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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
44948 SRR6324382 SRX3424135 SRS2715769 SRP125677 PRJNA419909 Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells GSE107369 Transcriptome Analysis Long non coding RNAs lncRNAs are increasingly regarded as a key role in regulating diverse biological processes in various tissues and species. So far no data is available on screening and functional prediction of lncRNAs in cold acclimation in fishes. Here we compared expression profiles of lncRNAs in zebrafish embryonic fibroblast cells ZF4 cultured at 28°C as control with that of cold acclimated cells cultured at 18°C for 30 days by high throughput sequencing. There are 8363 novel lncRNAs were identified. Including known and novel lncRNAs there are 347 lncRNAs up regulated and 342 lncRNAs down regulated in cold acclimated cells compared with that of control cells at 28°C. Among differentially expressed lncRNAs 74 and 61 were found only in control cells or in cold acclimated cells respectively. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses of genes adjacent to differentially expressed lncRNAs showed that enriched genes were involved in electron transport cell adhesion oxidation reduction process and so on. We predicted target genes of differentially expressed lncRNAs by looking for interactions between lncRNAs and mRNA and constructed a complex interaction network. In summary our genome wide systematic identification and function prediction of lncRNAs in zebrafish cells lays the foundation for future studies to elucidate crucial roles of lncRNAs in cold acclimation in fishes. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.   pubmed:29634734   ZF4 28 rep1 GSM2865566   tissue:ZF4 28|cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28°C|sample group:control ZF4 28 rep1 Illumina Casava1.8 software used for basecalling. Clean RNA seq reads for each sample were aligned by HISAT2 2.1.0 with default setting to the zebrafish genome assembly GRCz10 Transcripts were assembled by StringTie 1.3.3 with parameter “ G Danio rerio.GRCz10.88.gtf” all assemblies were merged together utilizing StringTie’s “merge” function CPC Coding Potential Calculator CNCI Coding Non Coding Index and Pfam were used to delete transcripts with coding potential The genes expression levels were estimated by FPKM fragments per kilobase of exon per million fragments mapped and assessed using StringTie Genome build: GRCz10 Supplementary files format and content: tab delimited text files include FPKM values for novel lncRNAs ZF4 28 For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 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 constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection ATCC CRL 2050; Driever and Rangini 1993. The cells were grown at 28 °C 5% CO2 in Dulbecco's modified Eagle's medium/F12 nutrient mix DMEM/F12 supplemented with 10% FBS 1% l glutamine 100 u/ml penicillin 100 μg/ml streptomycin. For cold treatment cells were grown at 18 °C 5% CO2 in the same medium for up to 30 days. All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd USA. cell line:ZF4|cell type:embryonic fibroblast cell line|cultured at:normal condition 28°C|sample group:control GSM2865566 GSM2865566: ZF4 28 rep1; Danio rerio; RNA Seq GSM2865566   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 constructed using the TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo Zero RS 122 2301/ RS 122 2302 Illumina. Libraries were pooled and sequenced using the Illumina HiSeq machine as 150 bp paired end sequencing reads. GEO Accession:GSM2865566 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA HiSeq X Ten   SRP125677     1_2.fq.gz 1_1.fq.gz fastq fastq 9364351500.0 31214505.0 GSM2865566 r1 0:150 1:150 A:2483908747;C:2191875885;G:2204013829;T:2484392803;N:160236 150 150     2483908747 2191875885 2204013829 2484392803 160236 SRX3424135 SRS2715769 SRA634103 GEO Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University 2 0.91474 0.91441 0.21056 0.20796 0.739 0.74477 0.52778 0.53276 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   China 2017-11-27 Undetermined Embryo Cell Line Cell Line