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Sample GSM450299 Query DataSets for GSM450299
Status Public on Feb 24, 2011
Title Epi-Sox2, rep2
Sample type RNA
Source name EpiSC GOF18 male (overexpressing Sox2) cultured in condition EpiSC medium (CM)
Organism Mus musculus
Characteristics gender: male
cell type: epiblast stem cells
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: 12h).
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 Biological replicate 2 of 2.
Data processing The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was performed 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.

Non-normalized data is available in the 'GSE17984_non-normalized_data.txt' file, which is linked to the Series GSE17984 record as a supplementary file.
Submission date Sep 04, 2009
Last update date Feb 24, 2011
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)
GSE17984 Epiblast stem cell subpopulations represent mouse embryos of distinct pregastrulation stages

Data table header descriptions
VALUE Quantile-normalized intensity

Data table
ILMN_1212607 1.618243
ILMN_1212612 2.043499
ILMN_1212619 4.547735
ILMN_1212628 1.604685
ILMN_1212632 3.563835
ILMN_1212636 11.004460
ILMN_1212637 7.002897
ILMN_1212645 5.036472
ILMN_1212648 6.827655
ILMN_1212653 2.360000
ILMN_1212672 6.951816
ILMN_1212682 1.476438
ILMN_1212683 0.919065
ILMN_1212685 1.881918
ILMN_1212692 7.119296
ILMN_1212693 4.221241
ILMN_1212695 1.831507
ILMN_1212698 2.103021
ILMN_1212702 5.735341
ILMN_1212703 3.238291

Total number of rows: 25697

Table truncated, full table size 553 Kbytes.

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

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