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Sample GSM385588 Query DataSets for GSM385588
Status Public on Dec 31, 2010
Title EpiSox2mE1, rep1
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 1 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 2.098204
ILMN_1212612 2.942440
ILMN_1212619 5.365537
ILMN_1212628 2.233777
ILMN_1212632 6.714653
ILMN_1212636 12.245101
ILMN_1212637 7.829484
ILMN_1212645 4.813879
ILMN_1212648 8.141290
ILMN_1212653 3.244184
ILMN_1212672 8.313176
ILMN_1212682 2.373291
ILMN_1212683 3.288956
ILMN_1212685 3.379710
ILMN_1212692 6.973847
ILMN_1212693 5.161110
ILMN_1212695 3.119607
ILMN_1212698 2.260100
ILMN_1212702 6.923426
ILMN_1212703 4.132626

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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