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Sample GSM450302 Query DataSets for GSM450302
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 2.023511
ILMN_1212612 1.466215
ILMN_1212619 3.525192
ILMN_1212628 2.282892
ILMN_1212632 4.637917
ILMN_1212636 11.322328
ILMN_1212637 6.591794
ILMN_1212645 2.974485
ILMN_1212648 6.367479
ILMN_1212653 2.330506
ILMN_1212672 6.458391
ILMN_1212682 1.730607
ILMN_1212683 2.267853
ILMN_1212685 1.199675
ILMN_1212692 7.920463
ILMN_1212693 4.501759
ILMN_1212695 1.503908
ILMN_1212698 1.559069
ILMN_1212702 4.066263
ILMN_1212703 2.009308

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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