|
| Status |
Public on Aug 19, 2015 |
| Title |
aub-_2-4h_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
2-4h aubHN2/aubQC42 embryos
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: embryos 2-4h
allele: aubHN2/aubQC42
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared with Trizol (Invitrogen) from 0-2 h and 2-4 h-embryos from wild-type, aubHN2/aubQC42 or spn-Ehls-03987/spn-E1 females crossed with wild-type males.
|
| Label |
Cy5
|
| Label protocol |
Experimental samples were labelled with Cy5 and the common reference sample (made by pooling equimolar amounts of RNA from all 18 experimental samples) was labelled with Cy3.
|
| |
|
| Channel 2 |
| Source name |
equimolar mix of all 18 samples
|
| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: pooled all stages
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared with Trizol (Invitrogen) from 0-2 h and 2-4 h-embryos from wild-type, aubHN2/aubQC42 or spn-Ehls-03987/spn-E1 females crossed with wild-type males.
|
| Label |
Cy3
|
| Label protocol |
Experimental samples were labelled with Cy5 and the common reference sample (made by pooling equimolar amounts of RNA from all 18 experimental samples) was labelled with Cy3.
|
| |
|
| |
| Hybridization protocol |
Samples were hybridized to Nimblegen Drosophila melanogaster 12 x 135 K microarrays
|
| Scan protocol |
Microarrays were scanned in Cy3 and Cy5 channels at 1 µm resolution using Innoscan900 scanner (Innopsys) and variable photomultiplier tube (PMT) settings to obtain maximal signal intensities. Nimblescan v2.5 software (Roche Nimblegen) was used for feature extraction
|
| Data processing |
The data were normalized using the VSN (Variance Stabilizing Normalization) method. Differentially expressed probes were identified using LIMMA and FDR (False Discovery Rate) set to 0.1%.
|
| |
|
| Submission date |
Jul 10, 2015 |
| Last update date |
Aug 19, 2015 |
| Contact name |
Simonelig Martine |
| E-mail(s) |
martine.simonelig@igh.cnrs.fr
|
| Organization name |
Institut de Genetique Humaine - CNRS
|
| Department |
Genetics and Development
|
| Lab |
mRNA Regulation and Development
|
| Street address |
141, rue de la Cardonille
|
| City |
MONTPELLIER |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL20683 |
| Series (2) |
| GSE70775 |
Transcriptomic analysis of wild-type, spn-E and aub mutant 0-2h- and 2-4h-embryos |
| GSE70778 |
Aubergine iCLIP and expression |
|
