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110 rows where experiment.library_layout = "SINGLE", technology = "unknown" and tissue_curation_coarse = "Muscular System"

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  • Muscular System · 110 ✖

tissue_curation 1

technology 1

  • unknown · 110 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

  • SINGLE · 110 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
10000 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   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                 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   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   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     479832533 470338808 443061655 493513324 124630 ERX6430470 ERS5060067 ERA6385885 I3S|European Nucleotide Archive I3S 1 0.95119   0.04224   0.79251   0.52332   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Portugal 2020-09-11 Adult Adult Muscle Muscular System
10001 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   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                 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   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   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     451489686 453210606 425250111 465282474 119973 ERX6430469 ERS5060066 ERA6385885 I3S|European Nucleotide Archive I3S 1 0.95698   0.02942   0.82126   0.56075   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Portugal 2020-09-11 Adult Adult Muscle Muscular System
34957 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.       Iso Seq RNA from Danio rerio C2 F2 F MUS21   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                 Iso Seq RNA from muscle C2 F2 F MUS21 C2 F2 F MUS21 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Muscle Muscular System
34963 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.       Iso Seq RNA from embryo zero hpf C2 F2 6   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                 Iso Seq RNA from embyo 6 hpf C2 F2 6 C2 F2 6 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Gastrula Embryo Muscle Muscular System
34966 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.       Iso Seq RNA from embryo zero hpf C2 F2 24   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                 Iso Seq RNA from embyo 24 hpf C2 F2 24 C2 F2 24 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Pharyngula Embryo Muscle Muscular System
34967 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.       Iso Seq RNA from Danio rerio C2 F2 M MUS22   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                 Iso Seq RNA from muscle C2 F2 M MUS22 C2 F2 M MUS22 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Muscle Muscular System
34968 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.       Iso Seq RNA from Danio rerio C2 F2 M mus2   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                 Iso Seq RNA from muscle C2 F2 M mus2 C2 F2 M mus2 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Muscle Muscular System
34976 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.       Iso Seq RNA from Danio rerio C2 F2 F MUS22   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                 Iso Seq RNA from muscle C2 F2 F MUS22 C2 F2 F MUS22 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Adult Adult Muscle Muscular System
34977 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.       Iso Seq RNA from embryo zero hpf C2 F2 12   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                 Iso Seq RNA from embyo 12 hpf C2 F2 12 C2 F2 12 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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                       T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Segmentation Embryo Muscle Muscular System
34978 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.       Iso Seq RNA from embryo zero hpf C2 F2 0   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                 Iso Seq RNA from embyo 0 hpf C2 F2 0 C2 F2 0 The long Read Sequencing libraries was sequenced using PacBio Sequel II     RNA-Seq TRANSCRIPTOMIC cDNA SINGLE PACBIO_SMRT Sequel II   SRP568323     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       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   0.00473   0.80371   0.50925   1489   T   long read pacbio pacbio_modern unknown cdna_unspecified unknown bulk unknown unknown   United States 2025-03-06 Zygote Embryo Muscle Muscular System
36665 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.   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   strain:Tubingen|label:PE: paired end SE: single end|development stage:muscle                 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.     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     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       872717534 808774955 1036781008 777391447 10908806 SRX257154 SRS405708 SRA072148 University of Utah|Brad Cairns Lab University of Utah 1 0.61428   0.09813   0.89305   0.6908   50   B   usable mapping rate illumina hiseq_era unknown rrna_depletion unknown bulk unknown unknown   United States 2013-05-07 Undetermined Embryo Muscle Muscular System
43214 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       NH FLI 231 muscle RNAseq GSM2736450   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   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.   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   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   SRP115129         2583426000.0 51668520.0 GSM2736450 r1 0:50 A:667888136;C:636156963;G:621733516;T:657492175;N:155210 50       667888136 636156963 621733516 657492175 155210 SRX3081927 SRS2420550 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94909   0.03382   0.82365   0.5257   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43215 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       NH FLI 230 muscle RNAseq GSM2736449   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   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.   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   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   SRP115129         2779212100.0 55584242.0 GSM2736449 r1 0:50 A:718950222;C:683346064;G:668977769;T:707772101;N:165944 50       718950222 683346064 668977769 707772101 165944 SRX3081926 SRS2420551 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94522   0.03238   0.83167   0.49244   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43216 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       NH FLI 229 muscle RNAseq GSM2736448   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   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.   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   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   SRP115129         2104798250.0 42095965.0 GSM2736448 r1 0:50 A:549002855;C:511883752;G:503492577;T:540292518;N:126548 50       549002855 511883752 503492577 540292518 126548 SRX3081925 SRS2420552 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94812   0.03693   0.8098   0.50299   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43217 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       NH FLI 228 muscle RNAseq GSM2736447   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   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.   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   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   SRP115129         2537225400.0 50744508.0 GSM2736447 r1 0:50 A:657205211;C:620581744;G:608842181;T:650441784;N:154480 50       657205211 620581744 608842181 650441784 154480 SRX3081924 SRS2420553 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94595   0.03741   0.8199   0.49555   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43218 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       NH FLI 227 muscle RNAseq GSM2736446   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   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.   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   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   SRP115129         2701413450.0 54028269.0 GSM2736446 r1 0:50 A:698144244;C:662872388;G:649328483;T:690924461;N:143874 50       698144244 662872388 649328483 690924461 143874 SRX3081923 SRS2420554 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95291   0.03821   0.80478   0.51532   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43219 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       NH FLI 226 muscle RNAseq GSM2736445   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   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.   strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1 GSM2736445 GSM2736445: NH FLI 226 muscle RNAseq; Danio rerio; RNA Seq GSM2736445   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   SRP115129         2315604100.0 46312082.0 GSM2736445 r1 0:50 A:599156215;C:569052284;G:554641515;T:592632081;N:122005 50       599156215 569052284 554641515 592632081 122005 SRX3081922 SRS2420555 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94732   0.0372   0.81903   0.50015   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43220 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       NH FLI 225 muscle RNAseq GSM2736444   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   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.   strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1 GSM2736444 GSM2736444: NH FLI 225 muscle RNAseq; Danio rerio; RNA Seq GSM2736444   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   SRP115129         2642773450.0 52855469.0 GSM2736444 r1 0:50 A:684408579;C:647493678;G:631806768;T:678927537;N:136888 50       684408579 647493678 631806768 678927537 136888 SRX3081921 SRS2420556 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95538   0.03743   0.81383   0.45235   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43221 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       NH FLI 223 muscle RNAseq GSM2736443   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   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.   strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1 GSM2736443 GSM2736443: NH FLI 223 muscle RNAseq; Danio rerio; RNA Seq GSM2736443   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   SRP115129         2311499450.0 46229989.0 GSM2736443 r1 0:50 A:599296521;C:566724822;G:549787552;T:595567871;N:122684 50       599296521 566724822 549787552 595567871 122684 SRX3081920 SRS2420557 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95367   0.03899   0.80452   0.52269   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43222 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       NH FLI 222 muscle RNAseq GSM2736442   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   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.   strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1 GSM2736442 GSM2736442: NH FLI 222 muscle RNAseq; Danio rerio; RNA Seq GSM2736442   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   SRP115129         2782496050.0 55649921.0 GSM2736442 r1 0:50 A:721432645;C:683389614;G:663351311;T:714203202;N:119278 50       721432645 683389614 663351311 714203202 119278 SRX3081919 SRS2420558 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96175   0.0358   0.81519   0.51692   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43223 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       NH FLI 221 muscle RNAseq GSM2736441   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   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.   strain:AB JxTu|tissue:muscle|age:3 years|Sex:male|perturbation:n1 GSM2736441 GSM2736441: NH FLI 221 muscle RNAseq; Danio rerio; RNA Seq GSM2736441   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   SRP115129         2628003500.0 52560070.0 GSM2736441 r1 0:50 A:689460991;C:636451918;G:620965937;T:681039592;N:85062 50       689460991 636451918 620965937 681039592 85062 SRX3081918 SRS2420559 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95172   0.03607   0.8144   0.52098   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43224 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       NH FLI 220 muscle RNAseq GSM2736440   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   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.   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   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   SRP115129         2716683150.0 54333663.0 GSM2736440 r1 0:50 A:708799192;C:663289162;G:642338014;T:702118631;N:138151 50       708799192 663289162 642338014 702118631 138151 SRX3081917 SRS2420560 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96405   0.03589   0.82442   0.54703   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43225 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       NH FLI 219 muscle RNAseq GSM2736439   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   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.   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   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   SRP115129         2532374300.0 50647486.0 GSM2736439 r1 0:50 A:663072795;C:618496710;G:602144102;T:648561930;N:98763 50       663072795 618496710 602144102 648561930 98763 SRX3081916 SRS2420562 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96219   0.03463   0.82412   0.49185   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43226 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       NH FLI 218 muscle RNAseq GSM2736438   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   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.   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   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   SRP115129         2378429500.0 47568590.0 GSM2736438 r1 0:50 A:625085605;C:576221380;G:561136630;T:615908269;N:77616 50       625085605 576221380 561136630 615908269 77616 SRX3081915 SRS2420561 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.93162   0.02832   0.8452   0.54129   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43227 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       NH FLI 216 muscle RNAseq GSM2736437   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   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.   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   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   SRP115129         2162753600.0 43255072.0 GSM2736437 r1 0:50 A:568419337;C:522327630;G:513098131;T:558839895;N:68607 50       568419337 522327630 513098131 558839895 68607 SRX3081914 SRS2420563 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95313   0.03331   0.83228   0.54377   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43228 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       NH FLI 215 muscle RNAseq GSM2736436   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   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.   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   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   SRP115129         2891187950.0 57823759.0 GSM2736436 r1 0:50 A:752283114;C:707486900;G:688534581;T:742791335;N:92020 50       752283114 707486900 688534581 742791335 92020 SRX3081913 SRS2420564 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.94558   0.03006   0.83234   0.52451   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43229 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       NH FLI 214 muscle RNAseq GSM2736435   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   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.   strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1 GSM2736435 GSM2736435: NH FLI 214 muscle RNAseq; Danio rerio; RNA Seq GSM2736435   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   SRP115129         2425847400.0 48516948.0 GSM2736435 r1 0:50 A:636153617;C:587566985;G:572222800;T:629815625;N:88373 50       636153617 587566985 572222800 629815625 88373 SRX3081912 SRS2420565 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95463   0.04122   0.79937   0.54522   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43230 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       NH FLI 213 muscle RNAseq GSM2736434   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   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.   strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1 GSM2736434 GSM2736434: NH FLI 213 muscle RNAseq; Danio rerio; RNA Seq GSM2736434   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   SRP115129         2696492200.0 53929844.0 GSM2736434 r1 0:50 A:705007995;C:654272683;G:639344493;T:697770444;N:96585 50       705007995 654272683 639344493 697770444 96585 SRX3081911 SRS2420566 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.89023   0.03515   0.82069   0.54881   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43231 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       NH FLI 212 muscle RNAseq GSM2736433   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   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.   strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1 GSM2736433 GSM2736433: NH FLI 212 muscle RNAseq; Danio rerio; RNA Seq GSM2736433   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   SRP115129         2048198000.0 40963960.0 GSM2736433 r1 0:50 A:534112663;C:499757837;G:485938398;T:528314868;N:74234 50       534112663 499757837 485938398 528314868 74234 SRX3081910 SRS2420567 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95513   0.03648   0.81945   0.54213   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43232 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       NH FLI 211 muscle RNAseq GSM2736432   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   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.   strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1 GSM2736432 GSM2736432: NH FLI 211 muscle RNAseq; Danio rerio; RNA Seq GSM2736432   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   SRP115129         2813928700.0 56278574.0 GSM2736432 r1 0:50 A:727919865;C:692905570;G:672803124;T:720199931;N:100210 50       727919865 692905570 672803124 720199931 100210 SRX3081909 SRS2420569 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95548   0.03587   0.81899   0.52766   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43233 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       NH FLI 210 muscle RNAseq GSM2736431   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   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.   strain:AB JxTu|tissue:muscle|age:1 year|Sex:male|perturbation:n1 GSM2736431 GSM2736431: NH FLI 210 muscle RNAseq; Danio rerio; RNA Seq GSM2736431   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   SRP115129         3216094850.0 64321897.0 GSM2736431 r1 0:50 A:842649849;C:784061705;G:756881143;T:832355348;N:146805 50       842649849 784061705 756881143 832355348 146805 SRX3081908 SRS2420568 SRA597918 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95942   0.04114   0.81387   0.53104   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43234 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   pubmed:34680427   NH FLI 273 muscle RNAseq GSM2736463   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   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.   strain:AB tert / |tissue:muscle|age:3 month|Sex:male GSM2736463 GSM2736463: NH FLI 273 muscle RNAseq; Danio rerio; RNA Seq GSM2736463   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   SRP115127         2963850210.0 58114710.0 GSM2736463 r1 0:51 A:760803485;C:733415284;G:713908770;T:755542381;N:180290 51       760803485 733415284 713908770 755542381 180290 SRX3081907 SRS2420524 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96002   0.03919   0.83329   0.50078   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43235 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   pubmed:34680427   NH FLI 271 muscle RNAseq GSM2736462   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   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.   strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male GSM2736462 GSM2736462: NH FLI 271 muscle RNAseq; Danio rerio; RNA Seq GSM2736462   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   SRP115127         2410790196.0 47270396.0 GSM2736462 r1 0:51 A:620498472;C:593943176;G:580010313;T:615793429;N:544806 51       620498472 593943176 580010313 615793429 544806 SRX3081906 SRS2420526 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95934   0.03584   0.82071   0.50583   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43236 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   pubmed:34680427   NH FLI 270 muscle RNAseq GSM2736461   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   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.   strain:AB wildtype|tissue:muscle|age:3 month|Sex:male GSM2736461 GSM2736461: NH FLI 270 muscle RNAseq; Danio rerio; RNA Seq GSM2736461   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   SRP115127         2902171881.0 56905331.0 GSM2736461 r1 0:51 A:663684682;C:805834958;G:779068076;T:653365321;N:218844 51       663684682 805834958 779068076 653365321 218844 SRX3081905 SRS2420525 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9802   0.2131   0.90009   0.65757   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43237 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   pubmed:34680427   NH FLI 264 muscle RNAseq GSM2736460   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   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.   strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male GSM2736460 GSM2736460: NH FLI 264 muscle RNAseq; Danio rerio; RNA Seq GSM2736460   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   SRP115127         3154946547.0 61861697.0 GSM2736460 r1 0:51 A:815694159;C:774994188;G:757046119;T:807013180;N:198901 51       815694159 774994188 757046119 807013180 198901 SRX3081904 SRS2420527 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96053   0.03781   0.81765   0.51653   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43238 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   pubmed:34680427   NH FLI 258 muscle RNAseq GSM2736459   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   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.   strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male GSM2736459 GSM2736459: NH FLI 258 muscle RNAseq; Danio rerio; RNA Seq GSM2736459   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   SRP115127         2005679856.0 39327056.0 GSM2736459 r1 0:51 A:506750501;C:503067671;G:491784049;T:503616846;N:460789 51       506750501 503067671 491784049 503616846 460789 SRX3081903 SRS2420528 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96065   0.05283   0.82649   0.52695   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43239 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   pubmed:34680427   NH FLI 257 muscle RNAseq GSM2736458   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   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.   strain:AB wildtype|tissue:muscle|age:3 month|Sex:male GSM2736458 GSM2736458: NH FLI 257 muscle RNAseq; Danio rerio; RNA Seq GSM2736458   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   SRP115127         2850491082.0 55891982.0 GSM2736458 r1 0:51 A:728039571;C:709536210;G:689699735;T:723071146;N:144420 51       728039571 709536210 689699735 723071146 144420 SRX3081902 SRS2420530 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95843   0.03933   0.82968   0.52274   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43240 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   pubmed:34680427   NH FLI 256 muscle RNAseq GSM2736457   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   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.   strain:AB tert / |tissue:muscle|age:3 month|Sex:male GSM2736457 GSM2736457: NH FLI 256 muscle RNAseq; Danio rerio; RNA Seq GSM2736457   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   SRP115127         2869226085.0 56259335.0 GSM2736457 r1 0:51 A:740499892;C:704499909;G:687477872;T:736568098;N:180314 51       740499892 704499909 687477872 736568098 180314 SRX3081901 SRS2420529 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96292   0.03576   0.81377   0.46796   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43241 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   pubmed:34680427   NH FLI 255 muscle RNAseq GSM2736456   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   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.   