GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM537510 Query DataSets for GSM537510
Status Public on Dec 08, 2010
Title ePSC C1, rep2
Sample type RNA
Source name C1
Organism Mus musculus
Characteristics cell type: epiblast stem cell-like induced pluripotent stem cell (EpiSC-like iPS cell; ePSC)
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 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
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 2.003499
ILMN_1212612 3.744171
ILMN_1212619 6.025387
ILMN_1212628 2.103592
ILMN_1212632 4.406329
ILMN_1212636 11.158637
ILMN_1212637 8.448112
ILMN_1212645 3.589038
ILMN_1212648 6.664113
ILMN_1212653 5.090309
ILMN_1212672 6.614817
ILMN_1212682 2.19885
ILMN_1212683 2.362801
ILMN_1212685 1.781279
ILMN_1212692 5.57312
ILMN_1212693 5.254764
ILMN_1212695 2.326993
ILMN_1212698 2.018283
ILMN_1212702 2.047903
ILMN_1212703 3.835887

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