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Sample GSM385578 Query DataSets for GSM385578
Status Public on Dec 31, 2010
Title Epi-Sox2f, rep1
Sample type RNA
 
Source name EpiSC OG2 female overexpressing Sox2
Organism Mus musculus
Characteristics gender: female
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 3.943367
ILMN_1212612 2.350758
ILMN_1212619 4.816564
ILMN_1212628 2.974865
ILMN_1212632 4.687044
ILMN_1212636 11.521866
ILMN_1212637 8.766959
ILMN_1212645 5.910975
ILMN_1212648 7.482253
ILMN_1212653 2.486877
ILMN_1212672 8.645005
ILMN_1212682 4.267336
ILMN_1212683 2.156940
ILMN_1212685 2.018935
ILMN_1212692 5.672772
ILMN_1212693 4.123592
ILMN_1212695 1.951961
ILMN_1212698 2.494345
ILMN_1212702 4.253840
ILMN_1212703 6.084072

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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