Series Summary for DCD000391SR

RNA-seq data from 8 different tissues (28dC): Global identification of the gene networks and cis-regulatory elements of the cold response in zebrafish

Survey

10.1093/nar/gkv780

GSE62221

The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. However, the cis- and trans-factors governing cold responses are not well characterized. We profiled transcriptional changes in eight zebrafish tissues exposed to mildly and severely cold temperatures using RNA-Seq. A total of 1943 differentially expressed genes (DEGs) were identified, from which 34 clusters representing distinct tissue and temperature response expression patterns were derived using the k-means fuzzy clustering algorithm.

True

mickael.dong

Jan. 11, 2018, 4:29 a.m.

Oct. 22, 2018, 3:36 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007062BS DCD000391SR tissue Liangbiao Lab, Shanghai Ocean University TU 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD002084AA DCD013675BR RNA-seq_Liangbiao_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002468SQ DCD002480TR Liangbiao Lab, Shanghai Ocean University Illumina HiSeq 2000 unstranded 09/04/2014
DCD008020DT: FASTQ
DCD008735DT: BIGWIG GRCz10/danRer10
DCD010753DT: LOG GRCz10/danRer10
DCD010754DT: TSV GRCz10/danRer10
DCD010755DT: TSV GRCz10/danRer10
DCD010756DT: BEDGRAPH GRCz10/danRer10
DCD010757DT: BEDGRAPH GRCz10/danRer10
DCD010758DT: BEDGRAPH GRCz10/danRer10
DCD010759DT: LOG GRCz10/danRer10
DCD010760DT: PDF GRCz10/danRer10
DCD010761DT: LOG GRCz10/danRer10
DCD010762DT: PDF GRCz10/danRer10
DCD010766DT: BEDGRAPH GRCz10/danRer10
DCD010778DT: BAM GRCz10/danRer10
DCD010779DT: BAM GRCz10/danRer10
DCD012846DT: LOG GRCz11/danRer11
DCD012847DT: TSV GRCz11/danRer11
DCD012848DT: TSV GRCz11/danRer11
DCD012849DT: BEDGRAPH GRCz11/danRer11
DCD012851DT: BIGWIG GRCz11/danRer11
DCD012852DT: PDF GRCz11/danRer11
DCD012853DT: LOG GRCz11/danRer11
DCD012854DT: PDF GRCz11/danRer11
DCD012855DT: LOG GRCz11/danRer11
DCD012856DT: BEDGRAPH GRCz11/danRer11
DCD012861DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007063BS DCD000391SR tissue Liangbiao Lab, Shanghai Ocean University TU 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD002085AA DCD013676BR RNA-seq_Liangbiao_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002469SQ DCD002481TR Liangbiao Lab, Shanghai Ocean University Illumina HiSeq 2000 unstranded 09/04/2014
DCD008021DT: FASTQ
DCD008742DT: BIGWIG GRCz10/danRer10
DCD010634DT: LOG GRCz10/danRer10
DCD010635DT: TSV GRCz10/danRer10
DCD010636DT: TSV GRCz10/danRer10
DCD010637DT: BEDGRAPH GRCz10/danRer10
DCD010638DT: BEDGRAPH GRCz10/danRer10
DCD010639DT: PDF GRCz10/danRer10
DCD010640DT: LOG GRCz10/danRer10
DCD010641DT: PDF GRCz10/danRer10
DCD010642DT: LOG GRCz10/danRer10
DCD010643DT: BEDGRAPH GRCz10/danRer10
DCD010645DT: BEDGRAPH GRCz10/danRer10
DCD010662DT: BAM GRCz10/danRer10
DCD012857DT: LOG GRCz11/danRer11
DCD012858DT: TSV GRCz11/danRer11
DCD012859DT: TSV GRCz11/danRer11
DCD012860DT: BEDGRAPH GRCz11/danRer11
DCD012862DT: BIGWIG GRCz11/danRer11
DCD012863DT: PDF GRCz11/danRer11
DCD012864DT: LOG GRCz11/danRer11
DCD012865DT: PDF GRCz11/danRer11
DCD012866DT: LOG GRCz11/danRer11
DCD012867DT: BEDGRAPH GRCz11/danRer11
DCD012883DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007064BS DCD000391SR tissue Liangbiao Lab, Shanghai Ocean University TU 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD002086AA DCD013677BR RNA-seq_Liangbiao_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002470SQ DCD002482TR Liangbiao Lab, Shanghai Ocean University Illumina HiSeq 2000 unstranded 09/04/2014
