sorted", null, "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", "Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.", "cell type:hepatocytes sorted|genotype:wt|time:96 hpf", "GSM6705351", "GSM6705351: hepatocytes 96hpf wt expt1 rep1; Danio rerio; RNA Seq", "GSM6705351 r1", "GSM6705351", "1", "Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. The SMART Seq v4 Ultra Low Input Kit for Sequencing Clontech kit was used for cDNA synthesis and amplification. Library prep was performed with the Nextera XT DNA Library Preparation Kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP405931", null, "loader:fastq load.py", "wt_expt1_rep1_R1.fastq.gz wt_expt1_rep1_R2.fastq.gz", "fastq fastq", 17241539100.0, 57471797.0, "GSM6705351 r1", "0:150 1:150", "A:4266092960;C:4150739925;G:4403086295;T:4420536893;N:1083027", 150, 150, null, null, 4266092960, 4150739925, 4403086295, 4420536893, 1083027, "SRX18122993", "SRS15624867", null, null, "Goessling Lab, Brigham and Women's Hospital", 2, 0.9395, 0.93854, 0.03615, 0.03586, 0.79715, 0.79906, 0.48099, 0.46325, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-11-02", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72451, "SRR22557572", "SRX18521038", "SRS15989662", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Kras mutant  5", "GSM6797836", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "Kras mutant  5", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "GSM6797836", "GSM6797836: Kras mutant  5; Danio rerio; RNA Seq", "GSM6797836 r1", "GSM6797836", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-K-5_S3_R1.fastq.gz WT-K-5_S3_R2.fastq.gz", "fastq fastq", 10898543916.0, 67633543.0, "GSM6797836 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX18521038", "SRS15989662", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.82302, 0.82403, 0.12041, 0.1167, 0.74911, 0.74897, 0.60698, 0.60654, 81, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72452, "SRR22557573", "SRX18521037", "SRS15989661", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Kras mutant  4", "GSM6797835", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "Kras mutant  4", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "GSM6797835", "GSM6797835: Kras mutant  4; Danio rerio; RNA Seq", "GSM6797835 r1", "GSM6797835", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-K-4_S2_R1.fastq.gz WT-K-4_S2_R2.fastq.gz", "fastq fastq", 7655029282.0, 47511116.0, "GSM6797835 r1", "0:80.57 1:80.55", "A:1892530644;C:1907240207;G:1927504602;T:1903942969;N:23810860", 80, 80, null, null, 1892530644, 1907240207, 1927504602, 1903942969, 23810860, "SRX18521037", "SRS15989661", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.80396, 0.80676, 0.11491, 0.11268, 0.75081, 0.75294, 0.60481, 0.60191, 81, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72453, "SRR22557574", "SRX18521036", "SRS15989660", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Kras mutant  3", "GSM6797834", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "Kras mutant  3", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "GSM6797834", "GSM6797834: Kras mutant  3; Danio rerio; RNA Seq", "GSM6797834 r1", "GSM6797834", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-K-3a_S9_R1.fastq.gz WT-K-3a_S9_R2.fastq.gz", "fastq fastq", 4679215613.0, 29024683.0, "GSM6797834 r1", "0:80.62 1:80.60", "A:1238886777;C:1096377570;G:1088561790;T:1240201926;N:15187550", 80, 80, null, null, 1238886777, 1096377570, 1088561790, 1240201926, 15187550, "SRX18521036", "SRS15989660", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.88846, 0.88798, 0.12969, 0.12529, 0.74566, 0.7455, 0.59597, 0.59105, 81, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72454, "SRR22557575", "SRX18521036", "SRS15989660", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Kras mutant  3", "GSM6797834", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "Kras mutant  3", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "GSM6797834", "GSM6797834: Kras mutant  3; Danio rerio; RNA Seq", "GSM6797834 r1", "GSM6797834", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-K-3b_S6_R1.fastq.gz WT-K-3b_S6_R2.fastq.gz", "fastq fastq", 126178415.0, 782575.0, "GSM6797834 r2", "0:80.62 1:80.61", "A:33725497;C:29453850;G:29082084;T:33561572;N:355412", 80, 80, null, null, 33725497, 29453850, 29082084, 33561572, 