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Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "hepatocyte specific gmfb overexpression  normal diet for 35 days", "RNAseq MASLD HepGOE ND rep1", "HepGOE ND rep1", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 9|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in HepGOE zebrafish of normal diet.", "HepGOE ND rep1", "HepGOE ND rep1", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_HepGOE_ND_rep1_1.fq.gz RNAseq_MASLD_HepGOE_ND_rep1_2.fq.gz", "fastq fastq", 6621268500.0, 22070895.0, "RNAseq MASLD HepGOE ND rep1 1.fq.gz", "0:150 1:150", "A:1711419517;C:1595902037;G:1611514825;T:1702282385;N:149736", 150, 150, null, null, 1711419517, 1595902037, 1611514825, 1702282385, 149736, "SRX27082406", "SRS23541574", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34399, "SRR31719831", "SRX27082405", "SRS23541573", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. However  the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study  total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "hepatocyte specific gmfb knockout  high fat  high cholesterol diet for 35 days", "RNAseq MASLD HepGKO HFC rep2", "HepGKO HFC rep2", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in HepGKO zebrafish of high fat  high cholesterol diet.", "HepGKO HFC rep2", "HepGKO HFC rep2", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_HepGKO_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep2_2.fq.gz", "fastq fastq", 5901646500.0, 19672155.0, "RNAseq MASLD HepGKO HFC rep2 1.fq.gz", "0:150 1:150", "A:1547939419;C:1401111812;G:1425197669;T:1527300198;N:97402", 150, 150, null, null, 1547939419, 1401111812, 1425197669, 1527300198, 97402, "SRX27082405", "SRS23541573", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34400, "SRR31719832", "SRX27082404", "SRS23541572", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. However  the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study  total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "hepatocyte specific gmfb knockout  high fat  high cholesterol diet for 35 days", "RNAseq MASLD HepGKO HFC rep1", "HepGKO HFC rep1", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in HepGKO zebrafish of high fat  high cholesterol diet.", "HepGKO HFC rep1", "HepGKO HFC rep1", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_HepGKO_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGKO_HFC_rep1_2.fq.gz", "fastq fastq", 6484178700.0, 21613929.0, "RNAseq MASLD HepGKO HFC rep1 1.fq.gz", "0:150 1:150", "A:1692850957;C:1545705390;G:1573644279;T:1671871368;N:106706", 150, 150, null, null, 1692850957, 1545705390, 1573644279, 1671871368, 106706, "SRX27082404", "SRS23541572", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34401, "SRR31719833", "SRX27082403", "SRS23541571", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. However  the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study  total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "hepatocyte specific gmfb knockout  normal diet for 35 days", "RNAseq MASLD HepGKO ND rep2", "HepGKO ND rep2", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in HepGKO zebrafish of normal diet.", "HepGKO ND rep2", "HepGKO ND rep2", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_HepGKO_ND_rep2_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep2_2.fq.gz", "fastq fastq", 6436941000.0, 21456470.0, "RNAseq MASLD HepGKO ND rep2 1.fq.gz", "0:150 1:150", "A:1671402056;C:1543860294;G:1570976721;T:1650596456;N:105473", 150, 150, null, null, 1671402056, 1543860294, 1570976721, 1650596456, 105473, "SRX27082403", "SRS23541571", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34402, "SRR31719834", "SRX27082402", "SRS23541570", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. However  the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study  total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "hepatocyte specific gmfb knockout  normal diet for 35 days", "RNAseq MASLD HepGKO ND rep1", "HepGKO ND rep1", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in HepGKO zebrafish of normal diet.", "HepGKO ND rep1", "HepGKO ND rep1", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_HepGKO_ND_rep1_1.fq.gz RNAseq_MASLD_HepGKO_ND_rep1_2.fq.gz", "fastq fastq", 6386174700.0, 21287249.0, "RNAseq MASLD HepGKO ND rep1 1.fq.gz", "0:150 1:150", "A:1662767742;C:1527603435;G:1545756971;T:1649944714;N:101838", 150, 150, null, null, 1662767742, 1527603435, 1545756971, 1649944714, 101838, "SRX27082402", "SRS23541570", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34403, "SRR31719835", "SRX27082401", "SRS23541569", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. However  the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study  total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "WT zebrafish  high fat  high cholesterol diet for 35 days", "RNAseq MASLD WT HFC rep2", "WT HFC rep2", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in WT zebrafish of high fat  high cholesterol diet.", "WT HFC rep2", "WT HFC rep2", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_WT_HFC_rep2_1.fq.gz RNAseq_MASLD_WT_HFC_rep2_2.fq.gz", "fastq fastq", 7088163900.0, 23627213.0, "RNAseq MASLD WT HFC rep2 1.fq.gz", "0:150 1:150", "A:1904609517;C:1635475353;G:1664944747;T:1882978732;N:155551", 150, 150, null, null, 1904609517, 1635475353, 1664944747, 1882978732, 155551, "SRX27082401", "SRS23541569", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34404, "SRR31719836", "SRX27082400", "SRS23541568", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. However  the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study  total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "WT zebrafish  high fat  high cholesterol diet for 35 days", "RNAseq MASLD WT HFC rep1", "WT HFC rep1", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in WT zebrafish of high fat  high cholesterol diet.", "WT HFC rep1", "WT HFC rep1", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_WT_HFC_rep1_1.fq.gz RNAseq_MASLD_WT_HFC_rep1_2.fq.gz", "fastq fastq", 7053396600.0, 23511322.0, "RNAseq MASLD WT HFC rep1 1.fq.gz", "0:150 1:150", "A:1862942395;C:1655266768;G:1688002812;T:1847030526;N:154099", 150, 150, null, null, 1862942395, 1655266768, 1688002812, 1847030526, 154099, "SRX27082400", "SRS23541568", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34405, "SRR31719837", "SRX27082399", "SRS23541567", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. However  the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study  total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "hepatocyte specific gmfb overexpression  high fat  high cholesterol diet for 35 days", "RNAseq MASLD HepGOE HFC rep2", "HepGOE HFC rep2", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 12|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in HepGOE zebrafish of high fat  high cholesterol diet.", "HepGOE HFC rep2", "HepGOE HFC rep2", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_HepGOE_HFC_rep2_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep2_2.fq.gz", "fastq fastq", 7004757600.0, 23349192.0, "RNAseq MASLD HepGOE HFC rep2 1.fq.gz", "0:150 1:150", "A:1846708800;C:1647727254;G:1676955416;T:1833207397;N:158733", 150, 150, null, null, 1846708800, 1647727254, 1676955416, 1833207397, 158733, "SRX27082399", "SRS23541567", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34406, "SRR31719838", "SRX27082398", "SRS23541566", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. 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Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "hepatocyte specific gmfb overexpression  high fat  high cholesterol diet for 35 days", "RNAseq MASLD HepGOE HFC rep1", "HepGOE HFC rep1", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 11|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in HepGOE zebrafish of high fat  high cholesterol diet.", "HepGOE HFC rep1", "HepGOE HFC rep1", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_HepGOE_HFC_rep1_1.fq.gz RNAseq_MASLD_HepGOE_HFC_rep1_2.fq.gz", "fastq fastq", 8211524400.0, 27371748.0, "RNAseq MASLD HepGOE HFC rep1 1.fq.gz", "0:150 1:150", "A:2217820195;C:1876471113;G:1906298333;T:2210753213;N:181546", 150, 150, null, null, 2217820195, 1876471113, 1906298333, 2210753213, 181546, "SRX27082398", "SRS23541566", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34407, "SRR31719839", "SRX27082397", "SRS23541565", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. However  the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study  total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "WT zebrafish  normal diet for 35 days", "RNAseq MASLD WT ND rep2", "WT ND rep2", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in WT zebrafish of normal diet.", "WT ND rep2", "WT ND rep2", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_WT_ND_rep2_1.fq.gz RNAseq_MASLD_WT_ND_rep2_2.fq.gz", "fastq fastq", 6966786300.0, 23222621.0, "RNAseq MASLD WT ND rep2 1.fq.gz", "0:150 1:150", "A:1855652140;C:1619780884;G:1651213951;T:1839982276;N:157049", 150, 150, null, null, 1855652140, 1619780884, 1651213951, 1839982276, 157049, "SRX27082397", "SRS23541565", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [34408, "SRR31719840", "SRX27082396", "SRS23541564", "SRP551495", "PRJNA1198392", "RNA seq data of zebrafish with gmfb knockout and overexpression in MASLD", "PRJNA1198392", "Other", "Glia maturation factor beta Gmfb  an actin filament debrancher  was first identified in the brain and has more recently been associated with liver diseases. However  the potential direct role of Gmfb in hepatocytes post chronic liver injury remains largely uninvestigated. In this study  total RNA was extracted from wild type or gmfb knockout and overexpression zebrafish liver in MASLD. And then RNA sequencing was performed in Novogene Co. Ltd. Beijing  China using the Illumina NovaSeq 6000 platform to unravel gmfb transcriptome changes in MASLD.", null, null, "WT zebrafish  normal diet for 35 days", "RNAseq MASLD WT ND rep1", "WT ND rep1", null, "strain:not collected|isolate:not collected|breed:AB|cultivar:not collected|ecotype:not collected|age:40 dpf stage:juvenile|collection date:2023 12 21|geo loc name:China:Guangzhou|sex:pooled male and female|tissue:liver|sample type:Total RNA|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Transcriptome of liver tissues in WT zebrafish of normal diet.", "WT ND rep1", "WT ND rep1", "Total RNA was extracted from liver tissue for RNA sequencing", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP551495", null, null, "RNAseq_MASLD_WT_ND_rep1_1.fq.gz RNAseq_MASLD_WT_ND_rep1_2.fq.gz", "fastq fastq", 7149668700.0, 23832229.0, "RNAseq MASLD WT ND rep1 1.fq.gz", "0:150 1:150", "A:1869145140;C:1695095352;G:1726444600;T:1858824841;N:158767", 150, 150, null, null, 1869145140, 1695095352, 1726444600, 1858824841, 158767, "SRX27082396", "SRS23541564", "SRA2034386", "Southern Medical University|Biomedical Research Center", "Southern Medical University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-12-15", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [42181, "SRR5482153", "SRX2765568", "SRS2149771", "SRP105243", "PRJNA383986", "Danio rerio Raw sequence