DCD008022DT: FASTQ
DCD008741DT: BIGWIG GRCz10/danRer10
DCD010524DT: LOG GRCz10/danRer10
DCD010525DT: TSV GRCz10/danRer10
DCD010526DT: TSV GRCz10/danRer10
DCD010528DT: BEDGRAPH GRCz10/danRer10
DCD010529DT: BEDGRAPH GRCz10/danRer10
DCD010530DT: PDF GRCz10/danRer10
DCD010531DT: LOG GRCz10/danRer10
DCD010532DT: PDF GRCz10/danRer10
DCD010533DT: LOG GRCz10/danRer10
DCD010534DT: BEDGRAPH GRCz10/danRer10
DCD010537DT: BEDGRAPH GRCz10/danRer10
DCD010562DT: BAM GRCz10/danRer10
DCD012868DT: LOG GRCz11/danRer11
DCD012869DT: TSV GRCz11/danRer11
DCD012870DT: TSV GRCz11/danRer11
DCD012871DT: BEDGRAPH GRCz11/danRer11
DCD012872DT: BEDGRAPH GRCz11/danRer11
DCD012874DT: PDF GRCz11/danRer11
DCD012875DT: LOG GRCz11/danRer11
DCD012876DT: PDF GRCz11/danRer11
DCD012877DT: LOG GRCz11/danRer11
DCD012878DT: BIGWIG GRCz11/danRer11
DCD012911DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007065BS DCD000391SR tissue Liangbiao Lab, Shanghai Ocean University TU 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD002087AA DCD013678BR RNA-seq_Liangbiao_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002471SQ DCD002483TR Liangbiao Lab, Shanghai Ocean University Illumina HiSeq 2000 unstranded 09/04/2014
DCD008023DT: FASTQ
DCD008765DT: BIGWIG GRCz10/danRer10
DCD010332DT: LOG GRCz10/danRer10
DCD010333DT: TSV GRCz10/danRer10
DCD010334DT: TSV GRCz10/danRer10
DCD010335DT: BEDGRAPH GRCz10/danRer10
DCD010336DT: BEDGRAPH GRCz10/danRer10
DCD010339DT: PDF GRCz10/danRer10
DCD010340DT: BEDGRAPH GRCz10/danRer10
DCD010341DT: LOG GRCz10/danRer10
DCD010342DT: LOG GRCz10/danRer10
DCD010343DT: PDF GRCz10/danRer10
DCD010348DT: BEDGRAPH GRCz10/danRer10
DCD010352DT: BAM GRCz10/danRer10
DCD012879DT: LOG GRCz11/danRer11
DCD012880DT: TSV GRCz11/danRer11
DCD012881DT: TSV GRCz11/danRer11
DCD012882DT: BEDGRAPH GRCz11/danRer11
DCD012884DT: BIGWIG GRCz11/danRer11
DCD012885DT: PDF GRCz11/danRer11
DCD012886DT: LOG GRCz11/danRer11
DCD012887DT: PDF GRCz11/danRer11
DCD012888DT: LOG GRCz11/danRer11
DCD012889DT: BEDGRAPH GRCz11/danRer11
DCD012916DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007066BS DCD000391SR tissue Liangbiao Lab, Shanghai Ocean University TU 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD002088AA DCD013679BR RNA-seq_Liangbiao_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002472SQ DCD002484TR Liangbiao Lab, Shanghai Ocean University Illumina HiSeq 2000 unstranded 09/04/2014
DCD008024DT: FASTQ
DCD008838DT: BIGWIG GRCz10/danRer10
DCD009420DT: LOG GRCz10/danRer10
DCD009421DT: TSV GRCz10/danRer10
DCD009422DT: TSV GRCz10/danRer10
DCD009424DT: BEDGRAPH GRCz10/danRer10
DCD009425DT: BEDGRAPH GRCz10/danRer10
DCD009426DT: PDF GRCz10/danRer10
DCD009427DT: LOG GRCz10/danRer10
DCD009428DT: BEDGRAPH GRCz10/danRer10
DCD009429DT: LOG GRCz10/danRer10
DCD009430DT: PDF GRCz10/danRer10
DCD009432DT: BEDGRAPH GRCz10/danRer10
DCD009446DT: BAM GRCz10/danRer10
DCD012890DT: LOG GRCz11/danRer11
DCD012891DT: TSV GRCz11/danRer11
DCD012892DT: TSV GRCz11/danRer11
DCD012893DT: BEDGRAPH GRCz11/danRer11
DCD012894DT: BEDGRAPH GRCz11/danRer11
DCD012895DT: BIGWIG GRCz11/danRer11
DCD012896DT: PDF GRCz11/danRer11
DCD012897DT: LOG GRCz11/danRer11
DCD012898DT: PDF GRCz11/danRer11
DCD012899DT: LOG GRCz11/danRer11
