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Sample GSM385574 Query DataSets for GSM385574
Status Public on Dec 31, 2010
Title F9-Sox2, rep1
Sample type RNA
 
Source name F9 embryonic carcinoma cell overexpressing Sox2
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 3.759614
ILMN_1212612 2.470713
ILMN_1212619 4.582812
ILMN_1212628 3.421580
ILMN_1212632 5.468545
ILMN_1212636 11.955612
ILMN_1212637 9.167531
ILMN_1212645 2.673042
ILMN_1212648 6.059979
ILMN_1212653 2.433046
ILMN_1212672 8.876213
ILMN_1212682 2.595599
ILMN_1212683 2.473192
ILMN_1212685 2.891513
ILMN_1212692 6.879953
ILMN_1212693 3.614580
ILMN_1212695 2.635717
ILMN_1212698 1.899632
ILMN_1212702 1.621873
ILMN_1212703 4.542922

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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