reads", "PRJNA383986", "Other", "The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.", null, null, null, "Danio rerio: Large harvested line  biological replicate 1  F2 offspring originating from wild caught population", "LS1 F2", null, "breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2008|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F2 individuals", "LS1 F2", "LS1 F2", "Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  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The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  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The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  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The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP105243", null, null, "RS2-F2-3_FCC4CMHACXX_L2_WHZEBagiNCBFRAAPEI-210_1.fq.gz RS2-F2-6-2_FCC4CMHACXX_L2_WHZEBagiNCBGRAAPEI-211_1.fq.gz RS2-F2-8_FCC4CMHACXX_L2_WHZEBagiNCBHRABPEI-212_1.fq.gz RS2-F2-9_FCC4CMHACXX_L3_WHZEBagiNCBIRABPEI-213_1.fq.gz", "fastq fastq fastq fastq", 11923597525.0, 243338725.0, "RS2 F2 9 FCC4CMHACXX L3 WHZEBagiNCBIRABPEI 213 1.fq.gz", "0:49", "A:3132507165;C:2819390547;G:2776793842;T:3193588286;N:1317685", 49, null, null, null, 3132507165, 2819390547, 2776793842, 3193588286, 1317685, "SRX2765564", "SRS2149768", "SRA557107", "University of Turku|Biology", "University of Turku", 1, 0.90986, null, 0.05269, null, 0.814, null, 0.36827, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2017-12-04", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [42185, "SRR5482149", "SRX2765563", "SRS2149767", "SRP105243", "PRJNA383986", "Danio rerio Raw sequence reads", "PRJNA383986", "Other", "The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.", null, null, null, "Danio rerio: Large harvested line  biological replicate 1  F5 offspring originating from wild caught population", "LS1 F5", null, "breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F5 individuals", "LS1 F5", "LS1 F5", "Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP105243", null, null, "LS1-15_FCC4C3HACXX_L1_WHZEBagiNBANRAAPEI-215_1.fq.gz LS1-2_FCC4BJ2ACXX_L5_WHZEBagiNBABRAAPEI-202_1.fq.gz LS1-6_FCC4BJ2ACXX_L6_WHZEBagiNBAFRAAPEI-207_1.fq.gz LS1-8_FCC4BJ2ACXX_L8_WHZEBagiNBAJRAAPEI-211_1.fq.gz", "fastq fastq fastq fastq", 12776192331.0, 260738619.0, "LS1 2 FCC4BJ2ACXX L5 WHZEBagiNBABRAAPEI 202 1.fq.gz", "0:49", "A:3371838433;C:3025006624;G:2934135898;T:3444117388;N:1093988", 49, null, null, null, 3371838433, 3025006624, 2934135898, 3444117388, 1093988, "SRX2765563", "SRS2149767", "SRA557107", "University of Turku|Biology", "University of Turku", 1, 0.88482, null, 0.04932, null, 0.813, null, 0.51224, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2017-12-04", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [42186, "SRR5482148", "SRX2765562", "SRS2149766", "SRP105243", "PRJNA383986", "Danio rerio Raw sequence reads", "PRJNA383986", "Other", "The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.", null, null, null, "Danio rerio: Large harvested line  biological replicate 2  F5 offspring originating from wild caught population", "LS2 F5", null, "breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2010|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a large harvested selection line F5 individuals", "LS2 F5", "LS2 F5", "Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  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The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  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The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  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The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP105243", null, null, "RS1-F11B-21_FCC4C2AACXX_L3_WHZEBagiNCAYRAAPEI-202_1.fq.gz RS1-F11B-23_FCC4C2AACXX_L4_WHZEBagiNCAZRAAPEI-203_1.fq.gz RS1-F11B-27_FCC4C2AACXX_L4_WHZEBagiNCBARAAPEI-205_1.fq.gz RS1-F11B-29_FCC4C2AACXX_L4_WHZEBagiNCBBRAAPEI-206_1.fq.gz", "fastq fastq fastq fastq", 11947679555.0, 243830195.0, "RS1 F11B 21 FCC4C2AACXX L3 WHZEBagiNCAYRAAPEI 202 1.fq.gz", "0:49", "A:3159477117;C:2827401119;G:2753495798;T:3206143470;N:1162051", 49, null, null, null, 3159477117, 2827401119, 2753495798, 3206143470, 1162051, "SRX2765557", "SRS2149760", "SRA557107", "University of Turku|Biology", "University of Turku", 1, 0.87877, null, 0.04488, null, 0.77445, null, 0.50852, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2017-12-04", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [42192, "SRR5482142", "SRX2765556", "SRS2149761", "SRP105243", "PRJNA383986", "Danio rerio Raw sequence reads", "PRJNA383986", "Other", "The goal of the experiment was to simulate the effect of size selective harvesting and captive rearing on gene expression in a controlled environment using zebrafish as a model species.", null, null, null, "Danio rerio: Random harvested line  biological replicate 2  F11 offspring originating from wild caught population", "RS2 F11", null, "breed:missing|dev stage:juvenile|sex:female|tissue:liver|death date:2014|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio: juvenile female liver RNA of 4 biological replicates from a random harvested selection line F11 individuals", "RS2 F11", "RS2 F11", "Total RNA from liver tissue of juvenile zebrafish was extracted according to the Trizol method with TRI reagent Sigma. The liver tissue was homogenized with a TissueLyser II homogenizer Qiagen. DNase treatment was performed to remove any genomic DNA from the samples. RNA was eluted in RNase free water and RNA concentrations and the integrity of RNA samples were determined using an Agilent 2100 Bioanalyzer.  Total RNA was processed by using Low Input Library Preparation Kit to prepare the RNA Seq library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP105243", null, null, "RS2-F11B-34_FCC4CMHACXX_L3_WHZEBagiNCBJRABPEI-214_1.fq.gz RS2-F11B-36_FCC4CMHACXX_L3_WHZEBagiNCBKRABPEI-215_1.fq.gz RS2-F11B-38_FCC4BY1ACXX_L1_WHZEBagiNCBLRABPEI-216_1.fq.gz RS2-F11B-40_FCC4BY1ACXX_L1_WHZEBagiNCBMRABPEI-218_1.fq.gz", "fastq fastq fastq fastq", 10619740698.0, 216729402.0, "RS2 F11B 38 FCC4BY1ACXX L1 WHZEBagiNCBLRABPEI 216 1.fq.gz", "0:49", "A:2799661065;C:2501316593;G:2465115836;T:2852970598;N:676606", 49, null, null, null, 2799661065, 2501316593, 2465115836, 2852970598, 676606, "SRX2765556", "SRS2149761", "SRA557107", "University of Turku|Biology", "University of Turku", 1, 0.8851, null, 0.04865, null, 0.80407, null, 0.54962, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "Finland", "2017-12-04", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53175, "SRR9708005", "SRX6465919", "SRS5126684", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week HBx Srcp53  DIO sample 2", "GSM3954323", null, "source name:8week HBx Srcp53  Overfed|strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed", "8week HBx Srcp53  DIO sample 2", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week HBx Srcp53  Overfed", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed", "GSM3954323", "GSM3954323: 8week HBx Srcp53  DIO sample 2; Danio rerio; RNA Seq", "GSM3954323", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954323", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "TriDIO11_1.fq.gz TriDIO11_2.fq.gz", "fastq fastq", 4249297200.0, 14164324.0, "GSM3954323 r1", "0:150 1:150", "A:1118373146;C:1004287869;G:1022623288;T:1103209208;N:803689", 150, 150, null, null, 1118373146, 1004287869, 1022623288, 1103209208, 803689, "SRX6465919", "SRS5126684", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.93432, 0.93585, 0.02504, 0.0252, 0.84147, 0.84404, 0.40759, 0.40621, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53176, "SRR9708004", "SRX6465918", "SRS5126685", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week HBx Srcp53  DIO sample 1", "GSM3954322", null, "source name:8week HBx Srcp53  Overfed|strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed", "8week HBx Srcp53  DIO sample 1", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week HBx Srcp53  Overfed", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Overfed", "GSM3954322", "GSM3954322: 8week HBx Srcp53  DIO sample 1; Danio rerio; RNA Seq", "GSM3954322", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954322", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "TriDIO7_1.fq.gz TriDIO7_2.fq.gz", "fastq fastq", 4138104000.0, 13793680.0, "GSM3954322 r1", "0:150 1:150", "A:1083497193;C:982815449;G:997572851;T:1073433464;N:785043", 150, 150, null, null, 1083497193, 982815449, 997572851, 1073433464, 785043, "SRX6465918", "SRS5126685", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.93773, 0.93872, 0.02225, 0.02227, 0.83976, 0.8434, 0.33808, 0.33225, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53177, "SRR9708003", "SRX6465917", "SRS5126683", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week HBx Srcp53  NOR sample 2", "GSM3954321", null, "source name:8week HBx Srcp53  Normal diet|strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Normal diet", "8week HBx Srcp53  NOR sample 2", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week HBx Srcp53  Normal diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Normal diet", "GSM3954321", "GSM3954321: 8week HBx Srcp53  NOR sample 2; Danio rerio; RNA Seq", "GSM3954321", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954321", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "TriNOR11_1.fq.gz TriNOR11_2.fq.gz", "fastq fastq", 4268302500.0, 14227675.0, "GSM3954321 r1", "0:150 1:150", "A:1117539537;C:1013234805;G:1028678990;T:1108041769;N:807399", 150, 150, null, null, 1117539537, 1013234805, 1028678990, 1108041769, 807399, "SRX6465917", "SRS5126683", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.9398, 0.9404, 0.01665, 0.01644, 0.84691, 0.84981, 0.23273, 0.23748, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53178, "SRR9708002", "SRX6465916", "SRS5126682", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week HBx Srcp53  NOR sample 1", "GSM3954320", null, "source name:8week HBx Srcp53  Normal diet|strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Normal diet", "8week HBx Srcp53  NOR sample 1", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week HBx Srcp53  Normal diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:HBx Srcp53 |tissue:Liver|diet:Normal diet", "GSM3954320", "GSM3954320: 8week HBx Srcp53  NOR sample 1; Danio rerio; RNA Seq", "GSM3954320", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954320", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "TriNOR3_1.fq.gz TriNOR3_2.fq.gz", "fastq fastq", 4035527100.0, 13451757.0, "GSM3954320 r1", "0:150 1:150", "A:1048654192;C:965234637;G:981448091;T:1039436158;N:754022", 150, 150, null, null, 1048654192, 965234637, 981448091, 1039436158, 754022, "SRX6465916", "SRS5126682", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.9318, 0.93291, 0.01634, 0.01669, 0.83155, 0.83431, 0.26548, 0.26993, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53179, "SRR9708001", "SRX6465915", "SRS5126681", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week Srcp53  FAT", "GSM3954319", null, "source name:8week Srcp53  High fat diet|strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:High fat diet", "8week Srcp53  FAT", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week Srcp53  High