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Sample GSM435174 Query DataSets for GSM435174
Status Public on Aug 17, 2010
Title Polysomal RNA purified from MEFs derived from a WT mouse rep 1
Sample type other
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 other
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 10.19750213
ILMN_2721178 8.87197337
ILMN_3033922 9.67745018
ILMN_3092673 11.12111325
ILMN_2816356 7.80944520
ILMN_2808939 9.27215476
ILMN_2634564 10.89552308
ILMN_2737647 7.71810738
ILMN_2734484 8.45303374
ILMN_2952292 8.52243978
ILMN_2699078 7.66244224
ILMN_1213681 8.28042013
ILMN_2735413 7.64435688
ILMN_2735415 7.65918396
ILMN_2891688 8.02808341
ILMN_2637698 10.28296387
ILMN_2674228 8.61485453
ILMN_2601546 7.70594177
ILMN_1230831 7.72284889
ILMN_2848071 7.82445751

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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