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Status |
Public on Apr 04, 2008 |
Title |
bh20061215m430v2_U_27_PKBa_-_-_R_MEF_24h_2 |
Sample type |
RNA |
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Source name |
MEF
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Organism |
Mus musculus |
Characteristics |
genotypes: wt PKBalpha, ko PKBalpha, ko/rescued PKBalpha gender: female passage: 45 gamma-IR: 10Gy recovery after IR: 4hrs, 24hrs
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Biomaterial provider |
Hemmings' Laboratory, FMI
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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.
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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.
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Extracted molecule |
total RNA |
Extraction protocol |
TRIZOL RNA extraction protocol, following the manufacturer's instructions.
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Label |
Biotin
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Label protocol |
The Affymetrix labelling protocol was used to label the material as per manufacturer's instructions.
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Hybridization protocol |
10ug of fragmented cRNA was hybridised to Affymetrix MOE430v2 GeneChips as per manufacturer's instructions.
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Scan protocol |
The chips were scanned in Affymetrix 7G scanner using an automated slide carosel.
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Description |
this sample is a knockout/reconstituted PKB alpha, treated, 24hrs
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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.
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Submission date |
Sep 24, 2007 |
Last update date |
Nov 29, 2007 |
Contact name |
Lana Bozulic |
E-mail(s) |
lana.bozulic@fmi.ch
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Phone |
0041 61 697 4046
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Organization name |
FMI
|
Street address |
Maulbeerstr 66
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City |
Basel |
ZIP/Postal code |
4058 |
Country |
Switzerland |
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Platform ID |
GPL1261 |
Series (1) |
GSE9146 |
Irradiation response in PKBalpha MEF |
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