fat diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:High fat diet", "GSM3954319", "GSM3954319: 8week Srcp53  FAT; Danio rerio; RNA Seq", "GSM3954319", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954319", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "Src_FAT4_1.fq.gz Src_FAT4_2.fq.gz", "fastq fastq", 4095939900.0, 13653133.0, "GSM3954319 r1", "0:150 1:150", "A:1080000914;C:966449452;G:980758473;T:1067958610;N:772451", 150, 150, null, null, 1080000914, 966449452, 980758473, 1067958610, 772451, "SRX6465915", "SRS5126681", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.9214, 0.92115, 0.02194, 0.02143, 0.86425, 0.86679, 0.19828, 0.19948, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53180, "SRR9708000", "SRX6465914", "SRS5126680", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week Srcp53  DIO", "GSM3954318", null, "source name:8week Srcp53  Overfed|strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Overfed", "8week Srcp53  DIO", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week Srcp53  Overfed", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Overfed", "GSM3954318", "GSM3954318: 8week Srcp53  DIO; Danio rerio; RNA Seq", "GSM3954318", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954318", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "SrcDIO11_1.fq.gz SrcDIO11_2.fq.gz", "fastq fastq", 4295950800.0, 14319836.0, "GSM3954318 r1", "0:150 1:150", "A:1118680365;C:1026334652;G:1040877221;T:1109247541;N:811021", 150, 150, null, null, 1118680365, 1026334652, 1040877221, 1109247541, 811021, "SRX6465914", "SRS5126680", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.93615, 0.93765, 0.01871, 0.01885, 0.87097, 0.87369, 0.29136, 0.29027, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53181, "SRR9707999", "SRX6465913", "SRS5126679", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week Srcp53  NOR sample 2", "GSM3954317", null, "source name:8week Srcp53  Normal diet|strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Normal diet", "8week Srcp53  NOR sample 2", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week Srcp53  Normal diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Normal diet", "GSM3954317", "GSM3954317: 8week Srcp53  NOR sample 2; Danio rerio; RNA Seq", "GSM3954317", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954317", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "Src_NOR9_1.fq.gz Src_NOR9_2.fq.gz", "fastq fastq", 3230924400.0, 10769748.0, "GSM3954317 r1", "0:150 1:150", "A:849542686;C:763912445;G:775517170;T:841572201;N:379898", 150, 150, null, null, 849542686, 763912445, 775517170, 841572201, 379898, "SRX6465913", "SRS5126679", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.92205, 0.92321, 0.02638, 0.02642, 0.83248, 0.83546, 0.33062, 0.32957, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53182, "SRR9707998", "SRX6465912", "SRS5126677", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week Srcp53  NOR sample 1", "GSM3954316", null, "source name:8week Srcp53  Normal diet|strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Normal diet", "8week Srcp53  NOR sample 1", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week Srcp53  Normal diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:Srcp53 |tissue:Liver|diet:Normal diet", "GSM3954316", "GSM3954316: 8week Srcp53  NOR sample 1; Danio rerio; RNA Seq", "GSM3954316", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954316", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "Src_NOR5_1.fq.gz Src_NOR5_2.fq.gz", "fastq fastq", 3622050600.0, 12073502.0, "GSM3954316 r1", "0:150 1:150", "A:952640423;C:856805394;G:867903368;T:944017329;N:684086", 150, 150, null, null, 952640423, 856805394, 867903368, 944017329, 684086, "SRX6465912", "SRS5126677", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.93859, 0.9386, 0.02248, 0.02285, 0.85638, 0.85853, 0.25471, 0.26321, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53183, "SRR9707997", "SRX6465911", "SRS5126678", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week HBxp53  FAT", "GSM3954315", null, "source name:8week HBxp53  High fat diet|strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:High fat diet", "8week HBxp53  FAT", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week HBxp53  High fat diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:High fat diet", "GSM3954315", "GSM3954315: 8week HBxp53  FAT; Danio rerio; RNA Seq", "GSM3954315", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954315", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "HBxFAT12_1.fq.gz HBxFAT12_2.fq.gz", "fastq fastq", 3496192800.0, 11653976.0, "GSM3954315 r1", "0:150 1:150", "A:913664496;C:831395771;G:845661828;T:904814682;N:656023", 150, 150, null, null, 913664496, 831395771, 845661828, 904814682, 656023, "SRX6465911", "SRS5126678", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.93627, 0.93829, 0.01608, 0.0163, 0.87203, 0.87588, 0.20914, 0.20793, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53184, "SRR9707996", "SRX6465910", "SRS5126676", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week HBxp53  DIO", "GSM3954314", null, "source name:8week HBxp53  Overfed|strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Overfed", "8week HBxp53  DIO", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week HBxp53  Overfed", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Overfed", "GSM3954314", "GSM3954314: 8week HBxp53  DIO; Danio rerio; RNA Seq", "GSM3954314", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954314", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "HBxDIO13_1.fq.gz HBxDIO13_2.fq.gz", "fastq fastq", 4161988500.0, 13873295.0, "GSM3954314 r1", "0:150 1:150", "A:1100750154;C:978574151;G:993521613;T:1088360923;N:781659", 150, 150, null, null, 1100750154, 978574151, 993521613, 1088360923, 781659, "SRX6465910", "SRS5126676", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.91603, 0.91663, 0.02493, 0.02524, 0.85867, 0.86137, 0.24463, 0.2477, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53185, "SRR9707995", "SRX6465909", "SRS5126675", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week HBxp53  NOR sample 2", "GSM3954313", null, "source name:8week HBxp53  Normal diet|strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Normal diet", "8week HBxp53  NOR sample 2", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week HBxp53  Normal diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Normal diet", "GSM3954313", "GSM3954313: 8week HBxp53  NOR sample 2; Danio rerio; RNA Seq", "GSM3954313", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954313", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "HBxNOR15_1.fq.gz HBxNOR15_2.fq.gz", "fastq fastq", 3412777800.0, 11375926.0, "GSM3954313 r1", "0:150 1:150", "A:897716581;C:805966386;G:818686771;T:889764566;N:643496", 150, 150, null, null, 897716581, 805966386, 818686771, 889764566, 643496, "SRX6465909", "SRS5126675", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.92812, 0.92863, 0.02875, 0.02888, 0.85626, 0.85918, 0.32689, 0.32969, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53186, "SRR9707994", "SRX6465908", "SRS5126674", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week HBxp53  NOR sample 1", "GSM3954312", null, "source name:8week HBxp53  Normal diet|strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Normal diet", "8week HBxp53  NOR sample 1", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week HBxp53  Normal diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:HBxp53 |tissue:Liver|diet:Normal diet", "GSM3954312", "GSM3954312: 8week HBxp53  NOR sample 1; Danio rerio; RNA Seq", "GSM3954312", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954312", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "HBx_NOR2_1.fq.gz HBx_NOR2_2.fq.gz", "fastq fastq", 3251877900.0, 10839593.0, "GSM3954312 r1", "0:150 1:150", "A:853585195;C:770775549;G:781707938;T:845195300;N:613918", 150, 150, null, null, 853585195, 770775549, 781707938, 845195300, 613918, "SRX6465908", "SRS5126674", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.93901, 0.93913, 0.02224, 0.02245, 0.86766, 0.87089, 0.23209, 0.23176, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53187, "SRR9707993", "SRX6465907", "SRS5126672", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week WT FAT", "GSM3954311", null, "source name:8week WT High fat diet|strain/background:AB|genotype/variation:WT|tissue:Liver|diet:High fat diet", "8week WT FAT", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week WT High fat diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:WT|tissue:Liver|diet:High fat diet", "GSM3954311", "GSM3954311: 8week WT FAT; Danio rerio; RNA Seq", "GSM3954311", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954311", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "WT_FAT12_1.fq.gz WT_FAT12_2.fq.gz", "fastq fastq", 3748358400.0, 12494528.0, "GSM3954311 r1", "0:150 1:150", "A:984937396;C:887127956;G:901610349;T:973974336;N:708363", 150, 150, null, null, 984937396, 887127956, 901610349, 973974336, 708363, "SRX6465907", "SRS5126672", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.92386, 0.92371, 0.0296, 0.02954, 0.85021, 0.85313, 0.26314, 0.25996, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53188, "SRR9707992", "SRX6465906", "SRS5126673", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week WT DIO", "GSM3954310", null, "source name:8week WT Overfed|strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Overfed", "8week WT DIO", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week WT Overfed", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Overfed", "GSM3954310", "GSM3954310: 8week WT DIO; Danio rerio; RNA Seq", "GSM3954310", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954310", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "WT_DIO16_1.fq.gz WT_DIO16_2.fq.gz", "fastq fastq", 4022575800.0, 13408586.0, "GSM3954310 r1", "0:150 1:150", "A:1061317698;C:947922063;G:961268985;T:1051306042;N:761012", 150, 150, null, null, 1061317698, 947922063, 961268985, 1051306042, 761012, "SRX6465906", "SRS5126673", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.92971, 0.93058, 0.02073, 0.02033, 0.86334, 0.86645, 0.22401, 0.22308, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53189, "SRR9707991", "SRX6465905", "SRS5126671", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week WT NOR sample 2", "GSM3954309", null, "source name:8week WT Normal diet|strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet", "8week WT NOR sample 2", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week WT Normal diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet", "GSM3954309", "GSM3954309: 8week WT NOR sample 2; Danio rerio; RNA Seq", "GSM3954309", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954309", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "WT_NOR20_1.fq.gz WT_NOR20_2.fq.gz", "fastq fastq", 3481565100.0, 11605217.0, "GSM3954309 r1", "0:150 1:150", "A:922872893;C:816859095;G:828168259;T:912998471;N:666382", 150, 150, null, null, 922872893, 816859095, 828168259, 912998471, 666382, "SRX6465905", "SRS5126671", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.92796, 0.92775, 0.02044, 0.0205, 0.85058, 0.85372, 0.24017, 