355412, "SRX18521036", "SRS15989660", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.89216, 0.8883, 0.13334, 0.12896, 0.74734, 0.74854, 0.596, 0.60101, 81, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72455, "SRR22557576", "SRX18521035", "SRS15989659", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Kras mutant  2", "GSM6797833", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "Kras mutant  2", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "GSM6797833", "GSM6797833: Kras mutant  2; Danio rerio; RNA Seq", "GSM6797833 r1", "GSM6797833", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-K-2a_S8_R1.fastq.gz WT-K-2a_S8_R2.fastq.gz", "fastq fastq", 3780404641.0, 23451132.0, "GSM6797833 r1", "0:80.61 1:80.59", "A:990271510;C:893620129;G:894553065;T:989503144;N:12456793", 80, 80, null, null, 990271510, 893620129, 894553065, 989503144, 12456793, "SRX18521035", "SRS15989659", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.88057, 0.88033, 0.12551, 0.12121, 0.75921, 0.75988, 0.5921, 0.6028, 81, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72456, "SRR22557577", "SRX18521035", "SRS15989659", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Kras mutant  2", "GSM6797833", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "Kras mutant  2", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "GSM6797833", "GSM6797833: Kras mutant  2; Danio rerio; RNA Seq", "GSM6797833 r1", "GSM6797833", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-K-2b_S5_R1.fastq.gz WT-K-2b_S5_R2.fastq.gz", "fastq fastq", 9606289747.0, 59586901.0, "GSM6797833 r2", "0:80.61 1:80.60", "A:2527629403;C:2272978634;G:2266766879;T:2511222021;N:27692810", 80, 80, null, null, 2527629403, 2272978634, 2266766879, 2511222021, 27692810, "SRX18521035", "SRS15989659", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.88377, 0.87989, 0.12629, 0.12147, 0.75852, 0.75887, 0.59511, 0.59638, 80, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72457, "SRR22557578", "SRX18521034", "SRS15989658", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Kras mutant  1", "GSM6797832", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "Kras mutant  1", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:kras mutant|treatment:Doxycycline 20mg/L from 2 dpf 7 dpf dpf", "GSM6797832", "GSM6797832: Kras mutant  1; Danio rerio; RNA Seq", "GSM6797832 r1", "GSM6797832", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-K-1_S7_R1.fastq.gz WT-K-1_S7_R2.fastq.gz", "fastq fastq", 6310086758.0, 39142872.0, "GSM6797832 r1", "0:80.61 1:80.59", "A:1661179611;C:1483976667;G:1479855032;T:1664432305;N:20643143", 80, 80, null, null, 1661179611, 1483976667, 1479855032, 1664432305, 20643143, "SRX18521034", "SRS15989658", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.88894, 0.88565, 0.13872, 0.13431, 0.74651, 0.74637, 0.58405, 0.58555, 81, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72458, "SRR22557579", "SRX18521033", "SRS15989657", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Wild type  3", "GSM6797831", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "Wild type  3", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "GSM6797831", "GSM6797831: Wild type  3; Danio rerio; RNA Seq", "GSM6797831 r1", "GSM6797831", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-3a_S3_R1.fastq.gz WT-3a_S3_R2.fastq.gz", "fastq fastq", 2105570529.0, 13074176.0, "GSM6797831 r1", "0:80.54 1:80.51", "A:506818232;C:537965374;G:544917139;T:507855461;N:8014323", 80, 80, null, null, 506818232, 537965374, 544917139, 507855461, 8014323, "SRX18521033", "SRS15989657", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.76593, 0.75368, 0.16216, 0.15545, 0.79297, 0.79446, 0.69178, 0.6927, 81, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72459, "SRR22557580", "SRX18521033", "SRS15989657", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Wild type  3", "GSM6797831", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "Wild type  3", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "GSM6797831", "GSM6797831: Wild type  3; Danio rerio; RNA Seq", "GSM6797831 r1", "GSM6797831", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-3b_S3_R1.fastq.gz WT-3b_S3_R2.fastq.gz", "fastq fastq", 9128143323.0, 56677544.0, "GSM6797831 r2", "0:80.54 1:80.51", "A:2190585466;C:2344261335;G:2371160371;T:2190984913;N:31151238", 80, 80, null, null, 