{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\" and tissue_curation_coarse = \"Muscular System\"", "rows": [[10000, "ERR6806877", "ERX6430470", "ERS5060067", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish muscle RNA seq replicate2 raw reads", "Zebrafish Muscle RNA seq replicate2", "SAMEA7301508", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301508|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Muscle RNA seq replicate2|common name:zebrafish|sample name:Zebrafish Muscle RNA seq replicate2|tissue type:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:330 8", "Muscle2", "1", "Total RNA extracted with TRIZOL from zebrafish muscle and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Muscle_Old_1.fastq.gz", "fastq", 1886870950.0, 37737419.0, "ena RUN I3S 23 09 2021 16:43:09:330 8", "0:50 1:0", "A:479832533;C:470338808;G:443061655;T:493513324;N:124630", 50, 0, null, null, 479832533, 470338808, 443061655, 493513324, 124630, "ERX6430470", "ERS5060067", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.95119, null, 0.04224, null, 0.79251, null, 0.52332, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Muscle", "Muscular System"], [10001, "ERR6806876", "ERX6430469", "ERS5060066", "ERP123913", "PRJEB40292", "Multidimensional chromatin profiling of zebrafish and human pancreas to uncover and validate disease related enhancers", "ena-STUDY-I3S-10-09-2020-08:12:35:299-4", "Other", "The pancreas is a central organ for human diseases. Most disease associated alleles overlap with non coding cis regulatory elements of DNA  suggesting that alterations in regulatory sequences contribute to pancreatic diseases. However  the interspecies identification of equivalent cis regulatory elements required for in vivo testing face fundamental challenges  including lack of sequence conservation. In this work  we performed a combined analysis of ATAC seq  ChIP seq  4C seq and HiChIP seq data from zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis regulatory elements  regardless of sequence conservation. To link cis regulation with the expression of target genes in the pancreas  we additionally integrated in our analysis own and public RNA seq data from zebrafish pancreatic cell types. Among several disease associated sequences  we identified a zebrafish ptf1a distal enhancer whose deletion generates pancreatic agenesis  demonstrating the causality of this condition in humans. Our results further demonstrate that this phenotype is a consequence of loss of pancreas progenitor cells. Overall  we show that chromatin profiling can uncover interspecies functional equivalency of cis regulatory elements  contributing to the prediction of new disease causative enhancers and their role in human disease.", "ChIP seq  ATAC seq  HiChIP seq  4C seq  RNA seq|chromatin accessibility|cis regulatory mutations|pancreas and pancreatic diseases|transcriptional enhancers|ENA FIRST PUBLIC:2020 09 11|ENA LAST UPDATE:2021 09 22", null, "Adult zebrafish muscle RNA seq replicate1 raw reads", "Zebrafish Muscle RNA seq replicate1", "SAMEA7301507", "I3S", "ENA first public:2021 09 23|ENA last update:2021 09 23|External Id:SAMEA7301507|INSDC center alias:I3S|INSDC center name:I3S|INSDC first public:2021 09 23T20:37:00Z|INSDC last update:2021 09 23T20:37:00Z|INSDC status:public|Submitter Id:Zebrafish Muscle RNA seq replicate1|common name:zebrafish|sample name:Zebrafish Muscle RNA seq replicate1|tissue type:muscle", null, null, null, null, null, null, null, null, "Illumina HiSeq 2000 sequencing", "ena EXPERIMENT I3S 23 09 2021 16:43:09:330 7", "Muscle1", "1", "Total RNA extracted with TRIZOL from zebrafish muscle and preprared for sequencing with the TruSeq kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "ERP123913", "Illumina HiSeq 2000 sequencing", "ENA FIRST PUBLIC:2021 09 23|ENA LAST UPDATE:2021 09 23", "Muscle_Young_1.fastq.gz", "fastq", 1795352850.0, 35907057.0, "ena RUN I3S 23 09 2021 16:43:09:330 7", "0:50 1:0", "A:451489686;C:453210606;G:425250111;T:465282474;N:119973", 50, 0, null, null, 451489686, 453210606, 425250111, 465282474, 119973, "ERX6430469", "ERS5060066", "ERA6385885", "I3S|European Nucleotide Archive", "I3S", 1, 0.95698, null, 0.02942, null, 0.82126, null, 0.56075, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Portugal", "2020-09-11", "Adult", "Adult", "Muscle", "Muscular System"], [34957, "SRR32588714", "SRX27895237", "SRS24266239", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 F MUS21", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:musle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from muscle", "C2 F2 F MUS21", "C2 F2 F MUS21", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m84270_240911_190611_s3.skera.flnc.fastq.gz", "fastq", 86382018375.0, 48203691.0, "m84270 240911 190611 s3.skera.flnc.fastq.gz", "0:1792.02", "A:25051251986;C:19022185989;G:19130320983;T:23178259417;N:0", 1792, null, null, null, 25051251986, 19022185989, 19130320983, 23178259417, 0, "SRX27895237", "SRS24266239", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Muscle", "Muscular System"], [34963, "SRR32588720", "SRX27895231", "SRS24266232", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from embryo zero hpf", "C2 F2 6", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 6 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from embyo 6 hpf", "C2 F2 6", "C2 F2 6", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m54313U_231108_155338.hifi_reads.flnc.fastq.gz", "fastq", 6758669497.0, 3269612.0, "m54313U 231108 155338.hifi reads.flnc.fastq.gz", "0:2067.12", "A:1903955333;C:1520080315;G:1594879456;T:1739754393;N:0", 2067, null, null, null, 1903955333, 1520080315, 1594879456, 1739754393, 0, "SRX27895231", "SRS24266232", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Gastrula", "Embryo", "Muscle", "Muscular System"], [34966, "SRR32588723", "SRX27895228", "SRS24266230", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from embryo zero hpf", "C2 F2 24", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 24 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from embyo 24 hpf", "C2 F2 24", "C2 F2 24", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m54313U_231109_165320.hifi_reads.flnc.fastq.gz", "fastq", 7642144881.0, 3850910.0, "m54313U 231109 165320.hifi reads.flnc.fastq.gz", "0:1984.50", "A:2137607023;C:1720821414;G:1812220379;T:1971496065;N:0", 1984, null, null, null, 2137607023, 1720821414, 1812220379, 1971496065, 0, "SRX27895228", "SRS24266230", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Pharyngula", "Embryo", "Muscle", "Muscular System"], [34967, "SRR32588724", "SRX27895227", "SRS24266228", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 M MUS22", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from muscle", "C2 F2 M MUS22", "C2 F2 M MUS22", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m64467e_240817_183852.hifi_reads.flnc.fastq.gz", "fastq", 14631605009.0, 3302436.0, "m64467e 240817 183852.hifi reads.flnc.fastq.gz", "0:4430.55", "A:4285049339;C:3157147611;G:3606320925;T:3583087134;N:0", 4430, null, null, null, 4285049339, 3157147611, 3606320925, 3583087134, 0, "SRX27895227", "SRS24266228", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Muscle", "Muscular System"], [34968, "SRR32588725", "SRX27895226", "SRS24266227", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 M mus2", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:male|tissue:Muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from muscle", "C2 F2 M mus2", "C2 F2 M mus2", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m84270_240913_150707_s2.skera.flnc.fastq.gz", "fastq", 105235491521.0, 56491114.0, "m84270 240913 150707 s2.skera.flnc.fastq.gz", "0:1862.87", "A:30649812728;C:23382133477;G:23762971602;T:27440573714;N:0", 1862, null, null, null, 30649812728, 23382133477, 23762971602, 27440573714, 0, "SRX27895226", "SRS24266227", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Muscle", "Muscular System"], [34976, "SRR32588733", "SRX27895218", "SRS24266220", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from Danio rerio", "C2 F2 F MUS22", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:9 month|dev stage:adult fish|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from muscle", "C2 F2 F MUS22", "C2 F2 F MUS22", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m64467e_240814_151650.hifi_reads.flnc.fastq.gz", "fastq", 12063904861.0, 3021713.0, "m64467e 240814 151650.hifi reads.flnc.fastq.gz", "0:3992.41", "A:3499589691;C:2629790020;G:2965002855;T:2969522295;N:0", 3992, null, null, null, 3499589691, 2629790020, 2965002855, 2969522295, 0, "SRX27895218", "SRS24266220", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Adult", "Adult", "Muscle", "Muscular System"], [34977, "SRR32588734", "SRX27895217", "SRS24266222", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from embryo zero hpf", "C2 F2 12", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 12 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:male|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from embyo 12 hpf", "C2 F2 12", "C2 F2 12", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m54313U_231111_191642.hifi_reads.flnc.fastq.gz", "fastq", 7627931284.0, 3897936.0, "m54313U 231111 191642.hifi reads.flnc.fastq.gz", "0:1956.92", "A:2146633241;C:1706673950;G:1799625470;T:1974998623;N:0", 1956, null, null, null, 2146633241, 1706673950, 1799625470, 1974998623, 0, "SRX27895217", "SRS24266222", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", null, null, null, null, null, null, null, null, null, null, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Segmentation", "Embryo", "Muscle", "Muscular System"], [34978, "SRR32588735", "SRX27895216", "SRS24266218", "SRP568323", "PRJNA1232602", "Telomere to telomere genome assemblies for commonly used zebrafish laboratory strains", "PRJNA1232602", "Other", "In this study  Iso Seq was performed on different zebrafish body organs  enabling a comprehensive view of organ specific transcriptomes. High quality PacBio Iso Seq long reads were generated from key zebrafish tissues  including the brain  testis  liver  eye  muscle  ovary  inner ear and kidney  to identify novel isoforms  tissue specific transcripts  and alternative splicing events. We also made available the Iso Seq data from embryos from different time points  hpf  0  6  12  and 24. This dataset enhances gene annotation  improves reference genome annotations  and provides insights into zebrafish organ specific gene expression.", null, null, null, "Iso Seq RNA from embryo zero hpf", "C2 F2 0", null, "strain:NHGRI2|isolate:Single paired cross|breed:Zebrafish|cultivar:wild type|ecotype:United States|age:time 0 hours|dev stage:Embyoys|collection date:2024 06|geo loc name:USA|sex:female|tissue:muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Iso Seq RNA from embyo 0 hpf", "C2 F2 0", "C2 F2 0", "The long Read Sequencing libraries was sequenced using PacBio Sequel II", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "PACBIO_SMRT", "Sequel