run_metadata: 47644

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
47644	SRR6798777	SRX3757614	SRS3013122	SRP133827	PRJNA436713	Inhibition of embryonic HSP 90 function causes variation of cold tolerance in zebrafish	GSE111359	Transcriptome Analysis	Accumulating evidence suggests that HSP90 plays roles in modulation of phenotype in vertebrate development which is closely involved in adaptation and evolution. In this study we showed that inhibition of embryonic HSP90 function either by a chemical inhibitor radicicol or low conductivity stress induced variation of cold tolerance in adult zebrafish. Overall design: Three zebrafish showing significantly increased survival times in cold from radicicol group and three zebrafish from control group were selected for RNA Seq. Muscle tissue was separated from above mentioned fishes and used as materials for RNA Seq.		pubmed:33343615		WT rep3	GSM3029083		source name:muscle tissues\|tissue:muscle\|treatment:DMSO	WT rep3	Illumina Casava1.8 software used for basecalling. The raw reads were trimmed and filtered using Seqtk https://github.com/lh3/seqtk. Low quality Q < 20 bases were trimmed from 3’ ends of the reads and the trimmed reads were filtered with read length ≥ 25 bp. Clean RNA Seq reads for each sample were aligned by HISAT2 2.0.4 with default setting to the zebrafish genome assembly using the Ensembl annotation DanRer10 Danio rerio.GRCz10.84.gtf 1. The number of reads mapped to the genes was counted by StringTie and normalized by TMM trimmed mean of M values method2. We next calculated fragments per kilobase per million mapped reads FPKM of each gene to indicate gene expression level. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for each gene	muscle tissues	Treatment with radicicol was initiated at 50% epiboly and continued to 48 hpf followed by the removal of the drug using three rinses the whole process was carried in the dark because the light sensitivity of radicicol. Control group were treated with identical doses of DMSO.	Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads.	Breeding fish were maintained at 28°C in a circulating water system on a 14 h light/10 h dark cycle. Embryos were collected by natural spawning and staged.	tissue:muscle\|treatment:DMSO	GSM3029083	GSM3029083: WT rep3; Danio rerio; RNA Seq	GSM3029083		1	Total RNA was extracted using TRIZOL Reagent 15596 018 Life technologies following the manufacturer's instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 Agilent technologies Santa Clara CA US. Qualified total RNA was further purified by RNAClean XP Kit A63987 Beckman Coulterand RNase Free DNase Set 79254 QIAGEN. Libraries were constructed using VAHTS Total RNA Seq（H/M/R Library PrepKit for Illumina NR603 02 Vazyme. Libraries were pooled and sequenced using the Illumina HiSeq X Ten machine as 150 bp paired end sequencing reads.	GEO Accession:GSM3029083	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	HiSeq X Ten		SRP133827			RLT3_1.fq.gz RLT3_2.fq.gz	fastq fastq	7458295500.0	24860985.0	GSM3029083 r1	0:150 1:150	A:1875422371;C:1858400851;G:1819493497;T:1904874518;N:104263	150	150			1875422371	1858400851	1819493497	1904874518	104263	SRX3757614	SRS3013122	SRA663830	GEO	School of basic medicine science, Zhejiang University	2	0.88642	0.88696	0.1881	0.18533	0.79537	0.80073	0.50351	0.48568	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	bulk	bulk		China	2018-03-02	Multi-stage	Embryo	Muscle	Muscular System