|
| Status |
Public on Oct 03, 2007 |
| Title |
bh20061128m430v2_A_16_pTN3-PKBa-2435 |
| Sample type |
RNA |
| |
|
| Source name |
FACS sorted DN3 thymocytes, PKBalpha-/-
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57Bl/6 backcross
Gender: Female
Age: 3 weeks
Tissue: DN3 thymocytes
Genotype: PKBalpha-/-
|
| Biomaterial provider |
FMI
|
| Treatment protocol |
The thymus was isolated and squeezed in PBS-2% FCS through a nylon membrane to extract the thymocytes. These cells were then FACS-sorted using FITC-CD25, PE-CD44, and Cy5-lineage markers to separate the DN3 thymocytes according to their surface antigens.
|
| Growth protocol |
Mice were group-housed with 12 h dark/light cycles and free access to food and water, in accordance to the Swiss Animal Protection Ordinance.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using PicoPureTM RNA isolation kit (Arcturus, Sunnyvale, CA, USA) according to manufacturer's instructions. RNA quality was controlled using the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).
|
| Label |
Biotin
|
| Label protocol |
The Affymetrix 2-cycle labelling kit was used to amplify and label the material as per manufacturer's instructions.
|
| |
|
| Hybridization protocol |
10 ug of fragmented cRNA was hybridised to Affymetrix MOE430v2 GeneChips as per manufacturer's instructions.
|
| Scan protocol |
The chips were scanned in an Affymetrix 7G scanner using an automated slide carosel.
|
| Description |
This sample is the pair of bh20061128m430v2_A_15_pTN3-PKBa-2432
|
| 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 normalized 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 |
May 22, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Brian A Hemmings |
| Organization name |
Friedrich Miescher Institute
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
CH-4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE7875 |
Deletion of PKBalpha/Akt1 affects thymic development |
|
| Relations |
| Reanalyzed by |
GSE119085 |
