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Sample GSM450296 Query DataSets for GSM450296
Status Public on Feb 24, 2011
Title EpiSC, rep1
Sample type RNA
Source name EpiSC GOF18 male
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
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 2.421125
ILMN_1212612 1.192865
ILMN_1212619 4.275046
ILMN_1212628 1.182348
ILMN_1212632 5.397326
ILMN_1212636 11.359144
ILMN_1212637 7.023803
ILMN_1212645 5.068468
ILMN_1212648 6.796601
ILMN_1212653 3.153690
ILMN_1212672 7.468779
ILMN_1212682 2.182810
ILMN_1212683 1.765963
ILMN_1212685 1.675626
ILMN_1212692 6.135342
ILMN_1212693 3.707775
ILMN_1212695 2.506564
ILMN_1212698 1.471428
ILMN_1212702 5.127568
ILMN_1212703 3.425563

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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