{"database": "metadata", "table": "run_metadata", "rows": [[47645, "SRR6798776", "SRX3757613", "SRS3013120", "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.", null, "pubmed:33343615", null, "WT rep2", "GSM3029082", null, "source name:muscle tissues|tissue:muscle|treatment:DMSO", "WT rep2", "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\u2019 ends of the reads and the trimmed reads were filtered with read length \u2265 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\u2019s 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\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "Breeding fish were maintained at 28\u00b0C 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", "GSM3029082", "GSM3029082: WT rep2; Danio rerio; RNA Seq", "GSM3029082", null, "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\uff08H/M/R Library PrepKit for Illumina NR603 02  Vazyme. Libraries were pooled and sequenced using the Illumina\u00a0HiSeq\u00a0X\u00a0Ten machine as 150 bp paired end sequencing reads.", "GEO Accession:GSM3029082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP133827", null, null, "RLT2_2.fq.gz RLT2_1.fq.gz", "fastq fastq", 9462767100.0, 31542557.0, "GSM3029082 r1", "0:150 1:150", "A:2301678607;C:2445064584;G:2361534540;T:2354357373;N:131996", 150, 150, null, null, 2301678607, 2445064584, 2361534540, 2354357373, 131996, "SRX3757613", "SRS3013120", "SRA663830", "GEO", "School of basic medicine science, Zhejiang University", 2, 0.91337, 0.91337, 0.17924, 0.17526, 0.78317, 0.79011, 0.50203, 0.51647, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "China", "2018-03-02", "Multi-stage", "Embryo", "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": ["47645"], "units": {}, "query_ms": 8.48132600003737}