|
Status |
Public on Aug 19, 2015 |
Title |
aub-_0-2h_rep4 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
0-2h aubHN2/aubQC42 embryos
|
Organism |
Drosophila melanogaster |
Characteristics |
developmental stage: embryos 0-2h 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 |
|