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Sample GSM450304 Query DataSets for GSM450304
Status Public on Feb 24, 2011
Title T9-EpiSC, rep1
Sample type RNA
Source name EpiSC T9 grown on medium-density CF1 MEFs in UM, 2d -Fgf2, harv. w/o MEFs
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 1.
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 1.657451
ILMN_1212612 2.366682
ILMN_1212619 3.023885
ILMN_1212628 1.289168
ILMN_1212632 4.865092
ILMN_1212636 11.422926
ILMN_1212637 8.052487
ILMN_1212645 2.114687
ILMN_1212648 6.237416
ILMN_1212653 3.423362
ILMN_1212672 6.637947
ILMN_1212682 2.574274
ILMN_1212683 0.998106
ILMN_1212685 1.500813
ILMN_1212692 4.439204
ILMN_1212693 4.178794
ILMN_1212695 1.457601
ILMN_1212698 2.287724
ILMN_1212702 2.806891
ILMN_1212703 2.752185

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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