0.24546, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [53190, "SRR9707990", "SRX6465904", "SRS5126670", "SRP215269", "PRJNA555341", "Obesity synergizes with HBx  Src and p53 mutation accelerate hepatocarcinogenesis [RNA seq]", "GSE134495", "Transcriptome Analysis", "Previous studies have identified liver cancer associated to NASH  diabetes  obesity  and some genetic risk factors. We want to investigate the synergism between diet and genetic risk factors in hepatocarcinogenesis using omics data of four background zebrafish in three types of diet. We found the fishes have more genetic risk factors at the same time  and have higher probability to accelerate cancer formation. Overfed and high fat diet will increase the chance. Moreover  the results showed metabolism and genetic information processing  including the pathways of fatty acid metabolism  steroid biosynthesis and ribosome biogenesis are highly affected in hepatocellular carcinoma. Overall design: Four background zebrafish in three types of diet: Wild type  HBxp53   Srcp53   and HBx Srcp53  zebrafish in normal  overfed  and high fat diet. RNA was prepared from liver and analyzed by RNAseq.", "parent bioproject:PRJNA555327", "pubmed:31795276", null, "8week WT NOR sample 1", "GSM3954308", null, "source name:8week WT Normal diet|strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet", "8week WT NOR sample 1", "Reads were trimmed and Read quality was checked using FastQC v0.11.5. Reads were aligned to the zebrafish genome GRCz10/danRer10 using HISAT2 v2.1.0 with parameters   mm   dta  x  1  2  S SAMtools v1.7 was then converted SAM files to BAM files and sorted. BAM files were transmitted to StringTie v1.3.4d for transcript assembly. The expression levels of all transcripts were estimated and calculated by StringTie and ballgown v2.16.0 in R v3.5.3. Genome build: GRCz10/danRer10 Supplementary files format and content: *.txt: Tab delimited text files include FPKM values for each Sample using ballgown package.", "8week WT Normal diet", "The three mpf of four types of fish were fed using three different feeding methods: normal diet  overfeeding and high fat diet. Normal diet: feeding with 0.5 ml of Artemia with a dropper one time daily. Overfeeding: feeding 12 fold of Artemia compared to NOR group by feeding with 2ml with a dropper three times daily. High fat feed: feeding with 0.5 ml of Artemia with a dropper one time daily  and high fat diet fish food one spoon  about 0.22g three times daily. For 8 weeks  the zebrafishes were sacrificed and liver specimens were collected.", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "The AB zebrafish strain Danio rerio  Tgfabp10a:src p53   Tgfabp10a:HBx p53   and Tgfabp10a:HBx src p53   were used and growth for 8 weeks.", "strain/background:AB|genotype/variation:WT|tissue:Liver|diet:Normal diet", "GSM3954308", "GSM3954308: 8week WT NOR sample 1; Danio rerio; RNA Seq", "GSM3954308", null, "1", "Total RNA was isolated by NucleoSpin\u00ae RNA kit MACHEREY NAGEL  US following the manufacturer manual  and RNA samples was eluted in 40 \u03bcl RNase free water. RNA quantity and purity were assessed using NanoDrop ND 1000. Pass criteria for absorbance ratios were established as A260/A280 > 1.8 and A260/A230 > 1.5 average to be acceptable. RNA integrity RIN# was determined by Agilent 2100 Bioanalyzer with RNA 6000 Nano Assay with passing criteria set at > 7. Libraries were prepared according to Illumina's instructions with the NEBNext Ultra RNA Library Prep Kit. Briefly  fragmentation was performed at elevated temperature using divalent cations post mRNA extraction. First and second strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase RNase H   and DNA Polymerase I and RNase H  respectively. NEBNext Adaptor were ligated to blunt ends of the cDNA fragments. Next  the adaptor ligated cDNA were treated with 3 \u03bcl USER Enzyme before PCR. Then  the PCR products were purified using AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.", "GEO Accession:GSM3954308", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP215269", null, null, "WT_NOR2_1.fq.gz WT_NOR2_2.fq.gz", "fastq fastq", 4215976200.0, 14053254.0, "GSM3954308 r1", "0:150 1:150", "A:1099428840;C:1005939535;G:1020758972;T:1089047539;N:801314", 150, 150, null, null, 1099428840, 1005939535, 1020758972, 1089047539, 801314, "SRX6465904", "SRS5126670", "SRA922815", "GEO", "National Chiao Tung University", 2, 0.92522, 0.92502, 0.02531, 0.02547, 0.87113, 0.8734, 0.28382, 0.28497, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "nebnext", "bulk", "unknown", "unknown", null, "Taiwan", "2019-07-18", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56067, "SRR10868218", "SRX7538241", "SRS5976905", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "WDFL rep2", "GSM4259038", null, "source name:Withdrawal Female Liver 2|strain:short fin  'AB' strain|condition:Withdrawal|Sex:female|tissue:Liver", "WDFL rep2", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Withdrawal Female Liver 2", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Withdrawal|Sex:Female|tissue:Liver", "GSM4259038", "GSM4259038: WDFL rep2; Danio rerio; RNA Seq", "GSM4259038", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259038", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "WDFL2_R2.fastq.gz WDFL2_R1.fastq.gz", "fastq fastq", 5978725600.0, 29893628.0, "GSM4259038 r1", "0:100 1:100", "A:1574223203;C:1415058444;G:1415352341;T:1571279633;N:2811979", 100, 100, null, null, 1574223203, 1415058444, 1415352341, 1571279633, 2811979, "SRX7538241", "SRS5976905", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.97373, 0.9727, 0.02754, 0.0273, 0.83717, 0.84053, 0.20675, 0.20492, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56068, "SRR10868217", "SRX7538240", "SRS5976904", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "WDFL rep1", "GSM4259037", null, "source name:Withdrawal Female Liver 1|strain:short fin  'AB' strain|condition:Withdrawal|Sex:female|tissue:Liver", "WDFL rep1", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Withdrawal Female Liver 1", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Withdrawal|Sex:Female|tissue:Liver", "GSM4259037", "GSM4259037: WDFL rep1; Danio rerio; RNA Seq", "GSM4259037", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259037", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "WDFL1_R1.fastq.gz WDFL1_R2.fastq.gz", "fastq fastq", 8803793400.0, 44018967.0, "GSM4259037 r1", "0:100 1:100", "A:2301352863;C:2094763989;G:2089744439;T:2313772264;N:4159845", 100, 100, null, null, 2301352863, 2094763989, 2089744439, 2313772264, 4159845, "SRX7538240", "SRS5976904", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.97269, 0.97147, 0.02717, 0.02755, 0.83948, 0.84206, 0.20335, 0.20575, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56069, "SRR10868216", "SRX7538239", "SRS5976903", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "WDML rep2", "GSM4259036", null, "source name:Withdrawal Male Liver 2|strain:short fin  'AB' strain|condition:Withdrawal|Sex:male|tissue:Liver", "WDML rep2", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Withdrawal Male Liver 2", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Withdrawal|Sex:Male|tissue:Liver", "GSM4259036", "GSM4259036: WDML rep2; Danio rerio; RNA Seq", "GSM4259036", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259036", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "WDML2_R2.fastq.gz WDML2_R1.fastq.gz", "fastq fastq", 7015689200.0, 35078446.0, "GSM4259036 r1", "0:100 1:100", "A:1779798478;C:1742766511;G:1769340834;T:1720182359;N:3601018", 100, 100, null, null, 1779798478, 1742766511, 1769340834, 1720182359, 3601018, "SRX7538239", "SRS5976903", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.94907, 0.94528, 0.03016, 0.03069, 0.79628, 0.79859, 0.53607, 0.53294, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56070, "SRR10868215", "SRX7538238", "SRS5976902", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "WDML rep1", "GSM4259035", null, "source name:Withdrawal Male Liver 1|strain:short fin  'AB' strain|condition:Withdrawal|Sex:male|tissue:Liver", "WDML rep1", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Withdrawal Male Liver 1", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Withdrawal|Sex:Male|tissue:Liver", "GSM4259035", "GSM4259035: WDML rep1; Danio rerio; RNA Seq", "GSM4259035", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259035", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "WDML1_R1.fastq.gz WDML1_R2.fastq.gz", "fastq fastq", 7147989000.0, 35739945.0, "GSM4259035 r1", "0:100 1:100", "A:1780372303;C:1815362554;G:1862406693;T:1686233575;N:3613875", 100, 100, null, null, 1780372303, 1815362554, 1862406693, 1686233575, 3613875, "SRX7538238", "SRS5976902", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.93918, 0.93766, 0.02982, 0.02971, 0.80535, 0.80913, 0.52958, 0.52331, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56071, "SRR10868214", "SRX7538237", "SRS5976901", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "ALFL rep2", "GSM4259034", null, "source name:Alcohol exposed Female Liver 2|strain:short fin  'AB' strain|condition:Alcohol exposed|Sex:female|tissue:Liver", "ALFL rep2", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Alcohol exposed Female Liver 2", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Alcohol exposed|Sex:Female|tissue:Liver", "GSM4259034", "GSM4259034: ALFL rep2; Danio rerio; RNA Seq", "GSM4259034", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259034", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "ALFL2_R1.fastq.gz ALFL2_R2.fastq.gz", "fastq fastq", 8678803800.0, 43394019.0, "GSM4259034 r1", "0:100 1:100", "A:2254928688;C:2084380554;G:2076784437;T:2258809206;N:3900915", 100, 100, null, null, 2254928688, 2084380554, 2076784437, 2258809206, 3900915, "SRX7538237", "SRS5976901", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.9695, 0.96915, 0.03085, 0.03134, 0.80908, 0.8127, 0.29284, 0.31107, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56072, "SRR10868213", "SRX7538236", "SRS5976900", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "ALFL rep1", "GSM4259033", null, "source name:Alcohol exposed Female Liver 1|strain:short fin  'AB' strain|condition:Alcohol exposed|Sex:female|tissue:Liver", "ALFL rep1", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Alcohol exposed Female Liver 1", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Alcohol exposed|Sex:Female|tissue:Liver", "GSM4259033", "GSM4259033: ALFL rep1; Danio rerio; RNA Seq", "GSM4259033", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259033", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "ALFL1_R2.fastq.gz ALFL1_R1.fastq.gz", "fastq fastq", 9562583000.0, 47812915.0, "GSM4259033 r1", "0:100 1:100", "A:2511938021;C:2281314685;G:2285416160;T:2479465786;N:4448348", 100, 100, null, null, 2511938021, 2281314685, 2285416160, 2479465786, 4448348, "SRX7538236", "SRS5976900", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.96678, 0.96014, 0.03186, 0.03232, 0.81205, 0.81832, 0.31507, 0.30599, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56073, "SRR10868212", "SRX7538235", "SRS5976899", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "ALML rep2", "GSM4259032", null, "source name:Alcohol exposed Male Liver 