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 | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007062BS | DCD000391SR | tissue | Liangbiao Lab, Shanghai Ocean University | TU | 90 Days-2 Years | brain | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002084AA | DCD013675BR | RNA-seq_Liangbiao_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002468SQ | DCD002480TR | Liangbiao Lab, Shanghai Ocean University | Illumina | HiSeq 2000 | TruSeq RNA Sample Prep Kit | ✔ | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007063BS | DCD000391SR | tissue | Liangbiao Lab, Shanghai Ocean University | TU | 90 Days-2 Years | gill | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002085AA | DCD013676BR | RNA-seq_Liangbiao_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002469SQ | DCD002481TR | Liangbiao Lab, Shanghai Ocean University | Illumina | HiSeq 2000 | TruSeq RNA Sample Prep Kit | ✔ | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007064BS | DCD000391SR | tissue | Liangbiao Lab, Shanghai Ocean University | TU | 90 Days-2 Years | heart | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002086AA | DCD013677BR | RNA-seq_Liangbiao_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002470SQ | DCD002482TR | Liangbiao Lab, Shanghai Ocean University | Illumina | HiSeq 2000 | TruSeq RNA Sample Prep Kit | ✔ | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007065BS | DCD000391SR | tissue | Liangbiao Lab, Shanghai Ocean University | TU | 90 Days-2 Years | intestine | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002087AA | DCD013678BR | RNA-seq_Liangbiao_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002471SQ | DCD002483TR | Liangbiao Lab, Shanghai Ocean University | Illumina | HiSeq 2000 | TruSeq RNA Sample Prep Kit | ✔ | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007066BS | DCD000391SR | tissue | Liangbiao Lab, Shanghai Ocean University | TU | 90 Days-2 Years | kidney | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002088AA | DCD013679BR | RNA-seq_Liangbiao_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002472SQ | DCD002484TR | Liangbiao Lab, Shanghai Ocean University | Illumina | HiSeq 2000 | TruSeq RNA Sample Prep Kit | ✔ | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007067BS | DCD000391SR | tissue | Liangbiao Lab, Shanghai Ocean University | TU | 90 Days-2 Years | liver | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002089AA | DCD013680BR | RNA-seq_Liangbiao_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002473SQ | DCD002485TR | Liangbiao Lab, Shanghai Ocean University | Illumina | HiSeq 2000 | TruSeq RNA Sample Prep Kit | ✔ | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | Hours Post Fertilization |
|---|---|---|---|---|---|---|---|
| DCD007068BS | DCD000391SR | tissue | Liangbiao Lab, Shanghai Ocean University | TU | 90 Days-2 Years | muscle | adult |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD002090AA | DCD013681BR | RNA-seq_Liangbiao_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002474SQ | DCD002486TR | Liangbiao Lab, Shanghai Ocean University | Illumina | HiSeq 2000 | TruSeq RNA Sample Prep Kit | ✔ | unstranded | 09/04/2014 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Controlled By | anatomical_term | Treatment | Hours Post Fertilization | Mutation Description |
|---|---|---|---|---|---|---|---|---|---|---|
| DCD007069BS | DCD000391SR | tissue | Liangbiao Lab, Shanghai Ocean University | TU | 90 Days-2 Years | spleen | — | adult | — |
| Applied Assay ID | Biosample Replicate | Assay | Controlled By |
|---|---|---|---|
| DCD002091AA | DCD013682BR | RNA-seq_Liangbiao_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|---|
| DCD002475SQ | DCD002487TR | Liangbiao Lab, Shanghai Ocean University | Illumina | HiSeq 2000 | TruSeq RNA Sample Prep Kit | ✔ | unstranded | — | 09/04/2014 |