strain:AB wildtype|tissue:muscle|age:3 month|Sex:male GSM2736456 GSM2736456: NH FLI 255 muscle RNAseq; Danio rerio; RNA Seq GSM2736456   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   SRP115127         2311606620.0 45325620.0 GSM2736456 r1 0:51 A:592225197;C:572857560;G:558400927;T:587974050;N:148886 51       592225197 572857560 558400927 587974050 148886 SRX3081900 SRS2420532 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95824   0.03419   0.82179   0.49852   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43242 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   pubmed:34680427   NH FLI 254 muscle RNAseq GSM2736455   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   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.   strain:AB tert / |tissue:muscle|age:3 month|Sex:male GSM2736455 GSM2736455: NH FLI 254 muscle RNAseq; Danio rerio; RNA Seq GSM2736455   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   SRP115127         1986993150.0 38960650.0 GSM2736455 r1 0:51 A:514733936;C:485548185;G:472926120;T:513678847;N:106062 51       514733936 485548185 472926120 513678847 106062 SRX3081899 SRS2420531 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.95349   0.04965   0.71573   0.44881   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43243 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   pubmed:34680427   NH FLI 253 muscle RNAseq GSM2736454   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   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.   strain:AB wildtype|tissue:muscle|age:3 month|Sex:male GSM2736454 GSM2736454: NH FLI 253 muscle RNAseq; Danio rerio; RNA Seq GSM2736454   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   SRP115127         2905674918.0 56974018.0 GSM2736454 r1 0:51 A:722299561;C:744825817;G:720256054;T:718060093;N:233393 51       722299561 744825817 720256054 718060093 233393 SRX3081898 SRS2420533 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96657   0.06755   0.83455   0.53052   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43244 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   pubmed:34680427   NH FLI 251 muscle RNAseq GSM2736453   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   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.   strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male GSM2736453 GSM2736453: NH FLI 251 muscle RNAseq; Danio rerio; RNA Seq GSM2736453   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   SRP115127         2767147800.0 54257800.0 GSM2736453 r1 0:51 A:704520098;C:691759511;G:671521216;T:699168042;N:178933 51       704520098 691759511 671521216 699168042 178933 SRX3081897 SRS2420534 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96137   0.07028   0.82404   0.53151   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43245 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   pubmed:34680427   NH FLI 235 muscle RNAseq GSM2736452   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   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.   strain:AB tert+/ |tissue:muscle|age:3 month|Sex:male GSM2736452 GSM2736452: NH FLI 235 muscle RNAseq; Danio rerio; RNA Seq GSM2736452   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   SRP115127         2293306290.0 44966790.0 GSM2736452 r1 0:51 A:546425257;C:612542551;G:591392826;T:542811435;N:134221 51       546425257 612542551 591392826 542811435 134221 SRX3081896 SRS2420535 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.96865   0.17032   0.79563   0.59765   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
43246 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   pubmed:34680427   NH FLI 234 muscle RNAseq GSM2736451   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   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.   strain:AB wildtype|tissue:muscle|age:3 month|Sex:male GSM2736451 GSM2736451: NH FLI 234 muscle RNAseq; Danio rerio; RNA Seq GSM2736451   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   SRP115127         2538754908.0 49779508.0 GSM2736451 r1 0:51 A:666217063;C:613097220;G:599972557;T:659289888;N:178180 51       666217063 613097220 599972557 659289888 178180 SRX3081895 SRS2420536 SRA597917 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.9546   0.06678   0.81937   0.4772   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Germany 2017-08-09 Adult Adult Muscle Muscular System
49268 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.   pubmed:30692930   Gr mutant swimming UOPT sample 3 GSM3396896   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle GSM3396896 GSM3396896: Gr mutant swimming UOPT sample 3; Danio rerio; RNA Seq GSM3396896   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 ºC. 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 μl 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 μg 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   SRP162257     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       56574599 63639902 59333109 68728919 135036 SRX4721396 SRS3806484 SRA780034 GEO ZF-screens BV 1 0.95963   0.03133   0.82144   0.50958   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49269 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.   pubmed:30692930   Gr mutant swimming UOPT sample 3 GSM3396896   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle GSM3396896 GSM3396896: Gr mutant swimming UOPT sample 3; Danio rerio; RNA Seq GSM3396896   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 ºC. 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 μl 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 μg 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   SRP162257     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       55999278 63022234 58753181 68048742 45066 SRX4721396 SRS3806484 SRA780034 GEO ZF-screens BV 1 0.9607   0.03061   0.81876   0.50656   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49270 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.   pubmed:30692930   Gr mutant swimming UOPT sample 2 GSM3396895   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle GSM3396895 GSM3396895: Gr mutant swimming UOPT sample 2; Danio rerio; RNA Seq GSM3396895   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 ºC. 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 μl 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 μg 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   SRP162257     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       48361086 57271498 53468696 60291615 121101 SRX4721395 SRS3806483 SRA780034 GEO ZF-screens BV 1 0.95734   0.02232   0.83037   0.46039   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49271 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.   pubmed:30692930   Gr mutant swimming UOPT sample 2 GSM3396895   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle GSM3396895 GSM3396895: Gr mutant swimming UOPT sample 2; Danio rerio; RNA Seq GSM3396895   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 ºC. 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 μl 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 μg 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   SRP162257     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       47895589 56699017 52953041 59691639 39890 SRX4721395 SRS3806483 SRA780034 GEO ZF-screens BV 1 0.95882   0.02375   0.82753   0.45523   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49272 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.   pubmed:30692930   Gr mutant swimming UOPT sample 1 GSM3396894   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle GSM3396894 GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq GSM3396894   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 ºC. 