{"database": "metadata", "table": "run_metadata", "rows": [[53170, "SRR9697469", "SRX6455746", "SRS5113421", "SRP215029", "PRJNA555064", "Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells", "GSE134399", "Transcriptome Analysis", "MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression  and are also involved in multiple stress conditions. However  the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study  high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28\u00b0C  30 days and cold acclimation 18\u00b0C  30 days conditions. A total of 414 miRNAs  349 known and 65 novel  were identified. Among those miRNAs  24 19 known and 5 novel were up regulated  and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation  cell junction  intracellular signal transduction  ECM receptor interaction and so on. Moreover  dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress  indicating the involvement of miRNA in cold acclimation. In summary  the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 \u00b0C as control and at 18 \u00b0C for 30 days  seperately. Each condition has three biological replica.", null, "pubmed:31923196", null, "ZF4 18 30d cold2", "GSM3946003", null, "tissue:embryonic fibroblast cells|cell line:ZF4|cell type:fibroblast cell line|growth temperature:cultured at 18 C for 30 days|treatment:cold treatment for 30 days", "ZF4 18 30d cold2", "Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5%  or with ploy A  contaminants  reads smaller than 17 nt or longer than 35 nt  and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10  ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation  clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The  miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs", "embryonic fibroblast cells", "For cold acclimation  ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18\u02daC  5% CO2  in the same medium for 30 days.", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.", "ZF4 cell line was from the American Type Culture Collection ATCC  CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B  Hyclone  Thermo Scientific supplemented with 10% fetal bovine serum 10099141  Gibco  Life technologies 1% penicillin streptomycin glutamine solution SV30082.01  Hyclone  Thermo Scientificat 28\u00b0C  5% CO2.", "cell line:ZF4|cell type:fibroblast cell line|growth temperature:cultured at 18 C for 30 days|treatment:cold treatment for 30 days", "GSM3946003", "GSM3946003: ZF4 18 30d cold2; Danio rerio; miRNA Seq", "GSM3946003", null, "1", "Total RNA was extracted using miRNeasy Mini Kit 217004  Qiagen and purified by RNAClean XP Kit A63987  Beckman Coulter and RNase Free DNase Set 79254  Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.", "GEO Accession:GSM3946003", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq X Ten", null, "SRP215029", null, null, "5.fq.gz", "fastq", 853031700.0, 17060634.0, "GSM3946003 r1", "0:50", "A:192338096;C:205750986;G:242627478;T:212299265;N:15875", 50, null, null, null, 192338096, 205750986, 242627478, 212299265, 15875, "SRX6455746", "SRS5113421", "SRA922199", "GEO", "Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University", 1, 0.00538, null, 0.00045, null, 0.99738, null, 0.47457, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-07-17", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "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": ["53170"], "units": {}, "query_ms": 8.509198989486322}