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Sample GSM435176 Query DataSets for GSM435176
Status Public on Aug 17, 2010
Title Polysomal RNA purified from MEFs derived from a WT mouse rep 2
Sample type other
Source name A5_rep2
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 10.49705940
ILMN_2721178 8.94740298
ILMN_3033922 9.64561049
ILMN_3092673 10.97943006
ILMN_2816356 7.95716771
ILMN_2808939 9.22164493
ILMN_2634564 11.00870068
ILMN_2737647 7.68011143
ILMN_2734484 8.31171546
ILMN_2952292 8.37257307
ILMN_2699078 7.67563196
ILMN_1213681 8.32393533
ILMN_2735413 7.62678775
ILMN_2735415 7.65509142
ILMN_2891688 8.23553630
ILMN_2637698 10.33072297
ILMN_2674228 8.84114819
ILMN_2601546 7.70576411
ILMN_1230831 7.69175249
ILMN_2848071 7.81494730

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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