RNA-seq data from 4 early developmental stages
Survey
10.1186/1471-213X-11-30
PRJEB2512
In this study we use RNA-Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% - 73% reads were successfully mapped to the zebrafish genome and 36% - 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1-cell stage. The largest number of common transcripts was observed between 1-cell stage and 16-cell stage. An enrichment of gene transcripts with molecular functions of DNA binding, protein folding and processing as well as metal ion binding was observed with progression of development.
True
mickael.dong
June 1, 2017, 4:06 a.m.
Aug. 14, 2018, 7:52 a.m.
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006937BS | DCD000336SR | whole organism | Kere Lab, Karolinska Institute | WT | 50%-epiboly | 5.25 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001924AA | DCD013449BR | small-RNA-seq_Kere_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Strand | Sequencing Date |
|---|---|---|---|---|---|---|
| DCD002275SQ | DCD002282TR | Kere Lab, Karolinska Institute | SOLiD | AB SOLiD System | unstranded | 06/09/2011 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Controlled By | anatomical_term | Treatment | Hours Post Fertilization | Mutation Description |
|---|---|---|---|---|---|---|---|---|---|---|
| DCD006938BS | DCD000336SR | whole organism | Kere Lab, Karolinska Institute | WT | 512-cell | — | — | 2.75 | — |
| Applied Assay ID | Biosample Replicate | Assay | Controlled By |
|---|---|---|---|
| DCD001923AA | DCD013450BR | small-RNA-seq_Kere_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|---|
| DCD002274SQ | DCD002281TR | Kere Lab, Karolinska Institute | SOLiD | AB SOLiD System | — | ✘ | unstranded | — | 06/09/2011 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006939BS | DCD000336SR | whole organism | Kere Lab, Karolinska Institute | WT | 16-cell | 1.5 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001922AA | DCD013451BR | small-RNA-seq_Kere_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Strand | Sequencing Date |
|---|---|---|---|---|---|---|
| DCD002273SQ | DCD002280TR | Kere Lab, Karolinska Institute | SOLiD | AB SOLiD System | unstranded | 06/09/2011 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006940BS | DCD000336SR | whole organism | Kere Lab, Karolinska Institute | WT | 1-cell | 0.75 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001921AA | DCD013452BR | small-RNA-seq_Kere_Lab_0001AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Strand | Sequencing Date |
|---|---|---|---|---|---|---|
| DCD002272SQ | DCD002279TR | Kere Lab, Karolinska Institute | SOLiD | AB SOLiD System | unstranded | 06/09/2011 |