{"database": "metadata", "table": "run_metadata", "rows": [[49281, "SRR7883092", "SRX4721392", "SRS3806480", "SRP162257", "PRJNA492308", "Cortisol acting through the glucocorticoid receptor is not responsible for exercise enhanced growth but does affect the white skeletal muscle transcriptome in zebrafish Danio rerio", "GSE120253", "Transcriptome Analysis", "Forced sustained swimming exercise at optimal speed enhances growth in many fish species  particularly through hypertrophy of the white skeletal muscle. The exact mechanism of this effect has not been resolved yet. To explore the mechanism  we first subjected wild type zebrafish to an exercise protocol validated for exercise enhanced growth  and showed that exercised zebrafish  which indeed showed enhanced growth  had higher cortisol levels than the non exercised controls. A central role was therefore hypothesized for the steroid hormone cortisol acting through the Glucocorticoid receptor Gr. Second  we subjected wild type zebrafish and zebrafish with a mutant Gr to exercise at optimal  suboptimal and super optimal speeds and compared them with non exercised controls. Exercised zebrafish showed growth enhancement at all speeds  with highest growth at optimal speeds. In the Gr mutant fish  exercise resulted in growth enhancement similar to wild type zebrafish  indicating that cortisol cannot be considered as a main determinant of exercise enhanced growth. Finally  the transcriptome of white skeletal muscle tissue was analysed by RNA sequencing. The results of this analysis showed that in the muscle tissue of Gr mutant fish a lower number of genes is regulated by exercise than in wild type fish 183 versus 351. A cluster of 36 genes was regulated by exercise in both wild type and mutant fish. In this cluster  genes involved in transcriptional regulation and protein ubiquitination were overrepresented. Since growth was enhanced similarly in both wild type fish and mutants  these processes may play an important role in exercise enhanced growth. Overall design: Deep sequencing transcriptome analysis of white muscle samples derived from wild type ++ or glucocorticoid receptor Gr mutant    Danio rerio specimens that were exposed to either a resting REST or a swimming UOPT regimen: wild type resting REST++; n=3  Gr mutant resting REST  ;  n=3  wild type swimming UOPT++; n=3  Gr mutant swimming UOPT  ; n=3.", null, "pubmed:30692930", null, "Wild type swimming UOPT++ sample 2", "GSM3396892", null, "source name:Wild type swimming UOPT++|biomaterial provider:[Origin of specimen] zebrafish facilities of the Institute of Biology Leiden Leiden  The Netherlands|tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "Wild type swimming UOPT++ sample 2", "Illumina Casava software used for basecalling: SCS2.2.38/RTA1.18.61 Illumina reads were aligned against the zebrafish genome sequence GRCz10.80 using TopHat version 2.0.5 Trapnell et al.  2009 The resulting files were filtered using SAMtools version 0.1.18 Li et al.  2009 to exclude secondary alignment of reads Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9 Anders and Huber  2014 Differentially expressed genes were identified using DESeq Anders and Huber  2010 and data were further processed using Microsoft Excel Genome build: Danio rerio.GRCz10.80 Supplementary files format and content: UOPT++ versus REST++ DiffExpr.txt  UOPT   versus REST   DiffExpr.txt  REST   versus REST++ DiffExpr.txt and UOPT   versus UOPT++ DiffExpr.txt: Microsoft Office Excel file .txt with the following columns: ENSEMBL ID; Associated Gene Name; Description; 6x sample x; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj", "Wild type swimming UOPT++", null, "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer\u2019s description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer\u2019s instructions Illumina  San Diego CA  USA.", null, "tissue:white muscle|genotype:Wild type|treatment:swimming|tissue:white muscle", "GSM3396892", "GSM3396892: Wild type swimming UOPT++ sample 2; Danio rerio; RNA Seq", "GSM3396892", null, "1", "White muscle fillet was dissected dorsally from the lateral line in the epaxial quadrant along the whole length of the fish and stored in RNAlater Ambion at  20 \u00baC. Tissue was lysed in QIAzol Lysis Reagent. A Qiagen TissueRuptor was used to cut up the tissue samples and RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's description Qiagen Benelux BV  Venlo  the Netherlands. RNA was eluted in 50 \u03bcl and quantified by Nanodrop Thermo Fisher Scientific  Amsterdam  the Netherlands. Integrity of the RNA was confirmed using an Agilent Bioanalyzer 2100 total RNA Nanoseries II chip Agilent  Amstelveen  Netherlands. Illumina RNAseq libraries were prepared from 1 \u03bcg total RNA using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.", "GEO Accession:GSM3396892", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162257", null, null, "ZFG-15-20_09_14125_GAGTGG_L002_R1_001.fastq.gz", "fastq", 273560328.0, 5363928.0, "GSM3396892 r4", "0:51", "A:64737712;C:67666247;G:65306231;T:75803211;N:46927", 51, null, null, null, 64737712, 67666247, 65306231, 75803211, 46927, "SRX4721392", "SRS3806480", "SRA780034", "GEO", "ZF-screens BV", 1, 0.95941, null, 0.03355, null, 0.82745, null, 0.54235, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2018-09-20", "Undetermined", "Undetermined", "Muscle", "Muscular System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "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"], "primary_keys": ["rowid"], "primary_key_values": ["49281"], "units": {}, "query_ms": 11.032428999897093}