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Sample GSM450298 Query DataSets for GSM450298
Status Public on Feb 24, 2011
Title Epi-Sox2, rep1
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 1 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
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)
GSE17984 Epiblast stem cell subpopulations represent mouse embryos of distinct pregastrulation stages

Data table header descriptions
ID_REF
VALUE Quantile-normalized intensity

Data table
ID_REF VALUE
ILMN_1212607 2.373085
ILMN_1212612 1.346942
ILMN_1212619 4.373521
ILMN_1212628 1.263623
ILMN_1212632 4.631640
ILMN_1212636 11.170099
ILMN_1212637 7.109792
ILMN_1212645 4.700943
ILMN_1212648 6.793620
ILMN_1212653 2.795808
ILMN_1212672 7.173771
ILMN_1212682 2.045729
ILMN_1212683 2.089581
ILMN_1212685 2.044029
ILMN_1212692 7.465818
ILMN_1212693 4.398271
ILMN_1212695 1.809783
ILMN_1212698 1.441848
ILMN_1212702 5.845508
ILMN_1212703 3.813212

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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