2190585466, 2344261335, 2371160371, 2190984913, 31151238, "SRX18521033", "SRS15989657", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.77404, 0.75436, 0.16495, 0.15691, 0.79681, 0.79744, 0.68436, 0.67659, 81, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72460, "SRR22557581", "SRX18521032", "SRS15989656", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Wild type  2", "GSM6797830", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "Wild type  2", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "GSM6797830", "GSM6797830: Wild type  2; Danio rerio; RNA Seq", "GSM6797830 r1", "GSM6797830", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-2a_S2_R1.fastq.gz WT-2a_S2_R2.fastq.gz", "fastq fastq", 2682376653.0, 16654401.0, "GSM6797830 r1", "0:80.55 1:80.52", "A:644284326;C:685500275;G:695634455;T:646783983;N:10173614", 80, 80, null, null, 644284326, 685500275, 695634455, 646783983, 10173614, "SRX18521032", "SRS15989656", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.78423, 0.77528, 0.15422, 0.15029, 0.78817, 0.78987, 0.68508, 0.68381, 79, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72461, "SRR22557582", "SRX18521032", "SRS15989656", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Wild type  2", "GSM6797830", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "Wild type  2", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "GSM6797830", "GSM6797830: Wild type  2; Danio rerio; RNA Seq", "GSM6797830 r1", "GSM6797830", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-2b_S2_R1.fastq.gz WT-2b_S2_R2.fastq.gz", "fastq fastq", 6301068867.0, 39119979.0, "GSM6797830 r2", "0:80.55 1:80.52", "A:1514393909;C:1612859108;G:1634563369;T:1517967148;N:21285333", 80, 80, null, null, 1514393909, 1612859108, 1634563369, 1517967148, 21285333, "SRX18521032", "SRS15989656", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.79021, 0.7744, 0.15988, 0.15392, 0.79155, 0.79448, 0.6869, 0.69002, 81, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72462, "SRR22557583", "SRX18521031", "SRS15989655", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Wild type  1", "GSM6797829", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "Wild type  1", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "GSM6797829", "GSM6797829: Wild type  1; Danio rerio; RNA Seq", "GSM6797829 r1", "GSM6797829", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-1a_S1_R1.fastq.gz WT-1a_S1_R2.fastq.gz", "fastq fastq", 4537290273.0, 28168268.0, "GSM6797829 r1", "0:80.55 1:80.52", "A:1108712847;C:1146457523;G:1155728370;T:1109471371;N:16920162", 80, 80, null, null, 1108712847, 1146457523, 1155728370, 1109471371, 16920162, "SRX18521031", "SRS15989655", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.79427, 0.78336, 0.15911, 0.15467, 0.78823, 0.7892, 0.68073, 0.6827, 81, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [72463, "SRR22557584", "SRX18521031", "SRS15989655", "SRP411740", "PRJNA909412", "Molecular characterisation of a mutant kras driven zebrafish model of hepatocellular carcinoma", "GSE220282", "Transcriptome Analysis", "We used doxycycline dox treatment to generate a larval model of hepatocellular carcinoma HCC22. In this model  we induced the expression of a single EGFP krasG12V transgene  denoted TOkrasG12VT/+ in developing livers by treating with doxycycline between 2 dpf 7 dpf dpf. This led to the accumulation of a constitutively active  EGFP tagged  potently oncogenic form of Kras specifically in hepatocytes  causing hepatocyte hyperplasia and a substantial increase in total liver volume. We used RNA sequencing to analyse the gene expression patterns of hepatocytes expressing the krasG12V transgene compared to wildtype WT livers expressing no transgene. We detected more than 6000 significantly upregulated genes in dox treated TOkrasG12VT/+ livers compared WT livers  and a further 6000+ genes were significantly downregulated. Of the upregulated genes  many were significantly enriched in KEGG pathways associated with highly proliferative cancers  including DNA replication  cell cycle and DNA damage repair. Geneset enrichment analysis identified a positive correlation between the differential gene expression data from the dox treated TOkrasG12VT/+ versus WT livers and the differential gene expression data for the HCC LIHC and healthy liver subsets available from