II", null, "SRP568323", null, null, "m54313U_231110_180503.hifi_reads.flnc.fastq.gz", "fastq", 8144050440.0, 3744842.0, "m54313U 231110 180503.hifi reads.flnc.fastq.gz", "0:2174.74", "A:2267401658;C:1836982566;G:1935470734;T:2104195482;N:0", 2174, null, null, null, 2267401658, 1836982566, 1935470734, 2104195482, 0, "SRX27895216", "SRS24266218", "SRA2089085", "National Human Genome Research Institute|Translational and Functional Genomics Branch", "National Human Genome Research Institute National Human Genome Research Institute", 1, 0.76793, null, 0.00473, null, 0.80371, null, 0.50925, null, 1489, null, "T", null, "long read", "pacbio", "pacbio_modern", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2025-03-06", "Zygote", "Embryo", "Muscle", "Muscular System"], [36665, "SRR800045", "SRX257154", "SRS405708", "SRP020008", "PRJNA193544", "Danio rerio strain:Tubingen Epigenomics", "PRJNA193544", "Other", "Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation ZGA. To better understand  we determined DNAme profiles of zebrafish gametes  multiple embryo stages flanking ZGA  and somatic muscle   and compared them to gene activity and histone modifications. First  sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly  in the oocyte many genes important for germline functions ie. piwil1 or early development ie. hox genes are DNA methylated. Remarkably  these maternal loci are demethylated during zygotic/cleavage stages to precisely the state observed in sperm  even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore  this cohort constitutes the genes/loci that acquire DNAme during development ie. ZGA to muscle. Finally  DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene/chromatin cohorts at ZGA  preventing their precocious expression. Thus  zebrafish achieve a 'totipotent' chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.", null, "pubmed:23663776", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", "Generic sample from Danio rerio", "muscle RNAseq totalRNARibominus", null, "strain:Tubingen|label:PE: paired end  SE: single end|development stage:muscle", null, null, null, null, null, null, null, null, "muscle RNAseq totalRNARibominus", "muscle RNAseq totalRNARibominus", "9084X1", "Total RNA was extracted using  Qiagen AllPrep DNA/RNA/Protein mini kit Cat # 80004  ribosomal RNA was depleted using RiboMinus kit A10837 08  Eukaryote Kit followed by directional RNA library preparation according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 1000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP020008", null, null, "muscle_RNAseq_totalRNARibominus_SE_9084X1_120420_SN141_0500_AD0TG5ACXX_5.txt.gz", "Illumina native", 3506573750.0, 70131475.0, "9084X1 120420 SN141 0500 AD0TG5ACXX 5", "0:50", "A:872717534;C:808774955;G:1036781008;T:777391447;N:10908806", 50, null, null, null, 872717534, 808774955, 1036781008, 777391447, 10908806, "SRX257154", "SRS405708", "SRA072148", "University of Utah|Brad Cairns Lab", "University of Utah", 1, 0.61428, null, 0.09813, null, 0.89305, null, 0.6908, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "rrna_depletion", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-05-07", "Undetermined", "Embryo", "Muscle", "Muscular System"], [43214, "SRR5921100", "SRX3081927", "SRS2420550", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 231 muscle RNAseq", "GSM2736450", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "NH FLI 231 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "GSM2736450", "GSM2736450: NH FLI 231 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736450", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736450", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2583426000.0, 51668520.0, "GSM2736450 r1", "0:50", "A:667888136;C:636156963;G:621733516;T:657492175;N:155210", 50, null, null, null, 667888136, 636156963, 621733516, 657492175, 155210, "SRX3081927", "SRS2420550", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94909, null, 0.03382, null, 0.82365, null, 0.5257, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43215, "SRR5921099", "SRX3081926", "SRS2420551", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 230 muscle RNAseq", "GSM2736449", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "NH FLI 230 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "GSM2736449", "GSM2736449: NH FLI 230 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736449", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736449", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2779212100.0, 55584242.0, "GSM2736449 r1", "0:50", "A:718950222;C:683346064;G:668977769;T:707772101;N:165944", 50, null, null, null, 718950222, 683346064, 668977769, 707772101, 165944, "SRX3081926", "SRS2420551", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94522, null, 0.03238, null, 0.83167, null, 0.49244, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43216, "SRR5921098", "SRX3081925", "SRS2420552", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 229 muscle RNAseq", "GSM2736448", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "NH FLI 229 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "GSM2736448", "GSM2736448: NH FLI 229 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736448", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736448", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2104798250.0, 42095965.0, "GSM2736448 r1", "0:50", "A:549002855;C:511883752;G:503492577;T:540292518;N:126548", 50, null, null, null, 549002855, 511883752, 503492577, 540292518, 126548, "SRX3081925", "SRS2420552", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94812, null, 0.03693, null, 0.8098, null, 0.50299, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43217, "SRR5921097", "SRX3081924", "SRS2420553", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 228 muscle RNAseq", "GSM2736447", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "NH FLI 228 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "GSM2736447", "GSM2736447: NH FLI 228 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736447", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736447", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2537225400.0, 50744508.0, "GSM2736447 r1", "0:50", "A:657205211;C:620581744;G:608842181;T:650441784;N:154480", 50, null, null, null, 657205211, 620581744, 608842181, 650441784, 154480, "SRX3081924", "SRS2420553", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94595, null, 0.03741, null, 0.8199, null, 0.49555, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43218, "SRR5921096", "SRX3081923", "SRS2420554", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 227 muscle RNAseq", "GSM2736446", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "NH FLI 227 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:swim tunnel", "GSM2736446", "GSM2736446: NH FLI 227 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736446", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736446", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2701413450.0, 54028269.0, "GSM2736446 r1", "0:50", "A:698144244;C:662872388;G:649328483;T:690924461;N:143874", 50, null, null, null, 698144244, 662872388, 649328483, 690924461, 143874, "SRX3081923", "SRS2420554", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95291, null, 0.03821, null, 0.80478, null, 0.51532, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43219, "SRR5921095", "SRX3081922", "SRS2420555", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 226 muscle RNAseq", "GSM2736445", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "NH FLI 226 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "GSM2736445", "GSM2736445: NH FLI 226 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736445", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736445", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2315604100.0, 46312082.0, "GSM2736445 r1", "0:50", "A:599156215;C:569052284;G:554641515;T:592632081;N:122005", 50, null, null, null, 599156215, 569052284, 554641515, 592632081, 122005, "SRX3081922", "SRS2420555", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94732, null, 0.0372, null, 0.81903, null, 0.50015, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43220, "SRR5921094", "SRX3081921", "SRS2420556", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 225 muscle RNAseq", "GSM2736444", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "NH FLI 225 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "GSM2736444", "GSM2736444: NH FLI 225 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736444", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736444", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2642773450.0, 52855469.0, "GSM2736444 r1", "0:50", "A:684408579;C:647493678;G:631806768;T:678927537;N:136888", 50, null, null, null, 684408579, 647493678, 631806768, 678927537, 136888, "SRX3081921", "SRS2420556", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95538, null, 0.03743, null, 0.81383, null, 0.45235, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43221, "SRR5921093", "SRX3081920", "SRS2420557", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 223 muscle RNAseq", "GSM2736443", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "NH FLI 223 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "GSM2736443", "GSM2736443: NH FLI 223 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736443", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736443", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2311499450.0, 46229989.0, "GSM2736443 r1", "0:50", "A:599296521;C:566724822;G:549787552;T:595567871;N:122684", 50, null, null, null, 599296521, 566724822, 549787552, 595567871, 122684, "SRX3081920", "SRS2420557", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95367, null, 0.03899, null, 0.80452, null, 0.52269, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43222, "SRR5921092", "SRX3081919", "SRS2420558", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 222 muscle RNAseq", "GSM2736442", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "NH FLI 222 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "GSM2736442", "GSM2736442: NH FLI 222 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736442", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736442", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2782496050.0, 55649921.0, "GSM2736442 r1", "0:50", "A:721432645;C:683389614;G:663351311;T:714203202;N:119278", 50, null, null, null, 721432645, 683389614, 663351311, 714203202, 119278, "SRX3081919", "SRS2420558", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96175, null, 0.0358, null, 0.81519, null, 0.51692, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43223, "SRR5921091", "SRX3081918", "SRS2420559", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 221 muscle RNAseq", "GSM2736441", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "NH FLI 221 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1", "GSM2736441", "GSM2736441: NH FLI 221 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736441", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736441", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2628003500.0, 52560070.0, "GSM2736441 r1", "0:50", "A:689460991;C:636451918;G:620965937;T:681039592;N:85062", 50, null, null, null, 689460991, 636451918, 620965937, 681039592, 85062, "SRX3081918", "SRS2420559", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95172, null, 0.03607, null, 0.8144, null, 0.52098, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43224, "SRR5921090", "SRX3081917", "SRS2420560", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 220 muscle RNAseq", "GSM2736440", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "NH FLI 220 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "GSM2736440", "GSM2736440: NH FLI 220 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736440", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2716683150.0, 54333663.0, "GSM2736440 r1", "0:50", "A:708799192;C:663289162;G:642338014;T:702118631;N:138151", 50, null, null, null, 708799192, 663289162, 642338014, 702118631, 138151, "SRX3081917", "SRS2420560", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96405, null, 0.03589, null, 0.82442, null, 0.54703, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43225, "SRR5921089", "SRX3081916", "SRS2420562", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 219 muscle RNAseq", "GSM2736439", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "NH FLI 219 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "GSM2736439", "GSM2736439: NH FLI 219 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736439", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2532374300.0, 50647486.0, "GSM2736439 r1", "0:50", "A:663072795;C:618496710;G:602144102;T:648561930;N:98763", 50, null, null, null, 663072795, 618496710, 602144102, 648561930, 98763, "SRX3081916", "SRS2420562", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96219, null, 0.03463, null, 0.82412, null, 0.49185, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43226, "SRR5921088", "SRX3081915", "SRS2420561", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 218 muscle RNAseq", "GSM2736438", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "NH FLI 218 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "GSM2736438", "GSM2736438: NH FLI 218 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736438", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736438", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2378429500.0, 47568590.0, "GSM2736438 r1", "0:50", "A:625085605;C:576221380;G:561136630;T:615908269;N:77616", 50, null, null, null, 625085605, 576221380, 561136630, 615908269, 77616, "SRX3081915", "SRS2420561", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.93162, null, 0.02832, null, 0.8452, null, 0.54129, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43227, "SRR5921087", "SRX3081914", "SRS2420563", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 216 muscle RNAseq", "GSM2736437", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "NH FLI 216 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "GSM2736437", "GSM2736437: NH FLI 216 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736437", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736437", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2162753600.0, 43255072.0, "GSM2736437 r1", "0:50", "A:568419337;C:522327630;G:513098131;T:558839895;N:68607", 50, null, null, null, 568419337, 522327630, 513098131, 558839895, 68607, "SRX3081914", "SRS2420563", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95313, null, 0.03331, null, 0.83228, null, 0.54377, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43228, "SRR5921086", "SRX3081913", "SRS2420564", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 215 muscle RNAseq", "GSM2736436", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "NH FLI 215 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:swim tunnel", "GSM2736436", "GSM2736436: NH FLI 215 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736436", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736436", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2891187950.0, 57823759.0, "GSM2736436 r1", "0:50", "A:752283114;C:707486900;G:688534581;T:742791335;N:92020", 50, null, null, null, 752283114, 707486900, 688534581, 742791335, 92020, "SRX3081913", "SRS2420564", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.94558, null, 0.03006, null, 0.83234, null, 0.52451, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43229, "SRR5921085", "SRX3081912", "SRS2420565", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 214 muscle RNAseq", "GSM2736435", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "NH FLI 214 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "GSM2736435", "GSM2736435: NH FLI 214 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736435", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736435", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2425847400.0, 48516948.0, "GSM2736435 r1", "0:50", "A:636153617;C:587566985;G:572222800;T:629815625;N:88373", 50, null, null, null, 636153617, 587566985, 572222800, 629815625, 88373, "SRX3081912", "SRS2420565", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95463, null, 0.04122, null, 0.79937, null, 0.54522, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43230, "SRR5921084", "SRX3081911", "SRS2420566", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 213 muscle RNAseq", "GSM2736434", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "NH FLI 213 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "GSM2736434", "GSM2736434: NH FLI 213 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736434", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736434", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2696492200.0, 53929844.0, "GSM2736434 r1", "0:50", "A:705007995;C:654272683;G:639344493;T:697770444;N:96585", 50, null, null, null, 705007995, 654272683, 639344493, 697770444, 96585, "SRX3081911", "SRS2420566", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.89023, null, 0.03515, null, 0.82069, null, 0.54881, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43231, "SRR5921083", "SRX3081910", "SRS2420567", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 212 muscle RNAseq", "GSM2736433", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "NH FLI 212 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "GSM2736433", "GSM2736433: NH FLI 212 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736433", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736433", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2048198000.0, 40963960.0, "GSM2736433 r1", "0:50", "A:534112663;C:499757837;G:485938398;T:528314868;N:74234", 50, null, null, null, 534112663, 499757837, 485938398, 528314868, 74234, "SRX3081910", "SRS2420567", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95513, null, 0.03648, null, 0.81945, null, 0.54213, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43232, "SRR5921082", "SRX3081909", "SRS2420569", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 211 muscle RNAseq", "GSM2736432", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "NH FLI 211 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "GSM2736432", "GSM2736432: NH FLI 211 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736432", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736432", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 2813928700.0, 56278574.0, "GSM2736432 r1", "0:50", "A:727919865;C:692905570;G:672803124;T:720199931;N:100210", 50, null, null, null, 727919865, 692905570, 672803124, 720199931, 100210, "SRX3081909", "SRS2420569", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95548, null, 0.03587, null, 0.81899, null, 0.52766, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43233, "SRR5921081", "SRX3081908", "SRS2420568", "SRP115129", "PRJNA397733", "Sequencing of Danio rerio muscle for 2 age groups post physical exercise", "GSE102430", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle for 2 age groups. The RNA seq data comprise 2 x 2 groups: two age groups  each with and without xxx exercise swim tunnel. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 20 samples in 2 x 2 groups: 1 year w/ physical execrise 5 samples  1 year w/o physical exercise 5 samples  3 year w/ physical exercise 5 samples  3 year w/o physical exercise 5 samples", null, null, null, "NH FLI 210 muscle RNAseq", "GSM2736431", null, "source name:muscle|strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "NH FLI 210 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1", "GSM2736431", "GSM2736431: NH FLI 210 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736431", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736431", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115129", null, null, null, null, 3216094850.0, 64321897.0, "GSM2736431 r1", "0:50", "A:842649849;C:784061705;G:756881143;T:832355348;N:146805", 50, null, null, null, 842649849, 784061705, 756881143, 832355348, 146805, "SRX3081908", "SRS2420568", "SRA597918", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95942, null, 0.04114, null, 0.81387, null, 0.53104, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43234, "SRR5921080", "SRX3081907", "SRS2420524", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 273 muscle RNAseq", "GSM2736463", null, "source name:muscle|strain:AB tert / |tissue:muscle|age:3 month|Sex:male", "NH FLI 273 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB tert / |tissue:muscle|age:3 month|Sex:male", "GSM2736463", "GSM2736463: NH FLI 273 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736463", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736463", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2963850210.0, 58114710.0, "GSM2736463 r1", "0:51", "A:760803485;C:733415284;G:713908770;T:755542381;N:180290", 51, null, null, null, 760803485, 733415284, 713908770, 755542381, 180290, "SRX3081907", "SRS2420524", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96002, null, 0.03919, null, 0.83329, null, 0.50078, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43235, "SRR5921079", "SRX3081906", "SRS2420526", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 271 muscle RNAseq", "GSM2736462", null, "source name:muscle|strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "NH FLI 271 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "GSM2736462", "GSM2736462: NH FLI 271 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736462", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736462", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2410790196.0, 47270396.0, "GSM2736462 r1", "0:51", "A:620498472;C:593943176;G:580010313;T:615793429;N:544806", 51, null, null, null, 620498472, 593943176, 580010313, 615793429, 544806, "SRX3081906", "SRS2420526", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95934, null, 