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Sample GSM537501 Query DataSets for GSM537501
Status Public on Dec 08, 2010
Title EpiSC GOF18, rep1
Sample type RNA
Source name EpiSC-GOF18
Organism Mus musculus
Characteristics cell type: epiblast stem cell (EpiSC)
potency: pluripotent
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 2.952479
ILMN_1212612 1.514188
ILMN_1212619 4.950043
ILMN_1212628 1.503541
ILMN_1212632 6.005085
ILMN_1212636 11.704244
ILMN_1212637 7.547557
ILMN_1212645 5.69316
ILMN_1212648 7.330985
ILMN_1212653 3.832662
ILMN_1212672 7.965351
ILMN_1212682 2.656381
ILMN_1212683 2.14764
ILMN_1212685 2.041932
ILMN_1212692 6.705139
ILMN_1212693 4.411128
ILMN_1212695 3.058408
ILMN_1212698 1.811578
ILMN_1212702 5.747169
ILMN_1212703 4.125569

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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