The Cancer Genome Atlas. We also found a positive correlation between the DEGs from the dox treated TOkrasG12VT/+ versus WT livers and a small HCC expression signature based on four patient samples carrying KRAS G12 or KRAS G13 mutations. These observations build on previous reports that dox treated TOkrasG12VT/+ zebrafish provide an authentic model of human HCC. Overall design: Paired end RNA sequencing data was generated for 8 samples of zebrafish liver. Of these samples  3 are wild type WT and 5 are kras mutants. Differential analyses were performed  identifying differentially expressed genes between the kras mutant and wild type groups. Please note  all WT and 2 of the mutant samples are sequenced over 2 runs.", null, "pubmed:36648336", null, "Wild type  1", "GSM6797829", null, "source name:Liver|tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "Wild type  1", "The\u00a0base calling and quality scoring were determined using Real Time Analysis on board software v2.4.6 Reads were aligned to the zebrafish genome by Rsubread version 2.10.5 Fragment read pair counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function Genes were identified using Ensembl annotation to the GRCz11 genome  version 101 Assembly: GRCz11 Supplementary files format and content: tab delimited text files wre written from the R prompt; columns represent Ensembl Gene ID  total gene length total base count of all exons and the number of fragments mapping to that gene", "Liver", "Treatment group received oxycycline 20mg/L from 2 dpf 7 dpf dpf", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", "E3 medium comprising 5mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSO4", "tissue:Liver|cell type:hepatocytes|genotype:Wild type|treatment:No treatment", "GSM6797829", "GSM6797829: Wild type  1; Danio rerio; RNA Seq", "GSM6797829 r1", "GSM6797829", "1", "Total RNA was extracted from individual micro dissected zebrafish livers using the RNeasy Micro Kit QIAGEN  #74004. RNA 100 ng per sample was used for RNA sequencing library preparation using the TruSeq RNA Sample Prep Kit with Ribo Zero depletion Illumina. Indexed libraries were sequenced on a NextSeq 500 instrument Illumina to generate 80 bp paired end reads and yielding at least 20 million reads per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP411740", null, null, "WT-1b_S1_R1.fastq.gz WT-1b_S1_R2.fastq.gz", "fastq fastq", 775190462.0, 4812296.0, "GSM6797829 r2", "0:80.56 1:80.53", "A:189393170;C:196728058;G:197734758;T:188746950;N:2587526", 80, 80, null, null, 189393170, 196728058, 197734758, 188746950, 2587526, "SRX18521031", "SRS15989655", "SRA1554907", "Walter and Eliza Hall Institute of Medical Research", "Walter and Eliza Hall Institute of Medical Research", 2, 0.79629, 0.78077, 0.15958, 0.1532, 0.78971, 0.7889, 0.68322, 0.68486, 81, 81, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Australia", "2022-12-06", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [75648, "SRR24755921", "SRX20532027", "SRS17840669", "SRP439951", "PRJNA977045", "Microbiota dysbiosis associated with type 2 diabetes like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish [I]", "GSE233631", "Transcriptome Analysis", "Mixtures of chlorinated persistent organic pollutants C POPs Mix are chemically related risk factors for type 2 diabetes mellitus T2DM; however  the effects of chronic exposure to C POPs Mix on microbial dysbiosis remain poorly understood. Herein  male and female zebrafish were exposed to C POPs Mix at a 1:1 ratio of five organochlorine pesticides and Aroclor 1254 at concentrations of 0.02  0.1  and 0.5 \u00b5g/L for 12 weeks. We measured T2DM indicators in blood and profiled microbial abundance  richness  and evenness in the gut as well as transcriptomic and metabolomic alterations in the liver. Exposure to C POPs Mix significantly increased blood glucose levels while decreasing the abundance and alpha diversity of microbial communities only in females at concentrations of 0.02 and 0.1 \u00b5g/L. The majorly identified microbial contributors to microbial dysbiosis were Bosea minatitlanensis  Rhizobium tibeticum  Bifidobacterium catenulatum  B. adolescentis  and Collinsella aerofaciens. PICRUSt results suggested that altered pathways were associated with glucose and lipid production and inflammation  which are linked to changes in the