0.03584, null, 0.82071, null, 0.50583, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43236, "SRR5921078", "SRX3081905", "SRS2420525", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 270 muscle RNAseq", "GSM2736461", null, "source name:muscle|strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "NH FLI 270 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "GSM2736461", "GSM2736461: NH FLI 270 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736461", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2902171881.0, 56905331.0, "GSM2736461 r1", "0:51", "A:663684682;C:805834958;G:779068076;T:653365321;N:218844", 51, null, null, null, 663684682, 805834958, 779068076, 653365321, 218844, "SRX3081905", "SRS2420525", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.9802, null, 0.2131, null, 0.90009, null, 0.65757, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43237, "SRR5921077", "SRX3081904", "SRS2420527", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 264 muscle RNAseq", "GSM2736460", null, "source name:muscle|strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "NH FLI 264 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "GSM2736460", "GSM2736460: NH FLI 264 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736460", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736460", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 3154946547.0, 61861697.0, "GSM2736460 r1", "0:51", "A:815694159;C:774994188;G:757046119;T:807013180;N:198901", 51, null, null, null, 815694159, 774994188, 757046119, 807013180, 198901, "SRX3081904", "SRS2420527", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96053, null, 0.03781, null, 0.81765, null, 0.51653, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43238, "SRR5921076", "SRX3081903", "SRS2420528", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 258 muscle RNAseq", "GSM2736459", null, "source name:muscle|strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "NH FLI 258 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "GSM2736459", "GSM2736459: NH FLI 258 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736459", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736459", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2005679856.0, 39327056.0, "GSM2736459 r1", "0:51", "A:506750501;C:503067671;G:491784049;T:503616846;N:460789", 51, null, null, null, 506750501, 503067671, 491784049, 503616846, 460789, "SRX3081903", "SRS2420528", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96065, null, 0.05283, null, 0.82649, null, 0.52695, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43239, "SRR5921075", "SRX3081902", "SRS2420530", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 257 muscle RNAseq", "GSM2736458", null, "source name:muscle|strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "NH FLI 257 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "GSM2736458", "GSM2736458: NH FLI 257 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736458", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736458", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2850491082.0, 55891982.0, "GSM2736458 r1", "0:51", "A:728039571;C:709536210;G:689699735;T:723071146;N:144420", 51, null, null, null, 728039571, 709536210, 689699735, 723071146, 144420, "SRX3081902", "SRS2420530", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95843, null, 0.03933, null, 0.82968, null, 0.52274, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43240, "SRR5921074", "SRX3081901", "SRS2420529", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 256 muscle RNAseq", "GSM2736457", null, "source name:muscle|strain:AB tert / |tissue:muscle|age:3 month|Sex:male", "NH FLI 256 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB tert / |tissue:muscle|age:3 month|Sex:male", "GSM2736457", "GSM2736457: NH FLI 256 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736457", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736457", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2869226085.0, 56259335.0, "GSM2736457 r1", "0:51", "A:740499892;C:704499909;G:687477872;T:736568098;N:180314", 51, null, null, null, 740499892, 704499909, 687477872, 736568098, 180314, "SRX3081901", "SRS2420529", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96292, null, 0.03576, null, 0.81377, null, 0.46796, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43241, "SRR5921073", "SRX3081900", "SRS2420532", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 255 muscle RNAseq", "GSM2736456", null, "source name:muscle|strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "NH FLI 255 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "GSM2736456", "GSM2736456: NH FLI 255 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736456", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736456", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2311606620.0, 45325620.0, "GSM2736456 r1", "0:51", "A:592225197;C:572857560;G:558400927;T:587974050;N:148886", 51, null, null, null, 592225197, 572857560, 558400927, 587974050, 148886, "SRX3081900", "SRS2420532", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95824, null, 0.03419, null, 0.82179, null, 0.49852, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43242, "SRR5921072", "SRX3081899", "SRS2420531", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 254 muscle RNAseq", "GSM2736455", null, "source name:muscle|strain:AB tert / |tissue:muscle|age:3 month|Sex:male", "NH FLI 254 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB tert / |tissue:muscle|age:3 month|Sex:male", "GSM2736455", "GSM2736455: NH FLI 254 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736455", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736455", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 1986993150.0, 38960650.0, "GSM2736455 r1", "0:51", "A:514733936;C:485548185;G:472926120;T:513678847;N:106062", 51, null, null, null, 514733936, 485548185, 472926120, 513678847, 106062, "SRX3081899", "SRS2420531", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.95349, null, 0.04965, null, 0.71573, null, 0.44881, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43243, "SRR5921071", "SRX3081898", "SRS2420533", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 253 muscle RNAseq", "GSM2736454", null, "source name:muscle|strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "NH FLI 253 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "GSM2736454", "GSM2736454: NH FLI 253 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736454", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736454", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2905674918.0, 56974018.0, "GSM2736454 r1", "0:51", "A:722299561;C:744825817;G:720256054;T:718060093;N:233393", 51, null, null, null, 722299561, 744825817, 720256054, 718060093, 233393, "SRX3081898", "SRS2420533", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96657, null, 0.06755, null, 0.83455, null, 0.53052, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43244, "SRR5921070", "SRX3081897", "SRS2420534", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 251 muscle RNAseq", "GSM2736453", null, "source name:muscle|strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "NH FLI 251 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "GSM2736453", "GSM2736453: NH FLI 251 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736453", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736453", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2767147800.0, 54257800.0, "GSM2736453 r1", "0:51", "A:704520098;C:691759511;G:671521216;T:699168042;N:178933", 51, null, null, null, 704520098, 691759511, 671521216, 699168042, 178933, "SRX3081897", "SRS2420534", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96137, null, 0.07028, null, 0.82404, null, 0.53151, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43245, "SRR5921069", "SRX3081896", "SRS2420535", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 235 muscle RNAseq", "GSM2736452", null, "source name:muscle|strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "NH FLI 235 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male", "GSM2736452", "GSM2736452: NH FLI 235 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736452", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736452", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2293306290.0, 44966790.0, "GSM2736452 r1", "0:51", "A:546425257;C:612542551;G:591392826;T:542811435;N:134221", 51, null, null, null, 546425257, 612542551, 591392826, 542811435, 134221, "SRX3081896", "SRS2420535", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.96865, null, 0.17032, null, 0.79563, null, 0.59765, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [43246, "SRR5921068", "SRX3081895", "SRS2420536", "SRP115127", "PRJNA397735", "Sequencing of Danio rerio muscle from tert mutants and controls", "GSE102431", "Transcriptome Analysis", "Comparison of gene expression profiles from Danio rerio muscle of wiltype AB and homozygous/heterozygous tert mutants AB tert /   AB tert+/. The RNA seq data comprise 3 groups. Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 13 samples in 3 groups: AB 5 samples  AB tert /  3 samples  AB tert+/  5 samples", null, "pubmed:34680427", null, "NH FLI 234 muscle RNAseq", "GSM2736451", null, "source name:muscle|strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "NH FLI 234 muscle RNAseq", "Sequence information was extracted in FastQ format using bcl2fastq software 1.8.4 data processing step. Reads were mapped using STAR 2.4.1d. Reads per gene were counted using featureCounts 1.4.6 p4. Counts were normalized to RPKM values as described in Mortazavi et al. 2008. Genome build: genome: GRCz10  and respective gene annotation GRCz10.84 Supplementary files format and content: The Excel files include raw counts sample counts.xls and RPKM values sample rpkms.xls of all genes for each sample.", "muscle", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", null, "strain:AB wildtype|tissue:muscle|age:3 month|Sex:male", "GSM2736451", "GSM2736451: NH FLI 234 muscle RNAseq; Danio rerio; RNA Seq", "GSM2736451", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq RNA Library Preparation Kit v2 following the manufacturer's instruction.", "GEO Accession:GSM2736451", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP115127", null, null, null, null, 2538754908.0, 49779508.0, "GSM2736451 r1", "0:51", "A:666217063;C:613097220;G:599972557;T:659289888;N:178180", 51, null, null, null, 666217063, 613097220, 599972557, 659289888, 178180, "SRX3081895", "SRS2420536", "SRA597917", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.9546, null, 0.06678, null, 0.81937, null, 0.4772, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2017-08-09", "Adult", "Adult", "Muscle", "Muscular System"], [49268, "SRR7883101", "SRX4721396", "SRS3806484", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT   sample 3", "GSM3396896", null, "source name:Gr mutant swimming