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Sample GSM537495 Query DataSets for GSM537495
Status Public on Dec 08, 2010
Title MEF, rep1
Sample type RNA
Source name MEF
Organism Mus musculus
Characteristics cell type: mouse embryonic fibroblast (MEF)
potency: unipotent
gender: female
Extracted molecule total RNA
Extraction protocol RNA samples to be analyzed on microarrays were prepared using Qiagen RNeasy columns with on-column DNA digestion.
Label biotin
Label protocol 500 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).
Hybridization protocol Standard Illumina hybridization protocol. Purified and labelled cRNA was hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina) according to the manufacturer's instructions. After washing, as recommended, chips were stained with streptavidin-Cy3 (GE Healthcare).
Scan protocol Standard Illumina scanning protocol. Chips were scanned using the iScan reader (Illumina) and accompanying software.
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 log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
Submission date Apr 26, 2010
Last update date Dec 08, 2010
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)
GSE21516 Direct Reprogramming of Fibroblasts into Epiblast Stem Cells

Data table header descriptions
VALUE Quantile-normalized intensity

Data table
ILMN_1212607 2.402667
ILMN_1212612 3.198277
ILMN_1212619 6.44456
ILMN_1212628 2.350907
ILMN_1212632 3.624804
ILMN_1212636 11.011636
ILMN_1212637 9.669339
ILMN_1212645 2.561238
ILMN_1212648 7.057106
ILMN_1212653 6.669054
ILMN_1212672 7.464552
ILMN_1212682 3.623339
ILMN_1212683 1.725512
ILMN_1212685 1.588659
ILMN_1212692 3.407963
ILMN_1212693 5.748875
ILMN_1212695 2.142783
ILMN_1212698 1.830651
ILMN_1212702 1.714469
ILMN_1212703 4.538342

Total number of rows: 25697

Table truncated, full table size 550 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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