2|strain:short fin  'AB' strain|condition:Alcohol exposed|Sex:male|tissue:Liver", "ALML rep2", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Alcohol exposed Male Liver 2", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Alcohol exposed|Sex:Male|tissue:Liver", "GSM4259032", "GSM4259032: ALML rep2; Danio rerio; RNA Seq", "GSM4259032", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259032", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "ALML2_R2.fastq.gz ALML2_R1.fastq.gz", "fastq fastq", 5920856200.0, 29604281.0, "GSM4259032 r1", "0:100 1:100", "A:1560024572;C:1398117012;G:1390600317;T:1568986226;N:3128073", 100, 100, null, null, 1560024572, 1398117012, 1390600317, 1568986226, 3128073, "SRX7538235", "SRS5976899", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.94976, 0.94841, 0.05469, 0.05628, 0.79415, 0.79864, 0.55278, 0.54546, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56074, "SRR10868211", "SRX7538234", "SRS5976898", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "ALML rep1", "GSM4259031", null, "source name:Alcohol exposed Male Liver 1|strain:short fin  'AB' strain|condition:Alcohol exposed|Sex:male|tissue:Liver", "ALML rep1", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Alcohol exposed Male Liver 1", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Alcohol exposed|Sex:Male|tissue:Liver", "GSM4259031", "GSM4259031: ALML rep1; Danio rerio; RNA Seq", "GSM4259031", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259031", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "ALML1_R1.fastq.gz ALML1_R2.fastq.gz", "fastq fastq", 6004949000.0, 30024745.0, "GSM4259031 r1", "0:100 1:100", "A:1546230434;C:1462161154;G:1452941715;T:1540051007;N:3564690", 100, 100, null, null, 1546230434, 1462161154, 1452941715, 1540051007, 3564690, "SRX7538234", "SRS5976898", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.95167, 0.95003, 0.04572, 0.04615, 0.79746, 0.80018, 0.48729, 0.48752, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56075, "SRR10868210", "SRX7538233", "SRS5976897", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "CTFL rep2", "GSM4259030", null, "source name:Control Female Liver 2|strain:short fin  'AB' strain|condition:Control|Sex:female|tissue:Liver", "CTFL rep2", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Control Female Liver 2", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Control|Sex:Female|tissue:Liver", "GSM4259030", "GSM4259030: CTFL rep2; Danio rerio; RNA Seq", "GSM4259030", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259030", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "CTFL2_R1.fastq.gz CTFL2_R2.fastq.gz", "fastq fastq", 8204545000.0, 41022725.0, "GSM4259030 r1", "0:100 1:100", "A:2141255352;C:1960063343;G:1940272991;T:2159263280;N:3690034", 100, 100, null, null, 2141255352, 1960063343, 1940272991, 2159263280, 3690034, "SRX7538233", "SRS5976897", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.96794, 0.96592, 0.03373, 0.03363, 0.83051, 0.83372, 0.26497, 0.27281, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56076, "SRR10868209", "SRX7538232", "SRS5976896", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "CTFL rep1", "GSM4259029", null, "source name:Control Female Liver 1|strain:short fin  'AB' strain|condition:Control|Sex:female|tissue:Liver", "CTFL rep1", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Control Female Liver 1", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Control|Sex:Female|tissue:Liver", "GSM4259029", "GSM4259029: CTFL rep1; Danio rerio; RNA Seq", "GSM4259029", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259029", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "CTFL1_R1.fastq.gz CTFL1_R2.fastq.gz", "fastq fastq", 7090165000.0, 35450825.0, "GSM4259029 r1", "0:100 1:100", "A:1885143566;C:1658541874;G:1661861079;T:1881339038;N:3279443", 100, 100, null, null, 1885143566, 1658541874, 1661861079, 1881339038, 3279443, "SRX7538232", "SRS5976896", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.95522, 0.95538, 0.03516, 0.03563, 0.81556, 0.81734, 0.32249, 0.3228, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56077, "SRR10868208", "SRX7538231", "SRS5976895", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "CTML rep2", "GSM4259028", null, "source name:Control Male Liver 2|strain:short fin  'AB' strain|condition:Control|Sex:male|tissue:Liver", "CTML rep2", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Control Male Liver 2", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Control|Sex:Male|tissue:Liver", "GSM4259028", "GSM4259028: CTML rep2; Danio rerio; RNA Seq", "GSM4259028", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259028", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "CTML2_R1.fastq.gz CTML2_R2.fastq.gz", "fastq fastq", 9796791200.0, 48983956.0, "GSM4259028 r1", "0:100 1:100", "A:2721758622;C:2238538476;G:2213513091;T:2622439538;N:541473", 100, 100, null, null, 2721758622, 2238538476, 2213513091, 2622439538, 541473, "SRX7538231", "SRS5976895", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.9236, 0.92195, 0.07857, 0.07792, 0.79095, 0.79431, 0.55394, 0.55633, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [56078, "SRR10868207", "SRX7538230", "SRS5976894", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "CTML rep1", "GSM4259027", null, "source name:Control Male Liver 1|strain:short fin  'AB' strain|condition:Control|Sex:male|tissue:Liver", "CTML rep1", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Control Male Liver 1", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Control|Sex:Male|tissue:Liver", "GSM4259027", "GSM4259027: CTML rep1; Danio rerio; RNA Seq", "GSM4259027", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259027", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "CTML1_R1.fastq.gz CTML1_R2.fastq.gz", "fastq fastq", 8984067200.0, 44920336.0, "GSM4259027 r1", "0:100 1:100", "A:2427722499;C:2092739125;G:2070318707;T:2392809051;N:477818", 100, 100, null, null, 2427722499, 2092739125, 2070318707, 2392809051, 477818, "SRX7538230", "SRS5976894", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.92804, 0.92566, 0.06599, 0.06574, 0.80728, 0.80791, 0.53925, 0.53265, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65887, "SRR15667963", "SRX11964789", "SRS9973857", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 6", "GSM5549117", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "liver  train overfeed 6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "GSM5549117", "GSM5549117: liver  train overfeed 6; Danio rerio; RNA Seq", "GSM5549117", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549117", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L24B_1.fq.gz L24B_2.fq.gz", "fastq fastq", 4893222400.0, 48932224.0, "GSM5549117 r1", "0:100 1:100", "A:1299363606;C:1127714226;G:1149448002;T:1316696566;N:0", 100, 100, null, null, 1299363606, 1127714226, 1149448002, 1316696566, 0, "SRX11964789", "SRS9973857", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94811, null, 0.06102, null, 0.81306, null, 0.58353, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65888, "SRR15667962", "SRX11964788", "SRS9973856", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 5", "GSM5549116", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "liver  train overfeed 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "GSM5549116", "GSM5549116: liver  train overfeed 5; Danio rerio; RNA Seq", "GSM5549116", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L23B_1.fq.gz L23B_2.fq.gz", "fastq fastq", 4864315800.0, 48643158.0, "GSM5549116 r1", "0:100 1:100", "A:1269157216;C:1139579077;G:1173873653;T:1281705854;N:0", 100, 100, null, null, 1269157216, 1139579077, 1173873653, 1281705854, 0, "SRX11964788", "SRS9973856", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94747, null, 0.0487, null, 0.81779, null, 0.56304, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65889, "SRR15667961", "SRX11964787", "SRS9973855", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 4", "GSM5549115", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "liver  train overfeed 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:male|strain:ABTL", "GSM5549115", "GSM5549115: liver  train overfeed 4; Danio rerio; RNA Seq", "GSM5549115", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L22B_1.fq.gz L22B_2.fq.gz", "fastq fastq", 4861767400.0, 48617674.0, "GSM5549115 r1", "0:100 1:100", "A:1272156595;C:1138672054;G:1163686667;T:1287252084;N:0", 100, 100, null, null, 1272156595, 1138672054, 1163686667, 1287252084, 0, "SRX11964787", "SRS9973855", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95316, null, 0.0514, null, 0.82008, null, 0.50642, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65890, "SRR15667960", "SRX11964786", "SRS9973854", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 3", "GSM5549114", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "liver  train overfeed 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "GSM5549114", "GSM5549114: liver  train overfeed 3; Danio rerio; RNA Seq", "GSM5549114", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L21B_1.fq.gz L21B_2.fq.gz", "fastq fastq", 4830571800.0, 48305718.0, "GSM5549114 r1", "0:100 1:100", "A:1279428022;C:1123545637;G:1144703564;T:1282894577;N:0", 100, 100, null, null, 1279428022, 1123545637, 1144703564, 1282894577, 0, "SRX11964786", "SRS9973854", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95734, null, 0.02001, null, 0.8868, null, 0.12725, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65891, "SRR15667959", "SRX11964785", "SRS9973853", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 2", "GSM5549113", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "liver  train overfeed 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "GSM5549113", "GSM5549113: liver  train overfeed 2; Danio rerio; RNA Seq", "GSM5549113", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L20B_1.fq.gz L20B_2.fq.gz", "fastq fastq", 4798900200.0, 47989002.0, "GSM5549113 r1", "0:100 1:100", "A:1264903507;C:1122454994;G:1142785530;T:1268756169;N:0", 100, 100, null, null, 1264903507, 1122454994, 1142785530, 1268756169, 0, "SRX11964785", "SRS9973853", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95953, null, 0.02579, null, 0.87251, null, 0.20039, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65892, "SRR15667958", "SRX11964784", "SRS9973852", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train overfeed 1", "GSM5549112", null, "source name:liver|tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "liver  train overfeed 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:overfeed|gender:female|strain:ABTL", "GSM5549112", "GSM5549112: liver  train overfeed 1; Danio rerio; RNA Seq", "GSM5549112", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L19B_1.fq.gz L19B_2.fq.gz", "fastq fastq", 4834397800.0, 48343978.0, "GSM5549112 r1", "0:100 1:100", "A:1279393804;C:1125815329;G:1148443590;T:1280745077;N:0", 100, 100, null, null, 1279393804, 1125815329, 1148443590, 1280745077, 0, "SRX11964784", "SRS9973852", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95933, null, 0.02008, null, 0.89483, null, 0.14592, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65893, "SRR15667957", "SRX11964783", "SRS9973851", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 