UOPT  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT   sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396896", "GSM3396896: Gr mutant swimming UOPT   sample 3; Danio rerio; RNA Seq", "GSM3396896", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396896", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_15_15105_CTTGTA_L001_R1_001.fastq.gz", "fastq", 248411565.0, 4870815.0, "GSM3396896 r1", "0:51", "A:56574599;C:63639902;G:59333109;T:68728919;N:135036", 51, null, null, null, 56574599, 63639902, 59333109, 68728919, 135036, "SRX4721396", "SRS3806484", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95963, null, 0.03133, null, 0.82144, null, 0.50958, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49269, "SRR7883102", "SRX4721396", "SRS3806484", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT   sample 3", "GSM3396896", null, "source name:Gr mutant swimming UOPT  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT   sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396896", "GSM3396896: Gr mutant swimming UOPT   sample 3; Danio rerio; RNA Seq", "GSM3396896", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396896", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_15_15105_CTTGTA_L002_R1_001.fastq.gz", "fastq", 245868501.0, 4820951.0, "GSM3396896 r2", "0:51", "A:55999278;C:63022234;G:58753181;T:68048742;N:45066", 51, null, null, null, 55999278, 63022234, 58753181, 68048742, 45066, "SRX4721396", "SRS3806484", "SRA780034", "GEO", "ZF-screens BV", 1, 0.9607, null, 0.03061, null, 0.81876, null, 0.50656, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49270, "SRR7883099", "SRX4721395", "SRS3806483", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT   sample 2", "GSM3396895", null, "source name:Gr mutant swimming UOPT  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT   sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396895", "GSM3396895: Gr mutant swimming UOPT   sample 2; Danio rerio; RNA Seq", "GSM3396895", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396895", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_14_15104_CAGATC_L001_R1_001.fastq.gz", "fastq", 219513996.0, 4304196.0, "GSM3396895 r1", "0:51", "A:48361086;C:57271498;G:53468696;T:60291615;N:121101", 51, null, null, null, 48361086, 57271498, 53468696, 60291615, 121101, "SRX4721395", "SRS3806483", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95734, null, 0.02232, null, 0.83037, null, 0.46039, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49271, "SRR7883100", "SRX4721395", "SRS3806483", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT   sample 2", "GSM3396895", null, "source name:Gr mutant swimming UOPT  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT   sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396895", "GSM3396895: Gr mutant swimming UOPT   sample 2; Danio rerio; RNA Seq", "GSM3396895", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396895", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_14_15104_CAGATC_L002_R1_001.fastq.gz", "fastq", 217279176.0, 4260376.0, "GSM3396895 r2", "0:51", "A:47895589;C:56699017;G:52953041;T:59691639;N:39890", 51, null, null, null, 47895589, 56699017, 52953041, 59691639, 39890, "SRX4721395", "SRS3806483", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95882, null, 0.02375, null, 0.82753, null, 0.45523, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49272, "SRR7883095", "SRX4721394", "SRS3806482", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT   sample 1", "GSM3396894", null, "source name:Gr mutant swimming UOPT  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT   sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396894", "GSM3396894: Gr mutant swimming UOPT   sample 1; Danio rerio; RNA Seq", "GSM3396894", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_11_14126_CGATGT_L001_R1_000.fastq.gz", "fastq", 76142847.0, 1492997.0, "GSM3396894 r1", "0:51", "A:17764968;C:19359482;G:17546237;T:21458644;N:13516", 51, null, null, null, 17764968, 19359482, 17546237, 21458644, 13516, "SRX4721394", "SRS3806482", "SRA780034", "GEO", "ZF-screens BV", 1, 0.94854, null, 0.03967, null, 0.81239, null, 0.52843, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49273, "SRR7883096", "SRX4721394", "SRS3806482", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT   sample 1", "GSM3396894", null, "source name:Gr mutant swimming UOPT  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT   sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396894", "GSM3396894: Gr mutant swimming UOPT   sample 1; Danio rerio; RNA Seq", "GSM3396894", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_11_14126_CGATGT_L002_R1_000.fastq.gz", "fastq", 75245655.0, 1475405.0, "GSM3396894 r2", "0:51", "A:17559056;C:19128796;G:17344883;T:21206265;N:6655", 51, null, null, null, 17559056, 19128796, 17344883, 21206265, 6655, "SRX4721394", "SRS3806482", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95076, null, 0.03952, null, 0.81057, null, 0.52805, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49274, "SRR7883097", "SRX4721394", "SRS3806482", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT   sample 1", "GSM3396894", null, "source name:Gr mutant swimming UOPT  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT   sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396894", "GSM3396894: Gr mutant swimming UOPT   sample 1; Danio rerio; RNA Seq", "GSM3396894", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_11_14126_CGATGT_L001_R1_001.fastq.gz", "fastq", 282942084.0, 5547884.0, "GSM3396894 r3", "0:51", "A:65346157;C:71914444;G:66015753;T:79625150;N:40580", 51, null, null, null, 65346157, 71914444, 66015753, 79625150, 40580, "SRX4721394", "SRS3806482", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95533, null, 0.03742, null, 0.81044, null, 0.52574, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49275, "SRR7883098", "SRX4721394", "SRS3806482", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant swimming UOPT   sample 1", "GSM3396894", null, "source name:Gr mutant swimming UOPT  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "Gr mutant swimming UOPT   sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant swimming UOPT  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle", "GSM3396894", "GSM3396894: Gr mutant swimming UOPT   sample 1; Danio rerio; RNA Seq", "GSM3396894", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396894", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_11_14126_CGATGT_L002_R1_001.fastq.gz", "fastq", 279101274.0, 5472574.0, "GSM3396894 r4", "0:51", "A:64447735;C:70937019;G:65137622;T:78531620;N:47278", 51, null, null, null, 64447735, 70937019, 65137622, 78531620, 47278, "SRX4721394", "SRS3806482", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95428, null, 0.03783, null, 0.81128, null, 0.52701, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49276, "SRR7883093", "SRX4721393", "SRS3806481", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 3", "GSM3396893", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396893", "GSM3396893: Wild type swimming UOPT++ sample 3; Danio rerio; RNA Seq", "GSM3396893", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396893", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_13_15103_GCCAAT_L001_R1_001.fastq.gz", "fastq", 354993966.0, 6960666.0, "GSM3396893 r1", "0:51", "A:84489335;C:86597253;G:84240000;T:99472362;N:195016", 51, null, null, null, 84489335, 86597253, 84240000, 99472362, 195016, "SRX4721393", "SRS3806481", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95532, null, 0.04239, null, 0.80653, null, 0.55623, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49277, "SRR7883094", "SRX4721393", "SRS3806481", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 3", "GSM3396893", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396893", "GSM3396893: Wild type swimming UOPT++ sample 3; Danio rerio; RNA Seq", "GSM3396893", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396893", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_13_15103_GCCAAT_L002_R1_001.fastq.gz", "fastq", 351290193.0, 6888043.0, "GSM3396893 r2", "0:51", "A:83629618;C:85716733;G:83395630;T:98483376;N:64836", 51, null, null, null, 83629618, 85716733, 83395630, 98483376, 64836, "SRX4721393", "SRS3806481", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95631, null, 0.04199, null, 0.8056, null, 0.54571, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49278, "SRR7883089", "SRX4721392", "SRS3806480", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 2", "GSM3396892", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396892", "GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq", "GSM3396892", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_09_14125_GAGTGG_L001_R1_000.fastq.gz", "fastq", 70889949.0, 1389999.0, "GSM3396892 r1", "0:51", "A:16926874;C:17543094;G:16728407;T:19679197;N:12377", 51, null, null, null, 16926874, 17543094, 16728407, 19679197, 12377, "SRX4721392", "SRS3806480", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95627, null, 0.03548, null, 0.82451, null, 0.53415, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49279, "SRR7883090", "SRX4721392", "SRS3806480", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 2", "GSM3396892", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396892", "GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq", "GSM3396892", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_09_14125_GAGTGG_L002_R1_000.fastq.gz", "fastq", 70218126.0, 1376826.0, "GSM3396892 r2", "0:51", "A:16757913;C:17378481;G:16577230;T:19498501;N:6001", 51, null, null, null, 16757913, 17378481, 16577230, 19498501, 6001, "SRX4721392", "SRS3806480", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95571, null, 0.03554, null, 0.82806, null, 0.50999, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49280, "SRR7883091", "SRX4721392", "SRS3806480", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 2", "GSM3396892", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396892", "GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq", "GSM3396892", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_09_14125_GAGTGG_L001_R1_001.fastq.gz", "fastq", 276251241.0, 5416691.0, "GSM3396892 r3", "0:51", "A:65379164;C:68332333;G:65926683;T:76572534;N:40527", 51, null, null, null, 65379164, 68332333, 65926683, 76572534, 40527, "SRX4721392", "SRS3806480", "SRA780034", "GEO", "ZF-screens BV", 1, 0.96013, null, 0.0352, null, 0.82814, null, 0.53974, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49281, "SRR7883092", "SRX4721392", "SRS3806480", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 2", "GSM3396892", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396892", "GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq", "GSM3396892", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_09_14125_GAGTGG_L002_R1_001.fastq.gz", "fastq", 273560328.0, 5363928.0, "GSM3396892 r4", "0:51", "A:64737712;C:67666247;G:65306231;T:75803211;N:46927", 