|
| Status |
Public on Apr 04, 2008 |
| Title |
bh20061215m430v2_U_12_PKBa_-_-_MEF_-_2 |
| Sample type |
RNA |
| |
|
| Source name |
mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotypes: wt PKBalpha, ko PKBalpha, ko/rescued PKBalpha
gender: female
passage: 45
gamma-IR: 10Gy
recovery after IR: 4hrs, 24hrs
|
| Biomaterial provider |
Hemmings' Laboratory, FMI
|
| Treatment protocol |
MEF were cultured for 24 hrs in standard conditions, before being gamma-irradiated with 10Gy. 4hrs or 24hrs after irradiation RNA was isolated using TRIZOL following manufacturer's instructions.
|
| Growth protocol |
MEF are grown in DMEM supplemented with 10%FCS, NEAA and L-glutamine. Cells are passaged every 3-4 days by splitting 1:5-1:10.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIZOL RNA extraction protocol, following the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
The Affymetrix labelling protocol was used to label the material as per manufacturer's instructions.
|
| |
|
| Hybridization protocol |
10ug of fragmented cRNA was hybridised to Affymetrix MOE430v2 GeneChips as per manufacturer's instructions.
|
| Scan protocol |
The chips were scanned in Affymetrix 7G scanner using an automated slide carosel.
|
| Description |
this sample is a knockout, untreated control
|
| Data processing |
Transcript expression values were estimated using the GC_RMA function provided by Refiner 3.1 (Genedata, Basel) and statistical analysis was performed using Analyst 3.1 (Genedata, Basel). Genedata's implementation of GC-RMA includes the generation of an Affymetrix detection p-value. A gene was considered to be reliably detected if it had a detection p-value ≤ 0.04 (Affymetrix default, marginal calls ignored) in at least 2/3 of the biological replicates of a condition. A power analysis of our experimental design showed we could expect to have a power of 0.8 to distinguish samples differing by 1.5-fold with a normal standard deviation less than 0.461 and it could resolve differences of 2-fold (power of 0.8) when the normalized standard deviation was less than 0.613.
|
| |
|
| Submission date |
Sep 24, 2007 |
| Last update date |
Nov 29, 2007 |
| Contact name |
Lana Bozulic |
| E-mail(s) |
lana.bozulic@fmi.ch
|
| Phone |
0041 61 697 4046
|
| Organization name |
FMI
|
| Street address |
Maulbeerstr 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE9146 |
Irradiation response in PKBalpha MEF |
|
