GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM537517 Query DataSets for GSM537517
Status Public on Dec 08, 2010
Title ePSC-RC2, rep1
Sample type RNA
Source name L4ePSRCre2
Organism Mus musculus
Characteristics cell type: EpiSC-like iPS cell reverted (ePSC reverted)
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 2.722201
ILMN_1212612 1.375712
ILMN_1212619 2.693944
ILMN_1212628 2.130379
ILMN_1212632 3.51636
ILMN_1212636 11.391067
ILMN_1212637 8.839243
ILMN_1212645 2.549771
ILMN_1212648 7.610711
ILMN_1212653 3.863174
ILMN_1212672 7.370583
ILMN_1212682 2.431694
ILMN_1212683 1.568604
ILMN_1212685 2.139706
ILMN_1212692 6.503267
ILMN_1212693 2.13886
ILMN_1212695 1.990889
ILMN_1212698 1.822468
ILMN_1212702 2.388036
ILMN_1212703 5.313989

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap