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Sample GSM450300 Query DataSets for GSM450300
Status Public on Feb 24, 2011
Title EpiSC-GFP-, rep1
Sample type RNA
 
Source name EpiSC E3 grown in CM and FACS-sorted for Oct4-GFP-
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 2.902393
ILMN_1212612 1.413378
ILMN_1212619 4.823127
ILMN_1212628 1.220201
ILMN_1212632 5.675693
ILMN_1212636 11.044734
ILMN_1212637 5.969924
ILMN_1212645 4.615420
ILMN_1212648 6.577973
ILMN_1212653 3.331045
ILMN_1212672 7.633204
ILMN_1212682 1.805523
ILMN_1212683 1.297087
ILMN_1212685 1.261738
ILMN_1212692 7.476582
ILMN_1212693 3.924473
ILMN_1212695 1.356967
ILMN_1212698 1.082026
ILMN_1212702 6.626388
ILMN_1212703 3.881416

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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