51, null, null, null, 64737712, 67666247, 65306231, 75803211, 46927, "SRX4721392", "SRS3806480", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95941, null, 0.03355, null, 0.82745, null, 0.54235, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49282, "SRR7883087", "SRX4721391", "SRS3806479", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 1", "GSM3396891", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396891", "GSM3396891: Wild type swimming UOPT++ sample 1; Danio rerio; RNA Seq", "GSM3396891", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396891", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_08_14124_CGTACG_L001_R1_001.fastq.gz", "fastq", 391510986.0, 7676686.0, "GSM3396891 r1", "0:51", "A:93242107;C:96684654;G:92114654;T:109292193;N:177378", 51, null, null, null, 93242107, 96684654, 92114654, 109292193, 177378, "SRX4721391", "SRS3806479", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95344, null, 0.05682, null, 0.80612, null, 0.46874, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49283, "SRR7883088", "SRX4721391", "SRS3806479", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 1", "GSM3396891", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396891", "GSM3396891: Wild type swimming UOPT++ sample 1; Danio rerio; RNA Seq", "GSM3396891", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396891", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_08_14124_CGTACG_L002_R1_001.fastq.gz", "fastq", 387065571.0, 7589521.0, "GSM3396891 r2", "0:51", "A:92211053;C:95616109;G:91125664;T:108078262;N:34483", 51, null, null, null, 92211053, 95616109, 91125664, 108078262, 34483, "SRX4721391", "SRS3806479", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95555, null, 0.05726, null, 0.80655, null, 0.50316, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49284, "SRR7883085", "SRX4721390", "SRS3806478", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST   sample 3", "GSM3396890", null, "source name:Gr mutant resting REST  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST   sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396890", "GSM3396890: Gr mutant resting REST   sample 3; Danio rerio; RNA Seq", "GSM3396890", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396890", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_06_14123_GTTTCG_L001_R1_001.fastq.gz", "fastq", 402333798.0, 7888898.0, "GSM3396890 r1", "0:51", "A:93056953;C:102519574;G:95945518;T:110623659;N:188094", 51, null, null, null, 93056953, 102519574, 95945518, 110623659, 188094, "SRX4721390", "SRS3806478", "SRA780034", "GEO", "ZF-screens BV", 1, 0.96072, null, 0.03044, null, 0.83151, null, 0.49904, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49285, "SRR7883086", "SRX4721390", "SRS3806478", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST   sample 3", "GSM3396890", null, "source name:Gr mutant resting REST  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST   sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396890", "GSM3396890: Gr mutant resting REST   sample 3; Danio rerio; RNA Seq", "GSM3396890", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396890", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_06_14123_GTTTCG_L002_R1_001.fastq.gz", "fastq", 397844166.0, 7800866.0, "GSM3396890 r2", "0:51", "A:92045457;C:101410388;G:94956743;T:109396044;N:35534", 51, null, null, null, 92045457, 101410388, 94956743, 109396044, 35534, "SRX4721390", "SRS3806478", "SRA780034", "GEO", "ZF-screens BV", 1, 0.96026, null, 0.03027, null, 0.82994, null, 0.49932, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49286, "SRR7883083", "SRX4721389", "SRS3806477", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST   sample 2", "GSM3396889", null, "source name:Gr mutant resting REST  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST   sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396889", "GSM3396889: Gr mutant resting REST   sample 2; Danio rerio; RNA Seq", "GSM3396889", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396889", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_05_14122_GTGGCC_L001_R1_001.fastq.gz", "fastq", 415265307.0, 8142457.0, "GSM3396889 r1", "0:51", "A:96524820;C:105111599;G:96647633;T:116788874;N:192381", 51, null, null, null, 96524820, 105111599, 96647633, 116788874, 192381, "SRX4721389", "SRS3806477", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95102, null, 0.04156, null, 0.79164, null, 0.52657, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49287, "SRR7883084", "SRX4721389", "SRS3806477", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST   sample 2", "GSM3396889", null, "source name:Gr mutant resting REST  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST   sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396889", "GSM3396889: Gr mutant resting REST   sample 2; Danio rerio; RNA Seq", "GSM3396889", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396889", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_05_14122_GTGGCC_L002_R1_001.fastq.gz", "fastq", 410798625.0, 8054875.0, "GSM3396889 r2", "0:51", "A:95514290;C:104001536;G:95684811;T:115561454;N:36534", 51, null, null, null, 95514290, 104001536, 95684811, 115561454, 36534, "SRX4721389", "SRS3806477", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95117, null, 0.04146, null, 0.79032, null, 0.51379, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49288, "SRR7883081", "SRX4721388", "SRS3806476", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST   sample 1", "GSM3396888", null, "source name:Gr mutant resting REST  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST   sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396888", "GSM3396888: Gr mutant resting REST   sample 1; Danio rerio; RNA Seq", "GSM3396888", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396888", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_04_14121_GGCTAC_L001_R1_001.fastq.gz", "fastq", 356273607.0, 6985757.0, "GSM3396888 r1", "0:51", "A:83067213;C:89144746;G:86927052;T:96973321;N:161275", 51, null, null, null, 83067213, 89144746, 86927052, 96973321, 161275, "SRX4721388", "SRS3806476", "SRA780034", "GEO", "ZF-screens BV", 1, 0.9514, null, 0.03636, null, 0.78064, null, 0.49277, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49289, "SRR7883082", "SRX4721388", "SRS3806476", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Gr mutant resting REST   sample 1", "GSM3396888", null, "source name:Gr mutant resting REST  |biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "Gr mutant resting REST   sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Gr mutant resting REST  ", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle", "GSM3396888", "GSM3396888: Gr mutant resting REST   sample 1; Danio rerio; RNA Seq", "GSM3396888", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396888", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_04_14121_GGCTAC_L002_R1_001.fastq.gz", "fastq", 353427042.0, 6929942.0, "GSM3396888 r2", "0:51", "A:82429330;C:88444066;G:86279627;T:96242734;N:31285", 51, null, null, null, 82429330, 88444066, 86279627, 96242734, 31285, "SRX4721388", "SRS3806476", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95127, null, 0.03685, null, 0.78125, null, 0.49716, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49290, "SRR7883079", "SRX4721387", "SRS3806475", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 3", "GSM3396887", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396887", "GSM3396887: Wild type resting REST++ sample 3; Danio rerio; RNA Seq", "GSM3396887", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396887", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_03_14120_TAGCTT_L001_R1_001.fastq.gz", "fastq", 407925846.0, 7998546.0, "GSM3396887 r1", "0:51", "A:95664418;C:101106745;G:99163612;T:111801493;N:189578", 51, null, null, null, 95664418, 101106745, 99163612, 111801493, 189578, "SRX4721387", "SRS3806475", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95163, null, 0.03911, null, 0.80308, null, 0.47176, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49291, "SRR7883080", "SRX4721387", "SRS3806475", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 3", "GSM3396887", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 3", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396887", "GSM3396887: Wild type resting REST++ sample 3; Danio rerio; RNA Seq", "GSM3396887", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396887", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_03_14120_TAGCTT_L002_R1_001.fastq.gz", "fastq", 403131897.0, 7904547.0, "GSM3396887 r2", "0:51", "A:94571267;C:99984137;G:98039941;T:110500771;N:35781", 51, null, null, null, 94571267, 99984137, 98039941, 110500771, 35781, "SRX4721387", "SRS3806475", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95153, null, 0.03927, null, 0.80081, null, 0.43253, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49292, "SRR7883077", "SRX4721386", "SRS3806474", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 2", "GSM3396886", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396886", "GSM3396886: Wild type resting REST++ sample 2; Danio rerio; RNA Seq", "GSM3396886", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396886", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_02_14119_GATCAG_L001_R1_001.fastq.gz", "fastq", 321180252.0, 6297652.0, "GSM3396886 r1", "0:51", "A:76187242;C:79646315;G:76288340;T:88907254;N:151101", 51, null, null, null, 76187242, 79646315, 76288340, 88907254, 151101, "SRX4721386", "SRS3806474", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95633, null, 0.0376, null, 0.82294, null, 0.48192, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49293, "SRR7883078", "SRX4721386", "SRS3806474", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 2", "GSM3396886", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396886", "GSM3396886: Wild type resting REST++ sample 2; Danio rerio; RNA Seq", "GSM3396886", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396886", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_02_14119_GATCAG_L002_R1_001.fastq.gz", "fastq", 318001371.0, 6235321.0, "GSM3396886 r2", "0:51", "A:75443385;C:78910190;G:75585800;T:88033421;N:28575", 51, null, null, null, 75443385, 78910190, 75585800, 88033421, 28575, "SRX4721386", "SRS3806474", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95684, null, 0.03736, null, 0.8228, null, 0.42199, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49294, "SRR7883075", "SRX4721385", "SRS3806473", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 1", "GSM3396885", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396885", "GSM3396885: Wild type resting REST++ sample 1; Danio rerio; RNA Seq", "GSM3396885", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396885", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_01_14118_ACTTGA_L001_R1_001.fastq.gz", "fastq", 332939526.0, 6528226.0, "GSM3396885 