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Sample GSM450301 Query DataSets for GSM450301
Status Public on Feb 24, 2011
Title EpiSC-GFP-, rep2
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 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
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 1.414692
ILMN_1212612 1.854818
ILMN_1212619 3.454306
ILMN_1212628 2.338553
ILMN_1212632 5.224564
ILMN_1212636 11.025012
ILMN_1212637 6.036216
ILMN_1212645 5.225461
ILMN_1212648 6.845003
ILMN_1212653 2.031977
ILMN_1212672 7.095373
ILMN_1212682 2.278066
ILMN_1212683 2.724525
ILMN_1212685 2.889669
ILMN_1212692 7.629423
ILMN_1212693 4.345842
ILMN_1212695 2.008803
ILMN_1212698 2.260923
ILMN_1212702 6.324167
ILMN_1212703 3.474797

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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