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Sample GSM385589 Query DataSets for GSM385589
Status Public on Dec 31, 2010
Title EpiSox2mE1, rep2
Sample type RNA
Source name EpiSC GOF18 male overexpressing Sox2 cultured in condition ESC medium (ESC like1)
Organism Mus musculus
Characteristics gender: male
Extracted molecule total RNA
Extraction protocol 300 ng of total DNA-free RNA was used as input for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 10h).
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.
Hybridization protocol Standard Illumina hybridization protocol.
Scan protocol Standard Illumina scanning protocol.
Description replicate 2 of 2.
Data processing The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Submission date Mar 23, 2009
Last update date Dec 31, 2010
Contact name Marcos J Ara├║zo-Bravo
Organization name Max Planck Institute for Molecular Biomedicine
Department Cell and Developmental Biology
Lab Computational Biology and Bioinformatics
Street address Rontgenstr. 20
City Muenster
ZIP/Postal code 48149
Country Germany
Platform ID GPL6885
Series (1)
GSE15358 Sox2 Levels Define Pluripotent Ground States and Reprogramming Potential

Data table header descriptions
VALUE Quantile normalized

Data table
ILMN_1212607 2.393008
ILMN_1212612 2.442054
ILMN_1212619 5.545751
ILMN_1212628 2.812836
ILMN_1212632 7.253066
ILMN_1212636 12.093965
ILMN_1212637 7.720779
ILMN_1212645 4.781860
ILMN_1212648 7.970296
ILMN_1212653 3.558561
ILMN_1212672 8.189108
ILMN_1212682 2.995323
ILMN_1212683 1.912810
ILMN_1212685 2.737549
ILMN_1212692 7.221940
ILMN_1212693 4.638385
ILMN_1212695 2.276402
ILMN_1212698 2.223499
ILMN_1212702 6.580984
ILMN_1212703 4.570299

Total number of rows: 25697

Table truncated, full table size 554 Kbytes.

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

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