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 μl 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 μg 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   SRP162257     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       17764968 19359482 17546237 21458644 13516 SRX4721394 SRS3806482 SRA780034 GEO ZF-screens BV 1 0.94854   0.03967   0.81239   0.52843   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49273 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.   pubmed:30692930   Gr mutant swimming UOPT sample 1 GSM3396894   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle GSM3396894 GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq GSM3396894   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 ºC. 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 μl 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 μg 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   SRP162257     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       17559056 19128796 17344883 21206265 6655 SRX4721394 SRS3806482 SRA780034 GEO ZF-screens BV 1 0.95076   0.03952   0.81057   0.52805   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49274 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.   pubmed:30692930   Gr mutant swimming UOPT sample 1 GSM3396894   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle GSM3396894 GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq GSM3396894   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 ºC. 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 μl 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 μg 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   SRP162257     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       65346157 71914444 66015753 79625150 40580 SRX4721394 SRS3806482 SRA780034 GEO ZF-screens BV 1 0.95533   0.03742   0.81044   0.52574   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49275 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.   pubmed:30692930   Gr mutant swimming UOPT sample 1 GSM3396894   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:swimming|tissue:white muscle GSM3396894 GSM3396894: Gr mutant swimming UOPT sample 1; Danio rerio; RNA Seq GSM3396894   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 ºC. 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 μl 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 μg 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   SRP162257     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       64447735 70937019 65137622 78531620 47278 SRX4721394 SRS3806482 SRA780034 GEO ZF-screens BV 1 0.95428   0.03783   0.81128   0.52701   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49276 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.   pubmed:30692930   Wild type swimming UOPT++ sample 3 GSM3396893   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle GSM3396893 GSM3396893: Wild type swimming UOPT++ sample 3; Danio rerio; RNA Seq GSM3396893   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 ºC. 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 μl 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 μg 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   SRP162257     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       84489335 86597253 84240000 99472362 195016 SRX4721393 SRS3806481 SRA780034 GEO ZF-screens BV 1 0.95532   0.04239   0.80653   0.55623   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49277 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.   pubmed:30692930   Wild type swimming UOPT++ sample 3 GSM3396893   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle GSM3396893 GSM3396893: Wild type swimming UOPT++ sample 3; Danio rerio; RNA Seq GSM3396893   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 ºC. 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 μl 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 μg 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   SRP162257     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       83629618 85716733 83395630 98483376 64836 SRX4721393 SRS3806481 SRA780034 GEO ZF-screens BV 1 0.95631   0.04199   0.8056   0.54571   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49278 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.   pubmed:30692930   Wild type swimming UOPT++ sample 2 GSM3396892   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle GSM3396892 GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq GSM3396892   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 ºC. 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 μl 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 μg 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   SRP162257     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       16926874 17543094 16728407 19679197 12377 SRX4721392 SRS3806480 SRA780034 GEO ZF-screens BV 1 0.95627   0.03548   0.82451   0.53415   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49279 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.   pubmed:30692930   Wild type swimming UOPT++ sample 2 GSM3396892   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle GSM3396892 GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq GSM3396892   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 ºC. 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 μl 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 μg 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   SRP162257     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       16757913 17378481 16577230 19498501 6001 SRX4721392 SRS3806480 SRA780034 GEO ZF-screens BV 1 0.95571   0.03554   0.82806   0.50999   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49280 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.   pubmed:30692930   Wild type swimming UOPT++ sample 2 GSM3396892   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle GSM3396892 GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq GSM3396892   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 ºC. 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 μl 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 μg 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   SRP162257     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       65379164 68332333 65926683 76572534 40527 SRX4721392 SRS3806480 SRA780034 GEO ZF-screens BV 1 0.96013   0.0352   0.82814   0.53974   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49281 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.   pubmed:30692930   Wild type swimming UOPT++ sample 2 GSM3396892   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle GSM3396892 GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq GSM3396892   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 ºC. 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 μl 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 μg 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   SRP162257     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       64737712 67666247 65306231 75803211 46927 SRX4721392 SRS3806480 SRA780034 GEO ZF-screens BV 1 0.95941   0.03355   0.82745   0.54235   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49282 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.   pubmed:30692930   Wild type swimming UOPT++ sample 1 GSM3396891   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle GSM3396891 GSM3396891: Wild type swimming UOPT++ sample 1; Danio rerio; RNA Seq GSM3396891   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 ºC. 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 μl 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 μg 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   SRP162257     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       93242107 96684654 92114654 109292193 177378 SRX4721391 SRS3806479 SRA780034 GEO ZF-screens BV 1 0.95344   0.05682   0.80612   0.46874   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49283 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.   pubmed:30692930   Wild type swimming UOPT++ sample 1 GSM3396891   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle GSM3396891 GSM3396891: Wild type swimming UOPT++ sample 1; Danio rerio; RNA Seq GSM3396891   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 ºC. 