transcriptome and metabolome of the zebrafish liver. Metagenomics outcomes revealed close relationships between intestinal and liver disruptions to T2DM related molecular pathways. Thus  microbial dysbiosis in T2DM triggered zebrafish occurred as a result of chronic exposure to C POPs Mix  indicating strong host\u2013microbiome interactions. Overall design: Samples consisted of the control group and three treatment groups exposed to 0.02  0.1  and 0.5 ug/L of C POPs Mix containing five OCPs and Aroclor1254 for the mechanistic study to demonstrate the relationship between microbiota dysbiosis and type 2 diabetes in C POPs Mix exposed zebrafish. Six female livers were pooled for each group and used to perform RNA seq on the Illumina HiSeq 2500 platform. For 16S rRNA seq analysis  total genomic DNAs were individually extracted from five intestines in each group and sequenced by Illumina Miseq system.", "parent bioproject:PRJNA977043", null, null, "C POPs Mix 0.5", "GSM7431682", null, "source name:Liver|tissue:Liver|Sex:female|treatment:Aroclor1254+5OCPs+DMSO|genotype:WT|time:84 days|geo loc name:missing|collection date:missing", "C POPs Mix 0.5", "Quality trimming was performed using FastQC v0.11.9 Quality based trimming was performed using cutadapt v2.8 Alignment was performed using STAR v2.7.1a Gene counts were performed with RSEM v1.3.3  featureCounts v2.0.0  HTSeq count v0.11.2  and Cufflinks v2.2.1 Normalization was performed using DESeq2 v1.26.0 and edgeR v3.2.1 Functional analysis was performed using goseq v1.38.0 and GOplot v1.0.2 Supplementary files format and content: FPKM count table is a CSV format.", "Liver", "A total of 360 zebrafish including 180 females and 180 males were randomly assigned to three tanks. Each tank per concentration was comprised of 15 females and 15 males. Adult zebrafish were exposed to 0.02  0.1  0.5 \u03bcg/L C POPs Mix for 12 weeks in an automatic flow through exposure system TOX MIXII  Hanalab  Daejeon  South Korea.", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", "Zebrafish Danio rerio  wild type AB strain aged 10\u201312 month were maintained in a flow through system Tecniplast  Buguggiate  Italy with a 14 h light/10 h dark photoperiod at a temperature of 28.5\u00b0C \u00b1 0.5\u00b0C and pH of 7.0\u20137.5. The zebrafish were fed thrice daily with Gemma micro 300 Skretting  West brook  Maine  USA.", "tissue:Liver|Sex:Female|treatment:Aroclor1254+5OCPs+DMSO|genotype:WT|time:84 days", "GSM7431682", "GSM7431682: C POPs Mix 0.5; Danio rerio; RNA Seq", "GSM7431682 r1", "GSM7431682", "1", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP439951", null, null, "0_05_1.fq.gz 0_05_2.fq.gz", "fastq fastq", 6648821430.0, 22015965.0, "GSM7431682 r1", "0:151 1:151", "A:1920128658;C:1379398635;G:1470489193;T:1878772397;N:32547", 151, 151, null, null, 1920128658, 1379398635, 1470489193, 1878772397, 32547, "SRX20532027", "SRS17840669", "SRA1645529", "Biology, University of Ottawa", "Biology, University of Ottawa", 2, 0.94277, 0.86585, 0.06146, 0.05619, 0.84524, 0.85173, 0.51097, 0.5215, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2023-05-28", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [75649, "SRR24755922", "SRX20532026", "SRS17840670", "SRP439951", "PRJNA977045", "Microbiota dysbiosis associated with type 2 diabetes like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish [I]", "GSE233631", "Transcriptome Analysis", "Mixtures of chlorinated persistent organic pollutants C POPs Mix are chemically related risk factors for type 2 diabetes mellitus T2DM; however  the effects of chronic exposure to C POPs Mix on microbial dysbiosis remain poorly understood. Herein  male and female zebrafish were exposed to C POPs Mix at a 1:1 ratio of five organochlorine pesticides and Aroclor 1254 at concentrations of 0.02  0.1  and 0.5 \u00b5g/L for 12 weeks. We measured T2DM indicators in blood and profiled microbial abundance  richness  and evenness in the gut as well as transcriptomic and metabolomic alterations in the liver. Exposure to C POPs Mix significantly increased blood glucose levels while decreasing the abundance and alpha diversity of microbial communities only in females at concentrations of 0.02 and 0.1 \u00b5g/L. The majorly identified microbial contributors to microbial dysbiosis were Bosea minatitlanensis  Rhizobium tibeticum  