run_metadata: 49288

This data as json

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
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