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 μl 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 μg 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   SRP162257     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       92211053 95616109 91125664 108078262 34483 SRX4721391 SRS3806479 SRA780034 GEO ZF-screens BV 1 0.95555   0.05726   0.80655   0.50316   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49284 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.   pubmed:30692930   Gr mutant resting REST sample 3 GSM3396890   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle GSM3396890 GSM3396890: Gr mutant resting REST sample 3; Danio rerio; RNA Seq GSM3396890   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 ºC. 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 μl 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 μg 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   SRP162257     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       93056953 102519574 95945518 110623659 188094 SRX4721390 SRS3806478 SRA780034 GEO ZF-screens BV 1 0.96072   0.03044   0.83151   0.49904   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49285 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.   pubmed:30692930   Gr mutant resting REST sample 3 GSM3396890   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle GSM3396890 GSM3396890: Gr mutant resting REST sample 3; Danio rerio; RNA Seq GSM3396890   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 ºC. 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 μl 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 μg 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   SRP162257     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       92045457 101410388 94956743 109396044 35534 SRX4721390 SRS3806478 SRA780034 GEO ZF-screens BV 1 0.96026   0.03027   0.82994   0.49932   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49286 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.   pubmed:30692930   Gr mutant resting REST sample 2 GSM3396889   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle GSM3396889 GSM3396889: Gr mutant resting REST sample 2; Danio rerio; RNA Seq GSM3396889   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 ºC. 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 μl 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 μg 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   SRP162257     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       96524820 105111599 96647633 116788874 192381 SRX4721389 SRS3806477 SRA780034 GEO ZF-screens BV 1 0.95102   0.04156   0.79164   0.52657   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49287 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.   pubmed:30692930   Gr mutant resting REST sample 2 GSM3396889   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle GSM3396889 GSM3396889: Gr mutant resting REST sample 2; Danio rerio; RNA Seq GSM3396889   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 ºC. 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 μl 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 μg 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   SRP162257     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       95514290 104001536 95684811 115561454 36534 SRX4721389 SRS3806477 SRA780034 GEO ZF-screens BV 1 0.95117   0.04146   0.79032   0.51379   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49288 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.   pubmed:30692930   Gr mutant resting REST sample 1 GSM3396888   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle GSM3396888 GSM3396888: Gr mutant resting REST sample 1; Danio rerio; RNA Seq GSM3396888   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 ºC. 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 μl 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 μg 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   SRP162257     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       83067213 89144746 86927052 96973321 161275 SRX4721388 SRS3806476 SRA780034 GEO ZF-screens BV 1 0.9514   0.03636   0.78064   0.49277   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49289 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.   pubmed:30692930   Gr mutant resting REST sample 1 GSM3396888   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   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Gr mutant|treatment:resting|tissue:white muscle GSM3396888 GSM3396888: Gr mutant resting REST sample 1; Danio rerio; RNA Seq GSM3396888   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 ºC. 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 μl 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 μg 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   SRP162257     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       82429330 88444066 86279627 96242734 31285 SRX4721388 SRS3806476 SRA780034 GEO ZF-screens BV 1 0.95127   0.03685   0.78125   0.49716   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49290 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.   pubmed:30692930   Wild type resting REST++ sample 3 GSM3396887   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle GSM3396887 GSM3396887: Wild type resting REST++ sample 3; Danio rerio; RNA Seq GSM3396887   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 ºC. 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 μl 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 μg 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   SRP162257     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       95664418 101106745 99163612 111801493 189578 SRX4721387 SRS3806475 SRA780034 GEO ZF-screens BV 1 0.95163   0.03911   0.80308   0.47176   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49291 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.   pubmed:30692930   Wild type resting REST++ sample 3 GSM3396887   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle GSM3396887 GSM3396887: Wild type resting REST++ sample 3; Danio rerio; RNA Seq GSM3396887   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 ºC. 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 μl 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 μg 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   SRP162257     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       94571267 99984137 98039941 110500771 35781 SRX4721387 SRS3806475 SRA780034 GEO ZF-screens BV 1 0.95153   0.03927   0.80081   0.43253   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49292 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.   pubmed:30692930   Wild type resting REST++ sample 2 GSM3396886   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle GSM3396886 GSM3396886: Wild type resting REST++ sample 2; Danio rerio; RNA Seq GSM3396886   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 ºC. 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 μl 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 μg 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   SRP162257     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       76187242 79646315 76288340 88907254 151101 SRX4721386 SRS3806474 SRA780034 GEO ZF-screens BV 1 0.95633   0.0376   0.82294   0.48192   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49293 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.   pubmed:30692930   Wild type resting REST++ sample 2 GSM3396886   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle GSM3396886 GSM3396886: Wild type resting REST++ sample 2; Danio rerio; RNA Seq GSM3396886   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 ºC. 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 μl 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 μg 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   SRP162257     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       75443385 78910190 75585800 88033421 28575 SRX4721386 SRS3806474 SRA780034 GEO ZF-screens BV 1 0.95684   0.03736   0.8228   0.42199   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49294 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.   pubmed:30692930   Wild type resting REST++ sample 1 GSM3396885   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle GSM3396885 GSM3396885: Wild type resting REST++ sample 1; Danio rerio; RNA Seq GSM3396885   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 ºC. 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 μl 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 μg 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   SRP162257     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       79370894 82057170 79743998 91615147 152317 SRX4721385 SRS3806473 SRA780034 GEO ZF-screens BV 1 0.9559   0.03764   0.81146   0.48877   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
