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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
38266 SRR1609749 SRX730402 SRS719623 SRP048807 PRJNA263496 Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish GSE62221 Transcriptome Analysis The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures ranging from normal 28°C to mild 18°C and severe 10°C cold using RNA seq. The tissues varied in the number of cold responsive genes of which the kidney appeared to be most sensitive whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes such as RNA splicing and proton transport as well tissue specific processes such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program DREME. Eleven motifs 6 known and 5 novel were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs such as the AP 1 and STAT1 binding sites are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures   pubmed:26227973   kidney10 GSM1523044   source name:kidney|tissue:kidney|temperature:10°C|strain:Tubingen|age:6 mpf kidney10 Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html which is a python based script was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... kidney fish were maintained 12h to adapt low temperatures and then killed by pithing Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:kidney|temperature:10°C|strain:Tubingen|age:6 mpf GSM1523044 GSM1523044: kidney10; Danio rerio; RNA Seq GSM1523044   1 Tissues were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM1523044 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP048807     kidney10_1.fq.gz kidney10_2.fq.gz fastq fastq 4315071200.0 21575356.0 GSM1523044 r1 0:100 1:100 A:1152823680;C:1012018705;G:1003451232;T:1146696176;N:81407 100 100     1152823680 1012018705 1003451232 1146696176 81407 SRX730402 SRS719623 SRA189240 GEO Shanghai Ocean University 2 0.95345 0.94751 0.05494 0.05445 0.7455 0.74856 0.53555 0.52518 100 100 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2014-10-09 Adult Adult Kidney Renal System