Bifidobacterium catenulatum  B. adolescentis  and Collinsella aerofaciens. PICRUSt results suggested that altered pathways were associated with glucose and lipid production and inflammation  which are linked to changes in the transcriptome and metabolome of the zebrafish liver. Metagenomics outcomes revealed close relationships between intestinal and liver disruptions to T2DM related molecular pathways. Thus  microbial dysbiosis in T2DM triggered zebrafish occurred as a result of chronic exposure to C POPs Mix  indicating strong host\u2013microbiome interactions. Overall design: Samples consisted of the control group and three treatment groups exposed to 0.02  0.1  and 0.5 ug/L of C POPs Mix containing five OCPs and Aroclor1254 for the mechanistic study to demonstrate the relationship between microbiota dysbiosis and type 2 diabetes in C POPs Mix exposed zebrafish. Six female livers were pooled for each group and used to perform RNA seq on the Illumina HiSeq 2500 platform. For 16S rRNA seq analysis  total genomic DNAs were individually extracted from five intestines in each group and sequenced by Illumina Miseq system.", "parent bioproject:PRJNA977043", null, null, "C POPs Mix 0.1", "GSM7431681", null, "source name:Liver|tissue:Liver|Sex:female|treatment:Aroclor1254+5OCPs+DMSO|genotype:WT|time:84 days|geo loc name:missing|collection date:missing", "C POPs Mix 0.1", "Quality trimming was performed using FastQC v0.11.9 Quality based trimming was performed using cutadapt v2.8 Alignment was performed using STAR v2.7.1a Gene counts were performed with RSEM v1.3.3  featureCounts v2.0.0  HTSeq count v0.11.2  and Cufflinks v2.2.1 Normalization was performed using DESeq2 v1.26.0 and edgeR v3.2.1 Functional analysis was performed using goseq v1.38.0 and GOplot v1.0.2 Supplementary files format and content: FPKM count table is a CSV format.", "Liver", "A total of 360 zebrafish including 180 females and 180 males were randomly assigned to three tanks. Each tank per concentration was comprised of 15 females and 15 males. Adult zebrafish were exposed to 0.02  0.1  0.5 \u03bcg/L C POPs Mix for 12 weeks in an automatic flow through exposure system TOX MIXII  Hanalab  Daejeon  South Korea.", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", "Zebrafish Danio rerio  wild type AB strain aged 10\u201312 month were maintained in a flow through system Tecniplast  Buguggiate  Italy with a 14 h light/10 h dark photoperiod at a temperature of 28.5\u00b0C \u00b1 0.5\u00b0C and pH of 7.0\u20137.5. The zebrafish were fed thrice daily with Gemma micro 300 Skretting  West brook  Maine  USA.", "tissue:Liver|Sex:Female|treatment:Aroclor1254+5OCPs+DMSO|genotype:WT|time:84 days", "GSM7431681", "GSM7431681: C POPs Mix 0.1; Danio rerio; RNA Seq", "GSM7431681 r1", "GSM7431681", "1", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP439951", null, null, "0_01_1.fq.gz 0_01_2.fq.gz", "fastq fastq", 7784390958.0, 25776129.0, "GSM7431681 r1", "0:151 1:151", "A:2100014723;C:1788734921;G:1852650656;T:2042895713;N:94945", 151, 151, null, null, 2100014723, 1788734921, 1852650656, 2042895713, 94945, "SRX20532026", "SRS17840670", "SRA1645529", "Biology, University of Ottawa", "Biology, University of Ottawa", 2, 0.90993, 0.91827, 0.02957, 0.02906, 0.86965, 0.86949, 0.26027, 0.26274, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2023-05-28", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [75650, "SRR24755923", "SRX20532025", "SRS17840668", "SRP439951", "PRJNA977045", "Microbiota dysbiosis associated with type 2 diabetes like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish [I]", "GSE233631", "Transcriptome Analysis", "Mixtures of chlorinated persistent organic pollutants C POPs Mix are chemically related risk factors for type 2 diabetes mellitus T2DM; however  the effects of chronic exposure to C POPs Mix on microbial dysbiosis remain poorly understood. Herein  male and female zebrafish were exposed to C POPs Mix at a 1:1 ratio of five organochlorine pesticides and Aroclor 1254 at concentrations of 0.02  0.1  and 0.5 \u00b5g/L for 12 weeks. We measured T2DM indicators in blood and profiled microbial abundance  richness  and evenness in the gut as well as transcriptomic and metabolomic alterations in the liver. Exposure to C POPs Mix significantly increased blood glucose levels while decreasing the abundance and