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Sample GSM702229 Query DataSets for GSM702229
Status Public on Apr 02, 2012
Title MEFS WT at Basal,biological rep2
Sample type RNA
 
Source name MEFS WT at Basal
Organism Mus musculus
Characteristics cell type: Primary murine embryonic fibroblasts (MEFs)
strain: C57Bl/6
genotype: Wild type
age: 13.5-day-old embryos
Treatment protocol Early passage (p.2) MEFs were washed twice with PBS1X solution, and then incubated in DMEM media containing 400 μM of H2O2 or 0.25μg/ml of Doxorubicin (SIGMA) at 37°C for four hours.
Growth protocol Primary murine embryonic fibroblasts (MEFs) were isolated from 13.5-day-old embryos according to standard procedures from WT, p53KO and p66ShcKO mice. MEFs were cultured in DMEM supplemented with 10% fetal bovine calf serum, 100µg/ml streptomycin, 100 µg/ml penicillin FBS, L-glutamine (2 mM) and incubated at 37°C in a humidified atmosphere containing 5% CO2 and normal oxygen tension (20%). For all the experiments MEFs at early passages (p.2) were used. Treatment: Early passage (p.2-5) MEFs were washed twice with PBS1X solution, and then incubated in DMEM media containing 400 μM of H2O2 or 0.25μg/ml of Doxorubicin (SIGMA) at 37°C for four hours.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cDNA were prepared according to the standard Affymetrix 3' IVTprotocol from 100 ng total RNA.
 
Hybridization protocol Following fragmentation,6 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MOE430PM strip array. GeneChip strip was washed and stained in the Affymetrix GeneAtlas instrument .
Scan protocol GeneChip strip images were acquired using the GeneAtlas Imaging Station.
Description Gene expression data from MEFs passage 2
GeneChip MOE430PM strip arrays on Affymetrix GeneAtlas instrument
Data processing The data were analyzed with Partek Genomics Suite v 6.5 using RMA algorithm.
 
Submission date Apr 06, 2011
Last update date Apr 02, 2012
Contact name Simone Paolo Minardi
E-mail(s) simone.minardi@ifom-ieo-campus.it
Phone +39 02 574303703
Organization name Cogentech
Department Microarray and NGS Unit
Street address Via Adamello
City Milano
State/province Italy
ZIP/Postal code 20139
Country Italy
 
Platform ID GPL11180
Series (2)
GSE28416 Expression data from mouse embryo fibroblast (MEFS)
GSE28418 Expression data from mouse tissues and MEFs: insights into the physiological activation of p53-p66Shc pathway

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
1415670_PM_at 9.92556
1415671_PM_at 9.72892
1415672_PM_at 10.4748
1415673_PM_at 9.15185
1415674_PM_a_at 9.2191
1415675_PM_at 8.11972
1415676_PM_a_at 10.413
1415677_PM_at 8.18941
1415678_PM_at 9.19314
1415679_PM_at 9.98016
1415680_PM_at 8.77255
1415681_PM_at 8.82834
1415682_PM_at 7.06416
1415683_PM_at 10.1688
1415684_PM_at 7.35376
1415685_PM_at 6.99294
1415686_PM_at 8.45061
1415687_PM_a_at 9.89217
1415688_PM_at 9.2014
1415689_PM_s_at 7.89351

Total number of rows: 45141

Table truncated, full table size 983 Kbytes.




Supplementary file Size Download File type/resource
GSM702229.cel.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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