|
| Status |
Public on Oct 31, 2011 |
| Title |
RNA_UNR IP3_dye swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
UNR_IP with Cytoplasmic extracts from male adult flies
|
| Organism |
Drosophila melanogaster |
| Characteristics |
gender: Male
|
| Extracted molecule |
cytoplasmic RNA |
| Extraction protocol |
Cytoplasmic extracts were prepared from adult flies as described in Wilhelm et al.(2000) J. Cell. Biol. 148:427-440, and used to immunoprecipitate UNR as described in Abaza et al. (2006) Genes Dev 20: 380-389. RNA was isolated from the immunoprecipitate using TRizol.
|
| Label |
Cy5
|
| Label protocol |
Probes were generated using the pico version of the ExpressArt mRNA Amplification Kit (Artus) following the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
UNR_IP with Cytoplasmic extracts from female adult flies
|
| Organism |
Drosophila melanogaster |
| Characteristics |
gender: Female
|
| Extracted molecule |
cytoplasmic RNA |
| Extraction protocol |
Cytoplasmic extracts were prepared from adult flies as described in Wilhelm et al.(2000) J. Cell. Biol. 148:427-440, and used to immunoprecipitate UNR as described in Abaza et al. (2006) Genes Dev 20: 380-389. RNA was isolated from the immunoprecipitate using TRizol.
|
| Label |
Cy3
|
| Label protocol |
Probes were generated using the pico version of the ExpressArt mRNA Amplification Kit (Artus) following the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
Microarrays were hybridized at the CRG Genomics Facility following the Corning protocol for UltraGaps slides.
|
| Scan protocol |
Microarrays were scanned using the Agilent scanner and the images were processed with GenePix image analysis software v6.0.
|
| Description |
214
Biological replicate 2 of 3. Dye swap. Cytoplasmic RNA associated with the RNA binding protein UNR in Female vs. in Male
|
| Data processing |
GPR files were analyzed with Limma package from BioConductor (Gentleman et al., 2004; Genome Biol 5, R80; Smyth, 2004; Statistical Applications in Genetics and Molecular Biology 3, Article 3) using the same criteria. Data was background corrected with the normexp method and normalized with OLIN (Futschik and Crompton, 2005; Bioinformatics 21, 1724-1726). Spots not fulfilling the quality thresholds (based on spot size, foreground versus background signals, saturation, coincidence between differently calculated ratio measures and R2 of regression ratio) were eliminated from further analysis
|
| |
|
| Submission date |
Jul 26, 2011 |
| Last update date |
Oct 31, 2011 |
| Contact name |
Francesco Mattia Mancuso |
| E-mail(s) |
francesco.mancuso@crg.eu
|
| Organization name |
CRG (Centre for Genomic Regulation)
|
| Street address |
C/ Dr. Aiguader, 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL3797 |
| Series (1) |
| GSE30963 |
Widespread Generation of Alternative UTRs Contributes to Sex-specific RNA Binding by UNR |
|
