NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM385575 Query DataSets for GSM385575
Status Public on Dec 31, 2010
Title F9-Sox2, rep2
Sample type RNA
 
Source name F9 embryonic carcinoma cell overexpressing Sox2
Organism Mus musculus
Characteristics gender: male
Extracted molecule total RNA
Extraction protocol 300 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: 10h).
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.
 
Hybridization protocol Standard Illumina hybridization protocol.
Scan protocol Standard Illumina scanning protocol.
Description replicate 2 of 2.
Data processing The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina), background correction was perform using the Affymetrix Robust Multi-array Analysis (RMA) background correction model, variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor.
 
Submission date Mar 23, 2009
Last update date Dec 31, 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)
GSE15358 Sox2 Levels Define Pluripotent Ground States and Reprogramming Potential

Data table header descriptions
ID_REF
VALUE Quantile normalized

Data table
ID_REF VALUE
ILMN_1212607 3.745323
ILMN_1212612 2.440025
ILMN_1212619 3.145363
ILMN_1212628 2.687837
ILMN_1212632 5.774892
ILMN_1212636 12.000200
ILMN_1212637 9.084535
ILMN_1212645 2.702283
ILMN_1212648 6.369031
ILMN_1212653 3.938415
ILMN_1212672 8.998720
ILMN_1212682 4.238340
ILMN_1212683 2.192512
ILMN_1212685 1.936983
ILMN_1212692 7.056021
ILMN_1212693 4.565720
ILMN_1212695 2.115190
ILMN_1212698 1.916965
ILMN_1212702 2.161437
ILMN_1212703 4.529047

Total number of rows: 25697

Table truncated, full table size 554 Kbytes.




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

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