r1", "0:51", "A:79370894;C:82057170;G:79743998;T:91615147;N:152317", 51, null, null, null, 79370894, 82057170, 79743998, 91615147, 152317, "SRX4721385", "SRS3806473", "SRA780034", "GEO", "ZF-screens BV", 1, 0.9559, null, 0.03764, null, 0.81146, null, 0.48877, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [49295, "SRR7883076", "SRX4721385", "SRS3806473", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type resting REST++ sample 1", "GSM3396885", null, "source name:Wild type resting REST++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "Wild type resting REST++ sample 1", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type resting REST++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle", "GSM3396885", "GSM3396885: Wild type resting REST++ sample 1; Danio rerio; RNA Seq", "GSM3396885", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396885", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_01_14118_ACTTGA_L002_R1_001.fastq.gz", "fastq", 328832853.0, 6447703.0, "GSM3396885 r2", "0:51", "A:78396828;C:81102360;G:78796819;T:90507746;N:29100", 51, null, null, null, 78396828, 81102360, 78796819, 90507746, 29100, "SRX4721385", "SRS3806473", "SRA780034", "GEO", "ZF-screens BV", 1, 0.9556, null, 0.03749, null, 0.81144, null, 0.48578, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"], [52955, "SRR9610848", "SRX6374057", "SRS5034866", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0WT S C RNA Seq", "GSM3910338", null, "source name:WT Standard Diet Muscle|Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle", "S0WT S C RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "WT Standard Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle", "GSM3910338", "GSM3910338: S0WT S C RNA Seq; Danio rerio; RNA Seq", "GSM3910338", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910338", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0WT_S_C__RNA_Seq_Directional_S46_L005_R1_001.fastq.gz", "fastq", 785460690.0, 15401190.0, "GSM3910338 r1", "0:51", "A:202991469;C:183350303;G:181337685;T:217696201;N:85032", 51, null, null, null, 202991469, 183350303, 181337685, 217696201, 85032, "SRX6374057", "SRS5034866", "SRA914604", "GEO", "University of Bern", 1, 0.93791, null, 0.05606, null, 0.75144, null, 0.53237, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52956, "SRR9610847", "SRX6374056", "SRS5034865", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0WT S B RNA Seq", "GSM3910337", null, "source name:WT Standard Diet Muscle|Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle", "S0WT S B RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "WT Standard Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle", "GSM3910337", "GSM3910337: S0WT S B RNA Seq; Danio rerio; RNA Seq", "GSM3910337", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910337", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0WT_S_B__RNA_Seq_Directional_S45_L005_R1_001.fastq.gz", "fastq", 1037581842.0, 20344742.0, "GSM3910337 r1", "0:51", "A:271421784;C:242201012;G:237079646;T:286766535;N:112865", 51, null, null, null, 271421784, 242201012, 237079646, 286766535, 112865, "SRX6374056", "SRS5034865", "SRA914604", "GEO", "University of Bern", 1, 0.93385, null, 0.05579, null, 0.73602, null, 0.50008, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52957, "SRR9610846", "SRX6374055", "SRS5034864", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0WT S 7 RNA Seq", "GSM3910336", null, "source name:WT Standard Diet Muscle|Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle", "S0WT S 7 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "WT Standard Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle", "GSM3910336", "GSM3910336: S0WT S 7 RNA Seq; Danio rerio; RNA Seq", "GSM3910336", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910336", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0WT_S_7__RNA_Seq_Directional_S48_L005_R1_001.fastq.gz", "fastq", 901161585.0, 17669835.0, "GSM3910336 r1", "0:51", "A:236551279;C:210199570;G:206723666;T:247589765;N:97305", 51, null, null, null, 236551279, 210199570, 206723666, 247589765, 97305, "SRX6374055", "SRS5034864", "SRA914604", "GEO", "University of Bern", 1, 0.93688, null, 0.05977, null, 0.80119, null, 0.50443, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52958, "SRR9610845", "SRX6374054", "SRS5034863", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0WT S 6 RNA Seq", "GSM3910335", null, "source name:WT Standard Diet Muscle|Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle", "S0WT S 6 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "WT Standard Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:WT|treatment:Standard Diet|tissue:Muscle", "GSM3910335", "GSM3910335: S0WT S 6 RNA Seq; Danio rerio; RNA Seq", "GSM3910335", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910335", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0WT_S_6__RNA_Seq_Directional_S47_L005_R1_001.fastq.gz", "fastq", 1075248759.0, 21083309.0, "GSM3910335 r1", "0:51", "A:297191939;C:247117436;G:237870203;T:292953815;N:115366", 51, null, null, null, 297191939, 247117436, 237870203, 292953815, 115366, "SRX6374054", "SRS5034863", "SRA914604", "GEO", "University of Bern", 1, 0.89528, null, 0.06728, null, 0.78634, null, 0.53098, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52959, "SRR9610844", "SRX6374053", "SRS5034862", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0WT DD 4 RNA Seq", "GSM3910334", null, "source name:WT Double Diet Muscle|Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle", "S0WT DD 4 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "WT Double Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle", "GSM3910334", "GSM3910334: S0WT DD 4 RNA Seq; Danio rerio; RNA Seq", "GSM3910334", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910334", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0WT_DD_4__RNA_Seq_Directional_S55_L005_R1_001.fastq.gz", "fastq", 907009602.0, 17784502.0, "GSM3910334 r1", "0:51", "A:241201134;C:204122008;G:208735432;T:252853431;N:97597", 51, null, null, null, 241201134, 204122008, 208735432, 252853431, 97597, "SRX6374053", "SRS5034862", "SRA914604", "GEO", "University of Bern", 1, 0.91061, null, 0.05033, null, 0.79545, null, 0.54457, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52960, "SRR9610843", "SRX6374052", "SRS5034861", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0WT DD 3 RNA Seq", "GSM3910333", null, "source name:WT Double Diet Muscle|Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle", "S0WT DD 3 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "WT Double Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle", "GSM3910333", "GSM3910333: S0WT DD 3 RNA Seq; Danio rerio; RNA Seq", "GSM3910333", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910333", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0WT_DD_3__RNA_Seq_Directional_S54_L005_R1_001.fastq.gz", "fastq", 1013135298.0, 19865398.0, "GSM3910333 r1", "0:51", "A:264389932;C:233507692;G:235911726;T:279216160;N:109788", 51, null, null, null, 264389932, 233507692, 235911726, 279216160, 109788, "SRX6374052", "SRS5034861", "SRA914604", "GEO", "University of Bern", 1, 0.92535, null, 0.04437, null, 0.81162, null, 0.49398, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52961, "SRR9610842", "SRX6374051", "SRS5034860", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0WT DD 2 RNA Seq", "GSM3910332", null, "source name:WT Double Diet Muscle|Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle", "S0WT DD 2 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "WT Double Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:WT|treatment:Double Diet|tissue:Muscle", "GSM3910332", "GSM3910332: S0WT DD 2 RNA Seq; Danio rerio; RNA Seq", "GSM3910332", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910332", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0WT_DD_2__RNA_Seq_Directional_S53_L005_R1_001.fastq.gz", "fastq", 856760832.0, 16799232.0, "GSM3910332 r1", "0:51", "A:228696407;C:206617559;G:191782242;T:229573977;N:90647", 51, null, null, null, 228696407, 206617559, 191782242, 229573977, 90647, "SRX6374051", "SRS5034860", "SRA914604", "GEO", "University of Bern", 1, 0.36358, null, 0.04768, null, 0.91303, null, 0.52314, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52962, "SRR9610841", "SRX6374050", "SRS5034859", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0KO S C RNA Seq", "GSM3910331", null, "source name:KO Standard Diet Muscle|Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle", "S0KO S C RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "KO Standard Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle", "GSM3910331", "GSM3910331: S0KO S C RNA Seq; Danio rerio; RNA Seq", "GSM3910331", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910331", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0KO_S_C__RNA_Seq_Directional_S51_L005_R1_001.fastq.gz", "fastq", 750414561.0, 14714011.0, "GSM3910331 r1", "0:51", "A:193243096;C:177276287;G:174035790;T:205777475;N:81913", 51, null, null, null, 193243096, 177276287, 174035790, 205777475, 81913, "SRX6374050", "SRS5034859", "SRA914604", "GEO", "University of Bern", 1, 0.94262, null, 0.05429, null, 0.75741, null, 0.51196, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52963, "SRR9610840", "SRX6374049", "SRS5034858", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0KO S B RNA Seq", "GSM3910330", null, "source name:KO Standard Diet Muscle|Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle", "S0KO S B RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "KO Standard Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle", "GSM3910330", "GSM3910330: S0KO S B RNA Seq; Danio rerio; RNA Seq", "GSM3910330", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910330", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0KO_S_B__RNA_Seq_Directional_S50_L005_R1_001.fastq.gz", "fastq", 862912350.0, 16919850.0, "GSM3910330 r1", "0:51", "A:223023468;C:203743702;G:200457097;T:235595080;N:93003", 51, null, null, null, 223023468, 203743702, 200457097, 235595080, 93003, "SRX6374049", "SRS5034858", "SRA914604", "GEO", "University of Bern", 1, 0.9374, null, 0.04142, null, 0.73111, null, 0.47223, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52964, "SRR9610839", "SRX6374048", "SRS5034857", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0KO S A RNA Seq", "GSM3910329", null, "source name:KO Standard Diet Muscle|Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle", "S0KO S A RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "KO Standard Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle", "GSM3910329", "GSM3910329: S0KO S A RNA Seq; Danio rerio; RNA Seq", "GSM3910329", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910329", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0KO_S_A__RNA_Seq_Directional_S49_L005_R1_001.fastq.gz", "fastq", 767697084.0, 15052884.0, "GSM3910329 r1", "0:51", "A:195880291;C:183023619;G:178202819;T:210507113;N:83242", 51, null, null, null, 