DCD012933DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007067BS DCD000391SR tissue Liangbiao Lab, Shanghai Ocean University TU 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD002089AA DCD013680BR RNA-seq_Liangbiao_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002473SQ DCD002485TR Liangbiao Lab, Shanghai Ocean University Illumina HiSeq 2000 unstranded 09/04/2014
DCD008025DT: FASTQ
DCD008848DT: BIGWIG GRCz10/danRer10
DCD009299DT: LOG GRCz10/danRer10
DCD009300DT: TSV GRCz10/danRer10
DCD009301DT: TSV GRCz10/danRer10
DCD009302DT: BEDGRAPH GRCz10/danRer10
DCD009303DT: BEDGRAPH GRCz10/danRer10
DCD009306DT: BEDGRAPH GRCz10/danRer10
DCD009307DT: BEDGRAPH GRCz10/danRer10
DCD009308DT: LOG GRCz10/danRer10
DCD009309DT: PDF GRCz10/danRer10
DCD009310DT: PDF GRCz10/danRer10
DCD009311DT: LOG GRCz10/danRer10
DCD009317DT: BAM GRCz10/danRer10
DCD012901DT: LOG GRCz11/danRer11
DCD012902DT: TSV GRCz11/danRer11
DCD012903DT: TSV GRCz11/danRer11
DCD012904DT: BEDGRAPH GRCz11/danRer11
DCD012905DT: BEDGRAPH GRCz11/danRer11
DCD012906DT: BIGWIG GRCz11/danRer11
DCD012907DT: PDF GRCz11/danRer11
DCD012908DT: LOG GRCz11/danRer11
DCD012909DT: PDF GRCz11/danRer11
DCD012910DT: LOG GRCz11/danRer11
DCD012938DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007068BS DCD000391SR tissue Liangbiao Lab, Shanghai Ocean University TU 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD002090AA DCD013681BR RNA-seq_Liangbiao_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002474SQ DCD002486TR Liangbiao Lab, Shanghai Ocean University Illumina HiSeq 2000 unstranded 09/04/2014
DCD008026DT: FASTQ
DCD008732DT: BIGWIG GRCz10/danRer10
DCD010730DT: LOG GRCz10/danRer10
DCD010731DT: TSV GRCz10/danRer10
DCD010732DT: TSV GRCz10/danRer10
DCD010733DT: BEDGRAPH GRCz10/danRer10
DCD010734DT: BEDGRAPH GRCz10/danRer10
DCD010735DT: PDF GRCz10/danRer10
DCD010736DT: LOG GRCz10/danRer10
DCD010737DT: BEDGRAPH GRCz10/danRer10
DCD010738DT: PDF GRCz10/danRer10
DCD010739DT: LOG GRCz10/danRer10
DCD010741DT: BEDGRAPH GRCz10/danRer10
DCD010767DT: BAM GRCz10/danRer10
DCD012912DT: LOG GRCz11/danRer11
DCD012913DT: TSV GRCz11/danRer11
DCD012914DT: TSV GRCz11/danRer11
DCD012915DT: BEDGRAPH GRCz11/danRer11
DCD012917DT: BEDGRAPH GRCz11/danRer11
DCD012918DT: PDF GRCz11/danRer11
DCD012919DT: LOG GRCz11/danRer11
DCD012920DT: PDF GRCz11/danRer11
DCD012921DT: LOG GRCz11/danRer11
DCD012922DT: BIGWIG GRCz11/danRer11
DCD012937DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007069BS DCD000391SR tissue Liangbiao Lab, Shanghai Ocean University TU 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD002091AA DCD013682BR RNA-seq_Liangbiao_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002475SQ DCD002487TR Liangbiao Lab, Shanghai Ocean University Illumina HiSeq 2000 unstranded 09/04/2014
DCD008027DT: FASTQ
DCD008754DT: BIGWIG GRCz10/danRer10
DCD010404DT: TSV GRCz10/danRer10
DCD010405DT: LOG GRCz10/danRer10
DCD010406DT: TSV GRCz10/danRer10
DCD010408DT: BEDGRAPH GRCz10/danRer10
DCD010409DT: BEDGRAPH GRCz10/danRer10
DCD010410DT: PDF GRCz10/danRer10
DCD010411DT: LOG GRCz10/danRer10
DCD010412DT: PDF GRCz10/danRer10
DCD010413DT: LOG GRCz10/danRer10
DCD010414DT: BEDGRAPH GRCz10/danRer10
DCD010416DT: BEDGRAPH GRCz10/danRer10
DCD010444DT: BAM GRCz10/danRer10
DCD012923DT: LOG GRCz11/danRer11
DCD012924DT: TSV GRCz11/danRer11
DCD012925DT: TSV GRCz11/danRer11
DCD012926DT: BEDGRAPH GRCz11/danRer11
DCD012927DT: BEDGRAPH GRCz11/danRer11
DCD012928DT: BIGWIG GRCz11/danRer11
DCD012929DT: PDF GRCz11/danRer11
DCD012930DT: LOG GRCz11/danRer11
DCD012931DT: PDF GRCz11/danRer11
DCD012932DT: LOG GRCz11/danRer11
DCD012948DT: BAM GRCz11/danRer11