49295 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.   pubmed:30692930   Wild type resting REST++ sample 1 GSM3396885   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++   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 ºC. 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 μl 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 μg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina San Diego CA USA.   tissue:white muscle|genotype:Wild type|treatment:resting|tissue:white muscle GSM3396885 GSM3396885: Wild type resting REST++ sample 1; Danio rerio; RNA Seq GSM3396885   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 ºC. 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 μl 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 μg 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   SRP162257     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       78396828 81102360 78796819 90507746 29100 SRX4721385 SRS3806473 SRA780034 GEO ZF-screens BV 1 0.9556   0.03749   0.81144   0.48578   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   Unknown 2018-09-20 Undetermined Undetermined Muscle Muscular System
52955 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°C.   pubmed:32496654   S0WT S C RNA Seq GSM3910338   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       202991469 183350303 181337685 217696201 85032 SRX6374057 SRS5034866 SRA914604 GEO University of Bern 1 0.93791   0.05606   0.75144   0.53237   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52956 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°C.   pubmed:32496654   S0WT S B RNA Seq GSM3910337   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       271421784 242201012 237079646 286766535 112865 SRX6374056 SRS5034865 SRA914604 GEO University of Bern 1 0.93385   0.05579   0.73602   0.50008   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52957 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°C.   pubmed:32496654   S0WT S 7 RNA Seq GSM3910336   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       236551279 210199570 206723666 247589765 97305 SRX6374055 SRS5034864 SRA914604 GEO University of Bern 1 0.93688   0.05977   0.80119   0.50443   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52958 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°C.   pubmed:32496654   S0WT S 6 RNA Seq GSM3910335   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       297191939 247117436 237870203 292953815 115366 SRX6374054 SRS5034863 SRA914604 GEO University of Bern 1 0.89528   0.06728   0.78634   0.53098   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52959 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°C.   pubmed:32496654   S0WT DD 4 RNA Seq GSM3910334   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       241201134 204122008 208735432 252853431 97597 SRX6374053 SRS5034862 SRA914604 GEO University of Bern 1 0.91061   0.05033   0.79545   0.54457   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52960 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°C.   pubmed:32496654   S0WT DD 3 RNA Seq GSM3910333   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       264389932 233507692 235911726 279216160 109788 SRX6374052 SRS5034861 SRA914604 GEO University of Bern 1 0.92535   0.04437   0.81162   0.49398   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52961 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°C.   pubmed:32496654   S0WT DD 2 RNA Seq GSM3910332   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       228696407 206617559 191782242 229573977 90647 SRX6374051 SRS5034860 SRA914604 GEO University of Bern 1 0.36358   0.04768   0.91303   0.52314   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52962 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°C.   pubmed:32496654   S0KO S C RNA Seq GSM3910331   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       193243096 177276287 174035790 205777475 81913 SRX6374050 SRS5034859 SRA914604 GEO University of Bern 1 0.94262   0.05429   0.75741   0.51196   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52963 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°C.   pubmed:32496654   S0KO S B RNA Seq GSM3910330   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       223023468 203743702 200457097 235595080 93003 SRX6374049 SRS5034858 SRA914604 GEO University of Bern 1 0.9374   0.04142   0.73111   0.47223   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52964 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°C.   pubmed:32496654   S0KO S A RNA Seq GSM3910329   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       195880291 183023619 178202819 210507113 83242 SRX6374048 SRS5034857 SRA914604 GEO University of Bern 1 0.93312   0.04579   0.72906   0.48412   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52965 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°C.   pubmed:32496654   S0KO S 6 RNA Seq GSM3910328   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       257642647 225459692 225710033 263073969 104911 SRX6374047 SRS5034856 SRA914604 GEO University of Bern 1 0.9235   0.05678   0.7779   0.51447   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52966 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°C.   pubmed:32496654   S0KO DD 7 RNA Seq GSM3910327   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       212421329 192524361 192658987 224881911 89760 SRX6374046 SRS5034855 SRA914604 GEO University of Bern 1 0.95061   0.04831   0.78013   0.52246   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52967 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°C.   pubmed:32496654   S0KO DD 6 RNA Seq GSM3910326   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       228413430 209052461 205760159 240648496 97030 SRX6374045 SRS5034854 SRA914604 GEO University of Bern 1 0.93764   0.04361   0.74777   0.45055   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52968 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°C.   pubmed:32496654   S0KO DD 3 RNA Seq GSM3910325   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       244456092 219466128 219111604 252630825 101813 SRX6374044 SRS5034853 SRA914604 GEO University of Bern 1 0.90131   0.0466   0.83477   0.50178   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
52969 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°C.   pubmed:32496654   S0KO DD 2 RNA Seq GSM3910324   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 “counts”. 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°C. 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   1 Adult zebrafish skeletal muscle were dissected and stored at 80°C. 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   SRP212268     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       223803666 200893790 201657972 237709184 92546 SRX6374043 SRS5034852 SRA914604 GEO University of Bern 1 0.9298   0.0537   0.82574   0.51143   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   Switzerland 2019-06-28 Multi-stage Multi-stage Muscle Muscular System
