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Sample GSM435173 Query DataSets for GSM435173
Status Public on Aug 17, 2010
Title Total RNA purified from MEFs derived from a WT mouse rep 1
Sample type RNA
Source name A5_rep1
Organism Mus musculus
Characteristics genotype: WT
Growth protocol MEFs were isolated from 14.5d pregnant females as previously described (Le Bacquer et al. 2007 The Journal of Clinical Investigation). WT and KI MEFs (5 x106) immortalized by passage were grown in DMEM supplemented with 10% FBS.
Extracted molecule total RNA
Extraction protocol Polysomal and total cytoplasmic RNA was isolated as described (Larsson et al. 2007, Cancer Research). Fractions containing mRNAs bound to >3 ribosomes were pooled and designated heavy polysomal RNA. RNA isolation procedure was performed in two independent experiments from one pair of KI and WT MEFs.
Label biotin
Label protocol 250ng RNA (polysomal or total) was labelled using the single round Illumina protocol
Hybridization protocol Standard hybridization optimized by Illumina
Scan protocol Standard scan protocoll optimized by Illumina
Description none
Data processing Data was transformed using Variance Stabilizing Transformation (VST) and normalized using Robust Spline Normalization (RSN) in the statistical environment R using the lumi package.
Submission date Jul 31, 2009
Last update date Aug 17, 2010
Contact name Ola Larsson
Phone +46 (0)8 517 73280
Organization name Karolinska Institutet
Department Department of oncology-pathology
Street address CCK, R8:01
City Stockholm
ZIP/Postal code 171 76
Country Sweden
Platform ID GPL6885
Series (1)
GSE17451 eIF4E phosphorylation promotes tumorigenesis and is associated with prostate cancer progression

Data table header descriptions
VALUE Normalized transformed log2 expression level

Data table
ILMN_2896528 12.25873986
ILMN_2721178 10.57480138
ILMN_3033922 10.26768738
ILMN_3092673 11.65027294
ILMN_2816356 7.65862723
ILMN_2808939 10.24579402
ILMN_2634564 11.10233769
ILMN_2737647 7.70091096
ILMN_2734484 8.54429470
ILMN_2952292 8.75619705
ILMN_2699078 7.64170270
ILMN_1213681 9.00929305
ILMN_2735413 7.64653946
ILMN_2735415 7.65061313
ILMN_2891688 9.74924951
ILMN_2637698 8.66688832
ILMN_2674228 10.49875330
ILMN_2601546 7.69395811
ILMN_1230831 7.69206469
ILMN_2848071 7.96350973

Total number of rows: 25697

Table truncated, full table size 604 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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