alpha diversity of microbial communities only in females at concentrations of 0.02 and 0.1 \u00b5g/L. The majorly identified microbial contributors to microbial dysbiosis were Bosea minatitlanensis  Rhizobium tibeticum  Bifidobacterium catenulatum  B. adolescentis  and Collinsella aerofaciens. PICRUSt results suggested that altered pathways were associated with glucose and lipid production and inflammation  which are linked to changes in the transcriptome and metabolome of the zebrafish liver. Metagenomics outcomes revealed close relationships between intestinal and liver disruptions to T2DM related molecular pathways. Thus  microbial dysbiosis in T2DM triggered zebrafish occurred as a result of chronic exposure to C POPs Mix  indicating strong host\u2013microbiome interactions. Overall design: Samples consisted of the control group and three treatment groups exposed to 0.02  0.1  and 0.5 ug/L of C POPs Mix containing five OCPs and Aroclor1254 for the mechanistic study to demonstrate the relationship between microbiota dysbiosis and type 2 diabetes in C POPs Mix exposed zebrafish. Six female livers were pooled for each group and used to perform RNA seq on the Illumina HiSeq 2500 platform. For 16S rRNA seq analysis  total genomic DNAs were individually extracted from five intestines in each group and sequenced by Illumina Miseq system.", "parent bioproject:PRJNA977043", null, null, "C POPs Mix 0.02", "GSM7431680", null, "source name:Liver|tissue:Liver|Sex:female|treatment:Aroclor1254+5OCPs+DMSO|genotype:WT|time:84 days|geo loc name:missing|collection date:missing", "C POPs Mix 0.02", "Quality trimming was performed using FastQC v0.11.9 Quality based trimming was performed using cutadapt v2.8 Alignment was performed using STAR v2.7.1a Gene counts were performed with RSEM v1.3.3  featureCounts v2.0.0  HTSeq count v0.11.2  and Cufflinks v2.2.1 Normalization was performed using DESeq2 v1.26.0 and edgeR v3.2.1 Functional analysis was performed using goseq v1.38.0 and GOplot v1.0.2 Supplementary files format and content: FPKM count table is a CSV format.", "Liver", "A total of 360 zebrafish including 180 females and 180 males were randomly assigned to three tanks. Each tank per concentration was comprised of 15 females and 15 males. Adult zebrafish were exposed to 0.02  0.1  0.5 \u03bcg/L C POPs Mix for 12 weeks in an automatic flow through exposure system TOX MIXII  Hanalab  Daejeon  South Korea.", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", "Zebrafish Danio rerio  wild type AB strain aged 10\u201312 month were maintained in a flow through system Tecniplast  Buguggiate  Italy with a 14 h light/10 h dark photoperiod at a temperature of 28.5\u00b0C \u00b1 0.5\u00b0C and pH of 7.0\u20137.5. The zebrafish were fed thrice daily with Gemma micro 300 Skretting  West brook  Maine  USA.", "tissue:Liver|Sex:Female|treatment:Aroclor1254+5OCPs+DMSO|genotype:WT|time:84 days", "GSM7431680", "GSM7431680: C POPs Mix 0.02; Danio rerio; RNA Seq", "GSM7431680 r1", "GSM7431680", "1", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP439951", null, null, "0_002_1.fq.gz 0_002_2.fq.gz", "fastq fastq", 5914888346.0, 19585723.0, "GSM7431680 r1", "0:151 1:151", "A:1677702242;C:1267414381;G:1330622303;T:1639121124;N:28296", 151, 151, null, null, 1677702242, 1267414381, 1330622303, 1639121124, 28296, "SRX20532025", "SRS17840668", "SRA1645529", "Biology, University of Ottawa", "Biology, University of Ottawa", 2, 0.94168, 0.86554, 0.05025, 0.04558, 0.76609, 0.77023, 0.43515, 0.43737, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2023-05-28", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"], [75651, "SRR24755924", "SRX20532024", "SRS17840667", "SRP439951", "PRJNA977045", "Microbiota dysbiosis associated with type 2 diabetes like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish [I]", "GSE233631", "Transcriptome Analysis", "Mixtures of chlorinated persistent organic pollutants C POPs Mix are chemically related risk factors for type 2 diabetes mellitus T2DM; however  the effects of chronic exposure to C POPs Mix on microbial dysbiosis remain poorly understood. Herein  male and female zebrafish were exposed to C POPs Mix at a 1:1 ratio of five organochlorine pesticides and Aroclor 1254 at concentrations of 0.02  0.1  and 0.5 \u00b5g/L for 12 weeks. We measured T2DM indicators in blood and