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| Status |
Public on Apr 01, 2010 |
| Title |
Technical variation between RNA isolations from individual embryos |
| Organism |
Danio rerio |
| Experiment type |
Expression profiling by array
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| Summary |
Transcriptome analysis during embryogenesis usually requires pooling of embryos to obtain sufficient RNA. Hence, the measured levels of gene-expression represent the average mRNA levels of pooled samples and the biological variation among individuals is lost for inclusion into statistical models used to analyze transcriptome data. This can irreversibly reduce the robustness, resolution and expressiveness of the experiment. Therefore, we developed a robust method to isolate abundant high-quality RNA from individual embryos to perform single embryo transcriptome analyses using the zebrafish as a model.
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| Overall design |
Zebrafish embryos were selected from the germ ring stage. RNA from 4 individual embryos and RNA from 4 pooled embryos and afterwards splitted material was isolated. These 8 samples were hybridized against a common reference made from a pool of 20 embryos.
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| Contributor(s) |
de Jong M, Rauwerda H, Bruning O, Verkooijen J, Spaink HP, Breit T |
| Citation(s) |
20233395 |
| |
| Submission date |
Aug 20, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
Mark de Jong |
| Organization name |
University of Amsterdam
|
| Street address |
Kruislaan 318
|
| City |
Amsterdam |
| ZIP/Postal code |
1098 SM |
| Country |
Netherlands |
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| Platforms (1) |
| GPL9060 |
Danio rerio dedicated 15k array |
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| Samples (8)
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| GSM442737 |
Semi-single embryo 1 vs Common reference 20 embryos |
| GSM442739 |
Single embryo 2 vs Common reference 20 embryos |
| GSM442740 |
Semi-single embryo 3 vs Common reference 20 embryos |
| GSM442741 |
Single embryo 4 vs Common reference 20 embryos |
| GSM442742 |
Single embryo 1 vs Common reference 20 embryos |
| GSM442743 |
Semi-single embryo 2 vs Common reference 20 embryos |
| GSM442744 |
Single embryo 3 vs Common reference 20 embryos |
| GSM442745 |
Semi-single embryo 4 vs Common reference 20 embryos |
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| Relations |
| BioProject |
PRJNA118365 |
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