Baseline expression from transcriptional profiling of zebrafish developmental stages
Survey
10.7554/eLife.30860
PRJEB12982
Establish baseline expression transcriptional signatures for zebrafish developmental stages. Total RNA was extracted from single wild type zebrafish embryos at a series of different developmental stages. RNA from 12 embryos was pooled to generate a replicate.The RNA was DNase treated. Stranded RNAseq libraries were constructed using the Illumina TruSeq Stranded RNA protocol with oligo dT pulldown.This data is part of a pre-publication release.
True
mickael.dong
May 2, 2017, 7:18 a.m.
Oct. 21, 2018, 6:40 p.m.
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006872BS | DCD000324SR | whole organism | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | HLF | 75%-epiboly | 8 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001818AA | DCD013304BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002220SQ | DCD002166TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001867AA | DCD013305BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002204SQ | DCD002225TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001811AA | DCD013306BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002172SQ | DCD002159TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001812AA | DCD013307BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002207SQ | DCD002180TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001817AA | DCD013308BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002188SQ | DCD002200TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006873BS | DCD000324SR | whole organism | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | HLF | 1-4 somites | 10.33 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001870AA | DCD013379BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002208SQ | DCD002198TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001871AA | DCD013380BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002162SQ | DCD002228TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001866AA | DCD013381BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002171SQ | DCD002220TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001868AA | DCD013382BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002244SQ | DCD002196TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001869AA | DCD013383BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002245SQ | DCD002226TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006874BS | DCD000324SR | whole organism | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | HLF | 50%-epiboly | 5.25 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001843AA | DCD013299BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002182SQ | DCD002176TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001813AA | DCD013300BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002184SQ | DCD002164TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001849AA | DCD013301BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002234SQ | DCD002175TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001844AA | DCD013302BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002183SQ | DCD002195TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001850AA | DCD013303BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002235SQ | DCD002216TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006875BS | DCD000324SR | whole organism | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | HLF | Shield | 6 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001810AA | DCD013369BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002177SQ | DCD002178TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001809AA | DCD013370BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002181SQ | DCD002148TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001816AA | DCD013371BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002222SQ | DCD002168TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001815AA | DCD013372BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002209SQ | DCD002145TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001814AA | DCD013373BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002178SQ | DCD002179TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | Hours Post Fertilization |
|---|---|---|---|---|---|---|
| DCD006876BS | DCD000324SR | whole organism | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | HLF | 1k-cell | 3 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001788AA | DCD013384BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002174SQ | DCD002191TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001789AA | DCD013385BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002219SQ | DCD002218TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001876AA | DCD013386BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002227SQ | DCD002182TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001787AA | DCD013387BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002163SQ | DCD002169TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |
| Applied Assay ID | Biosample Replicate | Assay |
|---|---|---|
| DCD001848AA | DCD013388BR | RNA-seq_Busch-Nentwich_Lab_0003AS |
| Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Paired End | Strand | Maximum Read Length | Sequencing Date |
|---|---|---|---|---|---|---|---|---|
| DCD002193SQ | DCD002158TR | Busch-Nentwich Lab, Wellcome Trust Sanger Institute | Illumina | HiSeq 2500 | ✔ | unstranded | 200 | 06/06/2016 |