55305 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.     fast muscle   pea fishm6   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                 RNASeq of zebrafish: adult female fast muscle pm6 pm6 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     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     512656433 497166196 475911685 561012780 111430 SRX7731318 SRS6151725 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.97101   0.06659   0.82745   0.46321   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55306 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.     fast muscle   pea fishm5   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                 RNASeq of zebrafish: adult female fast muscle pm5 pm5 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     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     351089576 337868838 315380752 380954376 72990 SRX7731317 SRS6151724 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.96194   0.09162   0.81126   0.51366   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55307 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. Ultimately this knowledge would be benefited for the industry to formulate sustainable diets based on terrestrial ingredients with properly addressing fish welfare concerns.     fast muscle   pea fishm4   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 replicate4|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle pm4 pm4 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     pm4.fastq.gz fastq 2118394512.0 27873612.0 pm4.fastq.gz 0:76 1:0 A:558144544;C:509998861;G:479358157;T:570769039;N:123911 76 0     558144544 509998861 479358157 570769039 123911 SRX7731316 SRS6151723 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.94888   0.12658   0.8252   0.41386   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55308 55308 SRR11092479 SRX7731315 SRS6151722 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.     fast muscle   pea fishm3   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 replicate3|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle pm3 pm3 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     pm3.fastq.gz fastq 2375673740.0 31258865.0 pm3.fastq.gz 0:76 1:0 A:515905187;C:691492864;G:615002075;T:553136912;N:136702 76 0     515905187 691492864 615002075 553136912 136702 SRX7731315 SRS6151722 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.95226   0.19981   0.88773   0.71487   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55309 55309 SRR11092480 SRX7731314 SRS6151721 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.     fast muscle   pea fishm2   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 replicate2|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle pm2 pm2 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     pm2.fastq.gz fastq 2107982056.0 27736606.0 pm2.fastq.gz 0:76 1:0 A:538632968;C:505291675;G:484605729;T:579329857;N:121827 76 0     538632968 505291675 484605729 579329857 121827 SRX7731314 SRS6151721 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.96281   0.07736   0.81493   0.50221   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55310 55310 SRR11092481 SRX7731313 SRS6151720 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.     fast muscle   pea fishm1   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 replicate1|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle pm1 pm1 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     pm1.fastq.gz fastq 2084337848.0 27425498.0 pm1.fastq.gz 0:76 1:0 A:525909797;C:504640406;G:488117980;T:565551059;N:118606 76 0     525909797 504640406 488117980 565551059 118606 SRX7731313 SRS6151720 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.96794   0.06893   0.83435   0.52321   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55311 55311 SRR11092482 SRX7731312 SRS6151719 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.     fast muscle   control fishm4   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:control replicate4|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle cm4 cm4 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     cm4.fastq.gz fastq 2263882984.0 29787934.0 cm4.fastq.gz 0:76 1:0 A:562502146;C:560431696;G:534631946;T:606194211;N:122985 76 0     562502146 560431696 534631946 606194211 122985 SRX7731312 SRS6151719 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.96339   0.07486   0.82958   0.51707   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55312 55312 SRR11092483 SRX7731311 SRS6151718 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.     fast muscle   control fishm3   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:control replicate3|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle cm3 cm3 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     cm3.fastq.gz fastq 2339617288.0 30784438.0 cm3.fastq.gz 0:76 1:0 A:622147797;C:548069187;G:533577104;T:635685680;N:137520 76 0     622147797 548069187 533577104 635685680 137520 SRX7731311 SRS6151718 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.94319   0.13419   0.81438   0.48694   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55313 55313 SRR11092484 SRX7731310 SRS6151717 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.     fast muscle   wheat fishm4   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:wheat replicate4|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle wm4 wm4 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     wm4.fastq.gz fastq 1985403024.0 26123724.0 wm4.fastq.gz 0:76 1:0 A:498747962;C:482453313;G:462097859;T:541996279;N:107611 76 0     498747962 482453313 462097859 541996279 107611 SRX7731310 SRS6151717 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.96249   0.06026   0.8367   0.51944   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55314 55314 SRR11092485 SRX7731309 SRS6151716 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.     fast muscle   wheat fishm3   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:wheat replicate3|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle wm3 wm3 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     wm3.fastq.gz fastq 1783867364.0 23471939.0 wm3.fastq.gz 0:76 1:0 A:450732711;C:435997554;G:411398964;T:485644552;N:93583 76 0     450732711 435997554 411398964 485644552 93583 SRX7731309 SRS6151716 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.95766   0.07889   0.83232   0.44279   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55315 55315 SRR11092486 SRX7731308 SRS6151715 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.     fast muscle   wheat fishm2   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:wheat replicate2|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle wm2 wm2 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     wm2.fastq.gz fastq 2142927996.0 28196421.0 wm2.fastq.gz 0:76 1:0 A:546469493;C:512054313;G:496423605;T:587858713;N:121872 76 0     546469493 512054313 496423605 587858713 121872 SRX7731308 SRS6151715 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.96705   0.07616   0.83067   0.42744   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55316 55316 SRR11092487 SRX7731307 SRS6151714 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.     fast muscle   wheat fishm1   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:wheat replicate1|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle wm1 wm1 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     wm1.fastq.gz fastq 2575961708.0 33894233.0 wm1.fastq.gz 0:76 1:0 A:715981531;C:567645285;G:554784963;T:737401160;N:148769 76 0     715981531 567645285 554784963 737401160 148769 SRX7731307 SRS6151714 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.94071   0.20468   0.81152   0.56581   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System
55317 55317 SRR11092488 SRX7731306 SRS6151713 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.     fast muscle   soy fishm6   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:soy replicate6|BioSampleModel:Model organism or animal                 RNASeq of zebrafish: adult female fast muscle sm6 sm6 Directional RNA libraries with PolyA mRNA enrichment     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 550   SRP226922     sm6.fastq.gz fastq 1476347044.0 19425619.0 sm6.fastq.gz 0:76 1:0 A:370448815;C:361460384;G:341504966;T:402855002;N:77877 76 0     370448815 361460384 341504966 402855002 77877 SRX7731306 SRS6151713 SRA1043309 Nord Universitet|Faculty of Biosciences and Aquaculture Nord Universitet 1 0.96435   0.06773   0.83049   0.50288   76   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Norway 2020-02-15 Adult Adult Muscle Muscular System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;