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Sample GSM385590 Query DataSets for GSM385590
Status Public on Dec 31, 2010
Title EpiSox2mE2, rep1
Sample type RNA
 
Source name EpiSC GOF18 male overexpressing Sox2 cultured in condition ESC medium (ESC like2)
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
E-mail(s) mararabra@yahoo.co.uk
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
ID_REF
VALUE Quantile normalized

Data table
ID_REF VALUE
ILMN_1212607 2.442494
ILMN_1212612 2.311693
ILMN_1212619 5.577139
ILMN_1212628 3.864695
ILMN_1212632 7.242626
ILMN_1212636 12.335602
ILMN_1212637 8.035917
ILMN_1212645 5.201103
ILMN_1212648 8.136105
ILMN_1212653 3.381540
ILMN_1212672 8.558614
ILMN_1212682 4.075461
ILMN_1212683 1.939208
ILMN_1212685 4.133570
ILMN_1212692 7.298366
ILMN_1212693 4.416699
ILMN_1212695 2.729970
ILMN_1212698 1.833856
ILMN_1212702 5.444547
ILMN_1212703 4.903153

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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