|
| Status |
Public on Aug 21, 2008 |
| Title |
cDeaf |
| Sample type |
RNA |
| |
|
| Source name |
cDeaf
|
| Organism |
Mus musculus |
| Characteristics |
C1 clone infected with Deaf-1-expressing retrovirus.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested from two independent clones (C1 and E1) infected with either control or Deaf-1-expressing retrovirus. RNA was purified using using the QIAGEN RNeasy Kit (Qiagen, Hilden, Germany)
and quality assessed by spectrophotometry and gel electrophoresis before
hybridisation to Affymetrix slides.
|
| Label |
biotin
|
| Label protocol |
Affymetrix IVT Labeling Kit
|
| |
|
| Hybridization protocol |
Affymetrix
|
| Scan protocol |
Affymetrix scanner 3000 7G
|
| Description |
Arrays were processed at the Australian Genome Research Facility (AGRF).
|
| Data processing |
Statistical analysis was undertaken using R (www.r-project.org) and Bioconductor
(www.bioconductor.org) software. The expression values were checked for quality and consistency using statistical quality assessment and were normalized using the RMA algorithm. Control probes and a small number (147) of probe-sets showing no variability between arrays were filtered out before subsequent analysis. For the differential expression analysis, the Deaf-1 and control samples for each clone were treated as paired observations, to reflect the biological variation between clones. Statistical significance was assessed using empirical Bayes moderated paired t-tests as implemented in the limma package within the Bioconductor software.
|
| |
|
| Submission date |
Aug 06, 2008 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Jane Visvader |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Victorian Breast Cancer Research Consortium
|
| Lab |
Lindeman/Visvader Lab
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3050 |
| Country |
Australia |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE12367 |
Deaf-1 regulated genes in the mouse mammary gland |
|
| Relations |
| Reanalyzed by |
GSE119085 |