6", "GSM5549111", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "liver  train ctrl 6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "GSM5549111", "GSM5549111: liver  train ctrl 6; Danio rerio; RNA Seq", "GSM5549111", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L18B_1.fq.gz L18B_2.fq.gz", "fastq fastq", 4821948400.0, 48219484.0, "GSM5549111 r1", "0:100 1:100", "A:1291565962;C:1101325255;G:1121237816;T:1307819367;N:0", 100, 100, null, null, 1291565962, 1101325255, 1121237816, 1307819367, 0, "SRX11964783", "SRS9973851", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94729, null, 0.06306, null, 0.81207, null, 0.58228, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65894, "SRR15667956", "SRX11964782", "SRS9973850", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 5", "GSM5549110", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "liver  train ctrl 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "GSM5549110", "GSM5549110: liver  train ctrl 5; Danio rerio; RNA Seq", "GSM5549110", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549110", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L17B_1.fq.gz L17B_2.fq.gz", "fastq fastq", 4803628200.0, 48036282.0, "GSM5549110 r1", "0:100 1:100", "A:1284799467;C:1098135007;G:1120469212;T:1300224514;N:0", 100, 100, null, null, 1284799467, 1098135007, 1120469212, 1300224514, 0, "SRX11964782", "SRS9973850", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.9496, null, 0.0625, null, 0.81456, null, 0.59107, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65895, "SRR15667955", "SRX11964781", "SRS9973849", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 4", "GSM5549109", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "liver  train ctrl 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:male|strain:ABTL", "GSM5549109", "GSM5549109: liver  train ctrl 4; Danio rerio; RNA Seq", "GSM5549109", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549109", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L16B_1.fq.gz L16B_2.fq.gz", "fastq fastq", 4810847400.0, 48108474.0, "GSM5549109 r1", "0:100 1:100", "A:1282522728;C:1105003262;G:1127602301;T:1295719109;N:0", 100, 100, null, null, 1282522728, 1105003262, 1127602301, 1295719109, 0, "SRX11964781", "SRS9973849", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94654, null, 0.05935, null, 0.81525, null, 0.55406, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65896, "SRR15667954", "SRX11964780", "SRS9973848", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 3", "GSM5549108", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "liver  train ctrl 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "GSM5549108", "GSM5549108: liver  train ctrl 3; Danio rerio; RNA Seq", "GSM5549108", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549108", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L15B_1.fq.gz L15B_2.fq.gz", "fastq fastq", 4985037400.0, 49850374.0, "GSM5549108 r1", "0:100 1:100", "A:1350433123;C:1126555415;G:1149552334;T:1358496528;N:0", 100, 100, null, null, 1350433123, 1126555415, 1149552334, 1358496528, 0, "SRX11964780", "SRS9973848", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94223, null, 0.05241, null, 0.81753, null, 0.38734, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65897, "SRR15667953", "SRX11964779", "SRS9973847", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 2", "GSM5549107", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "liver  train ctrl 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "GSM5549107", "GSM5549107: liver  train ctrl 2; Danio rerio; RNA Seq", "GSM5549107", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L14B_1.fq.gz L14B_2.fq.gz", "fastq fastq", 4804454800.0, 48044548.0, "GSM5549107 r1", "0:100 1:100", "A:1265573746;C:1124189778;G:1148662079;T:1266029197;N:0", 100, 100, null, null, 1265573746, 1124189778, 1148662079, 1266029197, 0, "SRX11964779", "SRS9973847", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95891, null, 0.02268, null, 0.88392, null, 0.17772, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65898, "SRR15667952", "SRX11964778", "SRS9973846", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  train ctrl 1", "GSM5549106", null, "source name:liver|tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "liver  train ctrl 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:trained|feed:ctrl|gender:female|strain:ABTL", "GSM5549106", "GSM5549106: liver  train ctrl 1; Danio rerio; RNA Seq", "GSM5549106", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549106", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L13B_1.fq.gz L13B_2.fq.gz", "fastq fastq", 4822830200.0, 48228302.0, "GSM5549106 r1", "0:100 1:100", "A:1276481281;C:1123835516;G:1144873235;T:1277640168;N:0", 100, 100, null, null, 1276481281, 1123835516, 1144873235, 1277640168, 0, "SRX11964778", "SRS9973846", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.96141, null, 0.0197, null, 0.89388, null, 0.1349, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65899, "SRR15667951", "SRX11964777", "SRS9973845", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 6", "GSM5549105", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "liver  ctrl overfeed 6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "GSM5549105", "GSM5549105: liver  ctrl overfeed 6; Danio rerio; RNA Seq", "GSM5549105", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549105", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L9B_1.fq.gz L9B_2.fq.gz", "fastq fastq", 4818164600.0, 48181646.0, "GSM5549105 r1", "0:100 1:100", "A:1279585168;C:1117941633;G:1137085086;T:1283552713;N:0", 100, 100, null, null, 1279585168, 1117941633, 1137085086, 1283552713, 0, "SRX11964777", "SRS9973845", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95794, null, 0.0217, null, 0.8772, null, 0.13327, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65900, "SRR15667950", "SRX11964776", "SRS9973844", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 5", "GSM5549104", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "liver  ctrl overfeed 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "GSM5549104", "GSM5549104: liver  ctrl overfeed 5; Danio rerio; RNA Seq", "GSM5549104", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L8B_1.fq.gz L8B_2.fq.gz", "fastq fastq", 4815366200.0, 48153662.0, "GSM5549104 r1", "0:100 1:100", "A:1274920749;C:1122213902;G:1140211257;T:1278020292;N:0", 100, 100, null, null, 1274920749, 1122213902, 1140211257, 1278020292, 0, "SRX11964776", "SRS9973844", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95864, null, 0.02123, null, 0.88805, null, 0.13863, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65901, "SRR15667949", "SRX11964775", "SRS9973843", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 4", "GSM5549103", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "liver  ctrl overfeed 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:female|strain:ABTL", "GSM5549103", "GSM5549103: liver  ctrl overfeed 4; Danio rerio; RNA Seq", "GSM5549103", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L7B_1.fq.gz L7B_2.fq.gz", "fastq fastq", 4806451200.0, 48064512.0, "GSM5549103 r1", "0:100 1:100", "A:1272428504;C:1119437887;G:1139899400;T:1274685409;N:0", 100, 100, null, null, 1272428504, 1119437887, 1139899400, 1274685409, 0, "SRX11964775", "SRS9973843", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.9605, null, 0.02337, null, 0.87625, null, 0.17173, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65902, "SRR15667948", "SRX11964774", "SRS9973842", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 3", "GSM5549102", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "liver  ctrl overfeed 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "GSM5549102", "GSM5549102: liver  ctrl overfeed 3; Danio rerio; RNA Seq", "GSM5549102", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L12B_1.fq.gz L12B_2.fq.gz", "fastq fastq", 4808986200.0, 48089862.0, "GSM5549102 r1", "0:100 1:100", "A:1282711930;C:1106482446;G:1126540026;T:1293251798;N:0", 100, 100, null, null, 1282711930, 1106482446, 1126540026, 1293251798, 0, "SRX11964774", "SRS9973842", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95163, null, 0.05783, null, 0.80872, null, 0.56282, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65903, "SRR15667947", "SRX11964773", "SRS9973841", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 2", "GSM5549101", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "liver  ctrl overfeed 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "GSM5549101", "GSM5549101: liver  ctrl overfeed 2; Danio rerio; RNA Seq", "GSM5549101", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549101", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L11B_1.fq.gz L11B_2.fq.gz", "fastq fastq", 4813626000.0, 48136260.0, "GSM5549101 r1", "0:100 1:100", "A:1280868095;C:1108012462;G:1126540954;T:1298204489;N:0", 100, 100, null, null, 1280868095, 1108012462, 1126540954, 1298204489, 0, "SRX11964773", "SRS9973841", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94831, null, 0.05349, null, 0.81513, null, 0.57243, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65904, "SRR15667946", "SRX11964772", "SRS9973840", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl overfeed 1", "GSM5549100", null, "source name:liver|tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "liver  ctrl overfeed 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:overfeed|gender:male|strain:ABTL", "GSM5549100", "GSM5549100: liver  ctrl overfeed 1; Danio rerio; RNA Seq", "GSM5549100", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L10B_1.fq.gz L10B_2.fq.gz", "fastq fastq", 4810219200.0, 48102192.0, "GSM5549100 r1", "0:100 1:100", "A:1291986049;C:1097301072;G:1114733041;T:1306199038;N:0", 100, 100, null, null, 1291986049, 1097301072, 1114733041, 1306199038, 0, "SRX11964772", "SRS9973840", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.9477, null, 0.06719, null, 0.80762, null, 0.56967, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65905, "SRR15667945", "SRX11964771", "SRS9973839", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 6", "GSM5549099", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "liver  ctrl ctrl 6", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "GSM5549099", "GSM5549099: liver  ctrl ctrl 6; Danio rerio; RNA Seq", "GSM5549099", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L6B_1.fq.gz L6B_2.fq.gz", "fastq fastq", 4800718000.0, 48007180.0, "GSM5549099 r1", "0:100 1:100", "A:1258342638;C:1122320482;G:1144931913;T:1275122967;N:0", 100, 100, null, null, 1258342638, 1122320482, 1144931913, 1275122967, 0, "SRX11964771", "SRS9973839", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.953, null, 0.05324, null, 0.81257, null, 0.58562, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65906, "SRR15667944", "SRX11964770", "SRS9973838", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 5", "GSM5549098", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "liver  ctrl ctrl 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "GSM5549098", "GSM5549098: liver  ctrl ctrl 5; Danio rerio; RNA Seq", "GSM5549098", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549098", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L5B_1.fq.gz