195880291, 183023619, 178202819, 210507113, 83242, "SRX6374048", "SRS5034857", "SRA914604", "GEO", "University of Bern", 1, 0.93312, null, 0.04579, null, 0.72906, null, 0.48412, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52965, "SRR9610838", "SRX6374047", "SRS5034856", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0KO S 6 RNA Seq", "GSM3910328", null, "source name:KO Standard Diet Muscle|Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle", "S0KO S 6 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "KO Standard Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:KO|treatment:Standard Diet|tissue:Muscle", "GSM3910328", "GSM3910328: S0KO S 6 RNA Seq; Danio rerio; RNA Seq", "GSM3910328", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910328", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0KO_S_6__RNA_Seq_Directional_S52_L005_R1_001.fastq.gz", "fastq", 971991252.0, 19058652.0, "GSM3910328 r1", "0:51", "A:257642647;C:225459692;G:225710033;T:263073969;N:104911", 51, null, null, null, 257642647, 225459692, 225710033, 263073969, 104911, "SRX6374047", "SRS5034856", "SRA914604", "GEO", "University of Bern", 1, 0.9235, null, 0.05678, null, 0.7779, null, 0.51447, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52966, "SRR9610837", "SRX6374046", "SRS5034855", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0KO DD 7 RNA Seq", "GSM3910327", null, "source name:KO Double Diet Muscle|Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle", "S0KO DD 7 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "KO Double Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle", "GSM3910327", "GSM3910327: S0KO DD 7 RNA Seq; Danio rerio; RNA Seq", "GSM3910327", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910327", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0KO_DD_7__RNA_Seq_Directional_S59_L005_R1_001.fastq.gz", "fastq", 822576348.0, 16128948.0, "GSM3910327 r1", "0:51", "A:212421329;C:192524361;G:192658987;T:224881911;N:89760", 51, null, null, null, 212421329, 192524361, 192658987, 224881911, 89760, "SRX6374046", "SRS5034855", "SRA914604", "GEO", "University of Bern", 1, 0.95061, null, 0.04831, null, 0.78013, null, 0.52246, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52967, "SRR9610836", "SRX6374045", "SRS5034854", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0KO DD 6 RNA Seq", "GSM3910326", null, "source name:KO Double Diet Muscle|Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle", "S0KO DD 6 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "KO Double Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle", "GSM3910326", "GSM3910326: S0KO DD 6 RNA Seq; Danio rerio; RNA Seq", "GSM3910326", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910326", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0KO_DD_6__RNA_Seq_Directional_S58_L005_R1_001.fastq.gz", "fastq", 883971576.0, 17332776.0, "GSM3910326 r1", "0:51", "A:228413430;C:209052461;G:205760159;T:240648496;N:97030", 51, null, null, null, 228413430, 209052461, 205760159, 240648496, 97030, "SRX6374045", "SRS5034854", "SRA914604", "GEO", "University of Bern", 1, 0.93764, null, 0.04361, null, 0.74777, null, 0.45055, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52968, "SRR9610835", "SRX6374044", "SRS5034853", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0KO DD 3 RNA Seq", "GSM3910325", null, "source name:KO Double Diet Muscle|Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle", "S0KO DD 3 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "KO Double Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle", "GSM3910325", "GSM3910325: S0KO DD 3 RNA Seq; Danio rerio; RNA Seq", "GSM3910325", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910325", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0KO_DD_3__RNA_Seq_Directional_S57_L005_R1_001.fastq.gz", "fastq", 935766462.0, 18348362.0, "GSM3910325 r1", "0:51", "A:244456092;C:219466128;G:219111604;T:252630825;N:101813", 51, null, null, null, 244456092, 219466128, 219111604, 252630825, 101813, "SRX6374044", "SRS5034853", "SRA914604", "GEO", "University of Bern", 1, 0.90131, null, 0.0466, null, 0.83477, null, 0.50178, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [52969, "SRR9610834", "SRX6374043", "SRS5034852", "SRP212268", "PRJNA551601", "Respiratory supercomplexes provide metabolic efficiency in zebrafish", "GSE133487", "Transcriptome Analysis", "The role of OXPHOS respiratory supercomplexes remains still unknown. To answer this question we use as a model a SCAF1 null allele model in zebrafish. SCAF1 cox7a2l is the only supercomplex assembly factor identified in vertebrates and it is involved in the physical link of III IV complexes. Therefore the SCAF1 null allele model lack all III IV interactions. We demonstrate that supercomplexes provide an advantage in the optimization of metabolic resources. Overall design: Muscle from females SCAF1?1 post the 6 weeks of a regime of standard diet or double diet  were dissected and stored at  80\u00b0C.", null, "pubmed:32496654", null, "S0KO DD 2 RNA Seq", "GSM3910324", null, "source name:KO Double Diet Muscle|Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle", "S0KO DD 2 RNA Seq", "Illumina HiSeq 2500 FASTQ files were checked for quality control metrics using FastQC version 0.11.8 Raw reads were pseudo mapped to the index created by Kallisto  using Danio rerio cDNA. Next  we used standard values for single end reads  with 100 bootstraps  fragment length 200bp and sd of fragments lengt was 30 bp. Genome build: Ensembl cDNA build 11  release 94 Supplementary files format and content: H5 and Tab delimited files containing the Ensembl transcript ID version Ensembl and the  length  eff length  est counts and tpm of  the \u201ccounts\u201d. To be imported using  tximport or sleuth.", "KO Double Diet Muscle", "Zebrafish were fed during 6 weeks in two different diets: standard diet S  gemma 300 3 times/day  double diet DD gemma 300 5 times/day", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "Zebrafish were grown at same density 13 fish in 2 l tanks", "Sex:female|genotype/variation:KO|treatment:Double Diet|tissue:Muscle", "GSM3910324", "GSM3910324: S0KO DD 2 RNA Seq; Danio rerio; RNA Seq", "GSM3910324", null, "1", "Adult zebrafish skeletal muscle were dissected and stored at  80\u00b0C. RNA was isolated using Trizol and purified Zymo RNA Clean & Concentrator kit. RNA purity was evaluated using Agilent Fragment Analyzer and used for the bar coded library generation. Illumina HiSeq 2500 SystemLibrary was sequenced in Illumina HiSeq 2500 System", "GEO Accession:GSM3910324", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP212268", null, null, "S0KO_DD_2__RNA_Seq_Directional_S56_L005_R1_001.fastq.gz", "fastq", 864157158.0, 16944258.0, "GSM3910324 r1", "0:51", "A:223803666;C:200893790;G:201657972;T:237709184;N:92546", 51, null, null, null, 223803666, 200893790, 201657972, 237709184, 92546, "SRX6374043", "SRS5034852", "SRA914604", "GEO", "University of Bern", 1, 0.9298, null, 0.0537, null, 0.82574, null, 0.51143, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Switzerland", "2019-06-28", "Multi-stage", "Multi-stage", "Muscle", "Muscular System"], [55305, "SRR11092476", "SRX7731318", "SRS6151725", "SRP226922", "PRJNA577226", "Danio rerio breed:AB Transcriptome or Gene expression", "PRJNA577226", "Other", "EpiGreen project investigated the nutrigenomic and nutriepigenomic effects of plant protein based diets on fish using zebrafish as a model. This study was also extended to a commercially important species  Atlantic salmon. Ultimately this knowledge would be benefited for the industry to formulate sustainable diets based on terrestrial ingredients with properly addressing fish welfare concerns.", null, null, "fast muscle", null, "pea fishm6", null, "strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:laboratory|age:6 month|dev stage:adult|sex:female|tissue:fast muscle|biomaterial provider:zebrafish lab  Nord University|birth location:zebrafish lab  Nord University|collected by:Anusha K.S.Dhanasiri Nord University|collection date:2017 09|health state:Healthy|treatment:pea replicate6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNASeq of zebrafish: adult female fast muscle", "pm6", "pm6", "Directional RNA libraries with PolyA mRNA enrichment", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP226922", null, null, "pm6.fastq.gz", "fastq", 2046858524.0, 26932349.0, "pm6.fastq.gz", "0:76 1:0", "A:512656433;C:497166196;G:475911685;T:561012780;N:111430", 76, 0, null, null, 512656433, 497166196, 475911685, 561012780, 111430, "SRX7731318", "SRS6151725", "SRA1043309", "Nord Universitet|Faculty of Biosciences and Aquaculture", "Nord Universitet", 1, 0.97101, null, 0.06659, null, 0.82745, null, 0.46321, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2020-02-15", "Adult", "Adult", "Muscle", "Muscular System"], [55306, "SRR11092477", "SRX7731317", "SRS6151724", "SRP226922", "PRJNA577226", "Danio rerio breed:AB Transcriptome or Gene expression", "PRJNA577226", "Other", "EpiGreen project investigated the nutrigenomic and nutriepigenomic effects of plant protein based diets on fish using zebrafish as a model. This study was also extended to a commercially important species  Atlantic salmon. Ultimately this knowledge would be benefited for the industry to formulate sustainable diets based on terrestrial ingredients with properly addressing fish welfare concerns.", null, null, "fast muscle", null, "pea fishm5", null, "strain:AB|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:laboratory|age:6 month|dev stage:adult|sex:female|tissue:fast muscle|biomaterial provider:zebrafish lab  Nord University|birth location:zebrafish lab  Nord University|collected by:Anusha K.S.Dhanasiri Nord University|collection date:2017 09|health state:Healthy|treatment:pea replicate5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNASeq of zebrafish: adult female fast muscle", "pm5", "pm5", "Directional RNA libraries with PolyA mRNA enrichment", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP226922", null, null, "pm5.fastq.gz", "fastq", 1385366532.0, 18228507.0, "pm5.fastq.gz", "0:76 1:0", "A:351089576;C:337868838;G:315380752;T:380954376;N:72990", 76, 0, null, null, 351089576, 337868838, 315380752, 380954376, 72990, "SRX7731317", "SRS6151724", "SRA1043309", "Nord Universitet|Faculty of Biosciences and Aquaculture", "Nord Universitet", 1, 0.96194, null, 0.09162, null, 0.81126, null, 0.51366, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2020-02-15", "Adult", "Adult", "Muscle", "Muscular System"], [55307, "SRR11092478", "SRX7731316", "SRS6151723", "SRP226922", "PRJNA577226", "Danio rerio breed:AB Transcriptome or Gene expression", "PRJNA577226", "Other", "EpiGreen project investigated the nutrigenomic and nutriepigenomic effects of plant protein based diets on fish using zebrafish as a model. This study was also extended to a commercially important species  Atlantic salmon. 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