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Sample GSM231178 Query DataSets for GSM231178
Status Public on Apr 04, 2008
Title bh20061215m430v2_U_17_PKBa_-_-_MEF_24h_1
Sample type RNA
 
Source name MEF
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, treated, 24hrs
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

Data table header descriptions
ID_REF
VALUE VALUE
ABS_CALL ABS_CALL
DETECTION P-VALUE P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 366.887 P 0.000581214
AFFX-BioB-M_at 517.574 P 4.42873e-05
AFFX-BioB-3_at 415.018 P 4.42873e-05
AFFX-BioC-5_at 1196.28 P 4.42873e-05
AFFX-BioC-3_at 1113.47 P 4.42873e-05
AFFX-BioDn-5_at 2546.56 P 4.42873e-05
AFFX-BioDn-3_at 4068.19 P 5.16732e-05
AFFX-CreX-5_at 10509.3 P 4.42873e-05
AFFX-CreX-3_at 13661.1 P 4.42873e-05
AFFX-DapX-5_at 14.4462 A 0.313693
AFFX-DapX-M_at 3.81589 A 0.876448
AFFX-DapX-3_at 2.70606 A 0.984832
AFFX-LysX-5_at 9.26166 A 0.724889
AFFX-LysX-M_at 5.54825 A 0.686292
AFFX-LysX-3_at 3.01423 A 0.672921
AFFX-PheX-5_at 0.533157 A 0.953518
AFFX-PheX-M_at 2.4073 A 0.904352
AFFX-PheX-3_at 14.2112 A 0.300591
AFFX-ThrX-5_at 4.25576 A 0.953533
AFFX-ThrX-M_at 2.27503 A 0.963443

Total number of rows: 45101

Table truncated, full table size 1386 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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