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Sample GSM537496 Query DataSets for GSM537496
Status Public on Dec 08, 2010
Title MEF, rep2
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 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 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
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)
GSE21516 Direct Reprogramming of Fibroblasts into Epiblast Stem Cells

Data table header descriptions
ID_REF
VALUE Quantile-normalized intensity

Data table
ID_REF VALUE
ILMN_1212607 3.088526
ILMN_1212612 2.378126
ILMN_1212619 5.884182
ILMN_1212628 1.503541
ILMN_1212632 3.893015
ILMN_1212636 11.068102
ILMN_1212637 9.443079
ILMN_1212645 1.99795
ILMN_1212648 7.015956
ILMN_1212653 6.679866
ILMN_1212672 6.927036
ILMN_1212682 2.353058
ILMN_1212683 2.131734
ILMN_1212685 2.371995
ILMN_1212692 4.04758
ILMN_1212693 6.226091
ILMN_1212695 1.507689
ILMN_1212698 2.064577
ILMN_1212702 1.921233
ILMN_1212703 4.943324

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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