L5B_2.fq.gz", "fastq fastq", 4806088800.0, 48060888.0, "GSM5549098 r1", "0:100 1:100", "A:1271888694;C:1114093824;G:1133421540;T:1286684742;N:0", 100, 100, null, null, 1271888694, 1114093824, 1133421540, 1286684742, 0, "SRX11964770", "SRS9973838", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95001, null, 0.05792, null, 0.807, null, 0.56126, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65907, "SRR15667943", "SRX11964769", "SRS9973837", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 4", "GSM5549097", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "liver  ctrl ctrl 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:male|strain:ABTL", "GSM5549097", "GSM5549097: liver  ctrl ctrl 4; Danio rerio; RNA Seq", "GSM5549097", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549097", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L4B_1.fq.gz L4B_2.fq.gz", "fastq fastq", 4793658200.0, 47936582.0, "GSM5549097 r1", "0:100 1:100", "A:1278328591;C:1101882376;G:1120230481;T:1293216752;N:0", 100, 100, null, null, 1278328591, 1101882376, 1120230481, 1293216752, 0, "SRX11964769", "SRS9973837", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.94635, null, 0.06821, null, 0.77814, null, 0.57203, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65908, "SRR15667942", "SRX11964768", "SRS9973836", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 3", "GSM5549096", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "liver  ctrl ctrl 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "GSM5549096", "GSM5549096: liver  ctrl ctrl 3; Danio rerio; RNA Seq", "GSM5549096", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549096", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L3B_1.fq.gz L3B_2.fq.gz", "fastq fastq", 4826663000.0, 48266630.0, "GSM5549096 r1", "0:100 1:100", "A:1279595092;C:1123953174;G:1141367365;T:1281747369;N:0", 100, 100, null, null, 1279595092, 1123953174, 1141367365, 1281747369, 0, "SRX11964768", "SRS9973836", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.9594, null, 0.02127, null, 0.88463, null, 0.12493, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65909, "SRR15667941", "SRX11964767", "SRS9973835", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 2", "GSM5549095", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "liver  ctrl ctrl 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "GSM5549095", "GSM5549095: liver  ctrl ctrl 2; Danio rerio; RNA Seq", "GSM5549095", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549095", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L2B_1.fq.gz L2B_2.fq.gz", "fastq fastq", 4825604600.0, 48256046.0, "GSM5549095 r1", "0:100 1:100", "A:1280321186;C:1120511740;G:1138899889;T:1285871785;N:0", 100, 100, null, null, 1280321186, 1120511740, 1138899889, 1285871785, 0, "SRX11964767", "SRS9973835", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95896, null, 0.0192, null, 0.88899, null, 0.11515, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [65910, "SRR15667940", "SRX11964766", "SRS9973834", "SRP334698", "PRJNA758884", "Metabolic and transcriptional adaptations improve physical performance of zebrafish", "GSE183023", "Transcriptome Analysis", "Background: Obesity is a worldwide public health problem with increasing prevalence and affects 80% of diabetes mellitus type 2 cases. Zebrafish Danio rerio are an established model organism for studying obesity and diabetes including diabetic microvascular complications. We aimed to determine whether physical activity is an appropriate tool to examine training effects in zebrafish and to analyse metabolic and transcriptional processes in trained zebrafish. Methods: A 2  and 8 weeks experimental training phase protocol with adult zebrafish in a swim tunnel system was established. We examined zebrafish basic characteristics before and post training such as body weight  body length and maximum speed and considered overfeeding as an additional parameter in the 8 weeks training protocol. Ultimately  the effects of training and overfeeding on blood glucose  muscle core metabolism and liver gene expression using RNA Seq were investigated. Results: Zebrafish maximum speed was correlated with body length and was significantly increased post 2 weeks of training. Maximum swim speed further increased post 8 weeks of training in both the normalfed and the overfed groups  but training was found not to be sufficient in preventing weight gain in overfed fish. Metabolome and transcriptome profiling in trained fish exhibited increased blood glucose levels in the short term and upregulated energy supply pathways in the long term. Conclusion: Swim training is a valuable tool to study effects of physical activity in zebrafish  which is accompanied by metabolic and transcriptional adaptations. Overall design: total RNA sequencing was performed with 24 zebrafish liver samples ABTL strain  including 6 control fish  6 overfed fish  6 trained fish  6 trained and overfed fish", null, "pubmed:34679716", null, "liver  ctrl ctrl 1", "GSM5549094", null, "source name:liver|tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "liver  ctrl ctrl 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates  generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.", "liver", "Fish of the overfeeding groups ctr overfeed and train overfeed were fed with 9 mL of living shrimps per fish spread over the morning 3 times 3 mL and 2 spoons of SDS 400 per tank in the postnoon. Fish of the training groups train ctrl and train overfeed were trained every other day from Monday to Friday alternating twice or thrice per week for 8 weeks 20 training sessions in total.", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "Zebrafish of the ABTL strain were reared and maintained at 28 \u00b0C and kept under 13 h light/11 h dark cycle in groups of 6 fish per tank.", "tissue:liver|training:ctrl|feed:ctrl|gender:female|strain:ABTL", "GSM5549094", "GSM5549094: liver  ctrl ctrl 1; Danio rerio; RNA Seq", "GSM5549094", null, "1", "Livers were removed and flash frozen on dry ice. RNA was isolated from liver samples using the RNeasy\u00ae Mini Kit from QIAGEN Hilden  Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", "GEO Accession:GSM5549094", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP334698", null, null, "L1B_1.fq.gz L1B_2.fq.gz", "fastq fastq", 4829756800.0, 48297568.0, "GSM5549094 r1", "0:100 1:100", "A:1282017434;C:1119791375;G:1138880812;T:1289067179;N:0", 100, 100, null, null, 1282017434, 1119791375, 1138880812, 1289067179, 0, "SRX11964766", "SRS9973834", "SRA1285419", "GEO", "ZMF, University Heidelberg", 1, 0.95838, null, 0.03146, null, 0.8479, null, 0.28451, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2021-08-30", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71670, "SRR21930613", "SRX17915137", "SRS15430839", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aminus6", "GSM6645224", null, "source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "Aminus6", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "GSM6645224", "GSM6645224: Aminus6; Danio rerio; RNA Seq", "GSM6645224 r1", "GSM6645224", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aminus6_S24_R1_001.fastq.gz Aminus6_S24_R2_001.fastq.gz", "fastq fastq", 6999317053.0, 46500434.0, "GSM6645224 r1", "0:75.15 1:75.37", "A:1800440367;C:1667972609;G:1696169122;T:1822834920;N:11900035", 75, 75, null, null, 1800440367, 1667972609, 1696169122, 1822834920, 11900035, "SRX17915137", "SRS15430839", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97713, 0.97834, 0.05347, 0.05209, 0.77285, 0.77516, 0.5586, 0.56518, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71671, "SRR21930614", "SRX17915136", "SRS15430838", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aminus5", "GSM6645223", null, "source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "Aminus5", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "GSM6645223", "GSM6645223: Aminus5; Danio rerio; RNA Seq", "GSM6645223 r1", "GSM6645223", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aminus5_S23_R1_001.fastq.gz Aminus5_S23_R2_001.fastq.gz", "fastq fastq", 6882375184.0, 45764657.0, "GSM6645223 r1", "0:75.05 1:75.33", "A:1748753730;C:1653160606;G:1699833991;T:1766084534;N:14542323", 75, 75, null, null, 1748753730, 1653160606, 1699833991, 1766084534, 14542323, "SRX17915136", "SRS15430838", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97955, 0.9807, 0.04149, 0.04021, 0.81251, 0.81499, 0.56267, 0.56974, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71672, "SRR21930615", "SRX17915135", "SRS15430837", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aminus4", "GSM6645222", null, "source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "Aminus4", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "GSM6645222", "GSM6645222: Aminus4; Danio rerio; RNA Seq", "GSM6645222 r1", "GSM6645222", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aminus4_S22_R1_001.fastq.gz Aminus4_S22_R2_001.fastq.gz", "fastq fastq", 6224741592.0, 41292003.0, "GSM6645222 r1", "0:75.33 1:75.42", "A:1571265090;C:1516463036;G:1536688036;T:1593637495;N:6687935", 75, 75, null, null, 1571265090, 1516463036, 1536688036, 1593637495, 6687935, "SRX17915135", "SRS15430837", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97898, 0.98108, 0.03911, 0.03771, 0.81653, 0.81947, 0.56503, 0.50775, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71673, "SRR21930616", "SRX17915134", "SRS15430836", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aminus3", "GSM6645221", null, "source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "Aminus3", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "GSM6645221", "GSM6645221: Aminus3; Danio rerio; RNA Seq", "GSM6645221 r1", "GSM6645221", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aminus3_S21_R1_001.fastq.gz Aminus3_S21_R2_001.fastq.gz", "fastq fastq", 6894036879.0, 45787003.0, "GSM6645221 r1", "0:75.18 1:75.39", "A:1733625309;C:1688222190;G:1692381570;T:1767645633;N:12162177", 75, 75, null, null, 1733625309, 1688222190, 1692381570, 1767645633, 12162177, "SRX17915134", "SRS15430836", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97919, 0.98055, 0.04869, 0.04724, 0.80647, 0.80866, 0.57236, 0.55519, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71674, "SRR21930617", "SRX17915133", "SRS15430835", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aminus2", "GSM6645220", null, "source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "Aminus2", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "GSM6645220", "GSM6645220: Aminus2; Danio rerio; RNA Seq", "GSM6645220 r1", "GSM6645220", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aminus2_S20_R1_001.fastq.gz Aminus2_S20_R2_001.fastq.gz", "fastq fastq", 6328688976.0, 42049798.0, "GSM6645220 r1", "0:75.16 1:75.34", "A:1583871529;C:1558452442;G:1563731549;T:1612985194;N:9648262", 75, 75, null, null, 1583871529, 1558452442, 1563731549, 1612985194, 9648262, "SRX17915133", "SRS15430835", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.98159, 0.98224, 0.04493, 0.04338, 0.80748, 0.81117, 0.54259, 