profiled microbial abundance  richness  and evenness in the gut as well as transcriptomic and metabolomic alterations in the liver. Exposure to C POPs Mix significantly increased blood glucose levels while decreasing the abundance and alpha diversity of microbial communities only in females at concentrations of 0.02 and 0.1 \u00b5g/L. The majorly identified microbial contributors to microbial dysbiosis were Bosea minatitlanensis  Rhizobium tibeticum  Bifidobacterium catenulatum  B. adolescentis  and Collinsella aerofaciens. PICRUSt results suggested that altered pathways were associated with glucose and lipid production and inflammation  which are linked to changes in the transcriptome and metabolome of the zebrafish liver. Metagenomics outcomes revealed close relationships between intestinal and liver disruptions to T2DM related molecular pathways. Thus  microbial dysbiosis in T2DM triggered zebrafish occurred as a result of chronic exposure to C POPs Mix  indicating strong host\u2013microbiome interactions. Overall design: Samples consisted of the control group and three treatment groups exposed to 0.02  0.1  and 0.5 ug/L of C POPs Mix containing five OCPs and Aroclor1254 for the mechanistic study to demonstrate the relationship between microbiota dysbiosis and type 2 diabetes in C POPs Mix exposed zebrafish. Six female livers were pooled for each group and used to perform RNA seq on the Illumina HiSeq 2500 platform. For 16S rRNA seq analysis  total genomic DNAs were individually extracted from five intestines in each group and sequenced by Illumina Miseq system.", "parent bioproject:PRJNA977043", null, null, "Control 0", "GSM7431679", null, "source name:Liver|tissue:Liver|Sex:female|treatment:DMSO|genotype:WT|time:84 days|geo loc name:missing|collection date:missing", "Control 0", "Quality trimming was performed using FastQC v0.11.9 Quality based trimming was performed using cutadapt v2.8 Alignment was performed using STAR v2.7.1a Gene counts were performed with RSEM v1.3.3  featureCounts v2.0.0  HTSeq count v0.11.2  and Cufflinks v2.2.1 Normalization was performed using DESeq2 v1.26.0 and edgeR v3.2.1 Functional analysis was performed using goseq v1.38.0 and GOplot v1.0.2 Supplementary files format and content: FPKM count table is a CSV format.", "Liver", "A total of 360 zebrafish including 180 females and 180 males were randomly assigned to three tanks. Each tank per concentration was comprised of 15 females and 15 males. Adult zebrafish were exposed to 0.02  0.1  0.5 \u03bcg/L C POPs Mix for 12 weeks in an automatic flow through exposure system TOX MIXII  Hanalab  Daejeon  South Korea.", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", "Zebrafish Danio rerio  wild type AB strain aged 10\u201312 month were maintained in a flow through system Tecniplast  Buguggiate  Italy with a 14 h light/10 h dark photoperiod at a temperature of 28.5\u00b0C \u00b1 0.5\u00b0C and pH of 7.0\u20137.5. The zebrafish were fed thrice daily with Gemma micro 300 Skretting  West brook  Maine  USA.", "tissue:Liver|Sex:Female|treatment:DMSO|genotype:WT|time:84 days", "GSM7431679", "GSM7431679: Control 0; Danio rerio; RNA Seq", "GSM7431679 r1", "GSM7431679", "1", "RNA was extracted using RNeasy Mini Kit Qiagen\u00ae  USA. RNA libraries were constructed using TruSeq RNA sample preparation kit Illumina  USA and quantified using KAPA library quantification kit Kapa Biosystems  USA according to the manufacturer's protocol The prepared RNA libraries were sequenced using the llumina HiSeq 2500 Illumina  USA platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP439951", null, null, "Control_1.fq.gz Control_2.fq.gz", "fastq fastq", 7663427274.0, 25375587.0, "GSM7431679 r1", "0:151 1:151", "A:2102047070;C:1720814862;G:1775607282;T:2064903634;N:54426", 151, 151, null, null, 2102047070, 1720814862, 1775607282, 2064903634, 54426, "SRX20532024", "SRS17840667", "SRA1645529", "Biology, University of Ottawa", "Biology, University of Ottawa", 2, 0.959, 0.89994, 0.04409, 0.04019, 0.84502, 0.84983, 0.30528, 0.30485, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Canada", "2023-05-28", "Multi-stage", "Multi-stage", "Liver", "Liver and Biliary System"]], "truncated": false, "filtered_table_rows_count": 100, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", 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