0.53675, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71675, "SRR21930618", "SRX17915132", "SRS15430834", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aminus1", "GSM6645219", null, "source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "Aminus1", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "GSM6645219", "GSM6645219: Aminus1; Danio rerio; RNA Seq", "GSM6645219 r1", "GSM6645219", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aminus1_S19_R1_001.fastq.gz Aminus1_S19_R2_001.fastq.gz", "fastq fastq", 7762770945.0, 51727376.0, "GSM6645219 r1", "0:74.75 1:75.32", "A:1894174587;C:1946921294;G:1972242071;T:1919829619;N:29603374", 74, 75, null, null, 1894174587, 1946921294, 1972242071, 1919829619, 29603374, "SRX17915132", "SRS15430834", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.9826, 0.98415, 0.06315, 0.0603, 0.824, 0.8257, 0.56313, 0.56424, 73, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71676, "SRR21930619", "SRX17915131", "SRS15430833", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aplus6", "GSM6645218", null, "source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "Aplus6", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "GSM6645218", "GSM6645218: Aplus6; Danio rerio; RNA Seq", "GSM6645218 r1", "GSM6645218", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aplus6_S18_R1_001.fastq.gz Aplus6_S18_R2_001.fastq.gz", "fastq fastq", 6587924798.0, 43792481.0, "GSM6645218 r1", "0:75.09 1:75.35", "A:1653688853;C:1603968356;G:1644621250;T:1672657500;N:12988839", 75, 75, null, null, 1653688853, 1603968356, 1644621250, 1672657500, 12988839, "SRX17915131", "SRS15430833", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97388, 0.97651, 0.04971, 0.04851, 0.82057, 0.82513, 0.57851, 0.58339, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71677, "SRR21930620", "SRX17915130", "SRS15430832", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aplus5", "GSM6645217", null, "source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "Aplus5", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "GSM6645217", "GSM6645217: Aplus5; Danio rerio; RNA Seq", "GSM6645217 r1", "GSM6645217", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aplus5_S17_R1_001.fastq.gz Aplus5_S17_R2_001.fastq.gz", "fastq fastq", 7309309046.0, 48586335.0, "GSM6645217 r1", "0:75.09 1:75.35", "A:1775647597;C:1845303690;G:1876798549;T:1796722054;N:14837156", 75, 75, null, null, 1775647597, 1845303690, 1876798549, 1796722054, 14837156, "SRX17915130", "SRS15430832", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97946, 0.98073, 0.08026, 0.07732, 0.82298, 0.8244, 0.57059, 0.57796, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71678, "SRR21930621", "SRX17915129", "SRS15430831", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aplus4", "GSM6645216", null, "source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "Aplus4", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "GSM6645216", "GSM6645216: Aplus4; Danio rerio; RNA Seq", "GSM6645216 r1", "GSM6645216", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aplus4_S16_R1_001.fastq.gz Aplus4_S16_R2_001.fastq.gz", "fastq fastq", 6589984047.0, 44071744.0, "GSM6645216 r1", "0:74.26 1:75.27", "A:1660708324;C:1563178084;G:1662308339;T:1661946771;N:41842529", 74, 75, null, null, 1660708324, 1563178084, 1662308339, 1661946771, 41842529, "SRX17915129", "SRS15430831", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97415, 0.97416, 0.04422, 0.04323, 0.81639, 0.82075, 0.5854, 0.58865, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71679, "SRR21930622", "SRX17915128", "SRS15430830", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aplus3", "GSM6645215", null, "source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "Aplus3", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "GSM6645215", "GSM6645215: Aplus3; Danio rerio; RNA Seq", "GSM6645215 r1", "GSM6645215", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aplus3_S15_R1_001.fastq.gz Aplus3_S15_R2_001.fastq.gz", "fastq fastq", 6881303008.0, 45881629.0, "GSM6645215 r1", "0:74.67 1:75.31", "A:1705776092;C:1687176683;G:1744678234;T:1714771420;N:28900579", 74, 75, null, null, 1705776092, 1687176683, 1744678234, 1714771420, 28900579, "SRX17915128", "SRS15430830", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97636, 0.97803, 0.04693, 0.04579, 0.82106, 0.82313, 0.57573, 0.57226, 74, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71680, "SRR21930623", "SRX17915127", "SRS15430829", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aplus2", "GSM6645214", null, "source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "Aplus2", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "GSM6645214", "GSM6645214: Aplus2; Danio rerio; RNA Seq", "GSM6645214 r1", "GSM6645214", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aplus2_S14_R1_001.fastq.gz Aplus2_S14_R2_001.fastq.gz", "fastq fastq", 6485624173.0, 43138712.0, "GSM6645214 r1", "0:75.02 1:75.32", "A:1640295930;C:1579957383;G:1589952337;T:1661697493;N:13721030", 75, 75, null, null, 1640295930, 1579957383, 1589952337, 1661697493, 13721030, "SRX17915127", "SRS15430829", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97327, 0.97467, 0.03267, 0.03179, 0.74434, 0.74675, 0.49993, 0.51727, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71681, "SRR21930624", "SRX17915126", "SRS15430828", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Aplus1", "GSM6645213", null, "source name:Liver|tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "Aplus1", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Tglfabp:eGFP T2A AAT|developmental stage:2 mpf", "GSM6645213", "GSM6645213: Aplus1; Danio rerio; RNA Seq", "GSM6645213 r1", "GSM6645213", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Aplus1_S13_R1_001.fastq.gz Aplus1_S13_R2_001.fastq.gz", "fastq fastq", 6817630277.0, 45605717.0, "GSM6645213 r1", "0:74.17 1:75.32", "A:1674389239;C:1667008346;G:1749740407;T:1678172490;N:48319795", 74, 75, null, null, 1674389239, 1667008346, 1749740407, 1678172490, 48319795, "SRX17915126", "SRS15430828", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97585, 0.97763, 0.04067, 0.03939, 0.79943, 0.80235, 0.54802, 0.55959, 74, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71682, "SRR21930625", "SRX17915125", "SRS15430827", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Zminus6", "GSM6645212", null, "source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "Zminus6", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "GSM6645212", "GSM6645212: Zminus6; Danio rerio; RNA Seq", "GSM6645212 r1", "GSM6645212", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Zminus6_S12_R1_001.fastq.gz Zminus6_S12_R2_001.fastq.gz", "fastq fastq", 7741229236.0, 51641892.0, "GSM6645212 r1", "0:74.56 1:75.34", "A:1947072330;C:1874720729;G:1913091115;T:1968158284;N:38186778", 74, 75, null, null, 1947072330, 1874720729, 1913091115, 1968158284, 38186778, "SRX17915125", "SRS15430827", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.98122, 0.98292, 0.04442, 0.04278, 0.80436, 0.80655, 0.56155, 0.58034, 76, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"], [71683, "SRR21930626", "SRX17915124", "SRS15430826", "SRP403013", "PRJNA891244", "Hepatic processing of Z variant a 1 antitrypsin alters ERAD capacity to regulate cholesterol biosynthesis in a zebrafish model", "GSE215899", "Transcriptome Analysis", "Homozygosity for the Z allele of a1 antitrypsin ZAAT predisposes affected individuals to developing liver disease as the serpin misfolds and forms insoluble polymers that accumulate in the endoplasmic reticulum ER of hepatocytes  resulting in gain of function hepatotoxicity. This prevents secretion of ZAAT leading to serum insufficiency. A zebrafish model expressing human ZAAT in the liver shows no signs of hepatic accumulation despite displaying serum insufficiency  suggesting defect in ZAAT secretion occurs independently of its tendency to accumulate in hepatocytes. In this study  global transcriptomic approach was used to identify pathways activated and operating in the ZAAT expressing zebrafish liver. The analysis provided strong evidence of suppressed Srebp2 mediated cholesterol biosynthesis. qPCR confirms this observation in the human liver cell line stably expressing ZAAT. We proposed that the engagement of misfolded ZAAT by the ER associated degradation ERAD system inhibits the turnover of Srebp2 repressing elements therefore hindering the activation of Srebp2. Overall design: Comparative gene expression profiling analysis of RNA seq data for transgenic zebrafish liver expressing wildtype or Z mutant human antitrypsin  and their non transgenic siblings.", null, "pubmed:36768797", null, "Zminus5", "GSM6645211", null, "source name:Liver|tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "Zminus5", "The fastq files were aligned to a custom genome GRCz11 that includes the AAT transgene ensembl release 92  curated to remove contigs  unknown and alternate chromsomes  using RNAsik pipeline version 1.4.7. A matching custom GTF annotation file was generated as well The RNAsik pipeline was run with the following parameters: \u2018 align star  paired  all\u2019 and used the combined fasta file and gtf file as input for the \u2018 fastaRef\u2019 and \u2018 gtfFile\u2019 parameters. The RNAsik pipeline uses STAR to align fastq files to the reference genome and then uses featureCounts to assign aligned reads to annotated genes. The raw counts were filtered to keep only genes with 100 in at least 3 samples. The data was then normalised to RPKM. Using multiple t tests  Z+ was tested against the 3 other groups  as well as p > 0.05 between the A  and Z  groups to ensure no difference in gene expression in non transgenic animals for it to be defined as a differential gene. A threshold on type I error from multiple tests was also applied so that the sum of the three p values do not exceed 0.01. Assembly: Ensembl GRCz11 modified to include the AAT transgene Supplementary files format and content: comma separated file containing raw counts for each sample", "Liver", null, "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", "Zebrafish were maintained at 28\u00b0C on a 14 h light/10 h dark cycle", "tissue:Liver|strain:Non transgenic sibling|developmental stage:2 mpf", "GSM6645211", "GSM6645211: Zminus5; Danio rerio; RNA Seq", "GSM6645211 r1", "GSM6645211", "1", "Total RNA was isolated from fish liver using Trizol lysis reagent Sigma Aldrich followed by isopropanol precipitation and the RNA pellet washed with 70% v/v ethanol. PolyA RNA seq libraries prepared using Ilumina TruSeq Stranded mRNA Sample prep kit following manufacturer's protocols.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP403013", null, null, "Zminus5_S11_R1_001.fastq.gz Zminus5_S11_R2_001.fastq.gz", "fastq fastq", 7001244905.0, 46579742.0, "GSM6645211 r1", "0:74.99 1:75.32", "A:1764508171;C:1705392619;G:1719391191;T:1794863129;N:17089795", 74, 75, null, null, 1764508171, 1705392619, 1719391191, 1794863129, 17089795, "SRX17915124", "SRS15430826", "SRA1521803", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", "Monash Bioinformatics Platform, Monash Bioinformatics Platform", 2, 0.97841, 0.97975, 0.04435, 0.04344, 0.80523, 0.80704, 0.56559, 0.55911, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Australia", "2022-10-17", "Juvenile", "Juvenile", "Liver", "Liver and Biliary System"]], 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