NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM406311 Query DataSets for GSM406311
Status Public on Jul 29, 2009
Title ESC rep1
Sample type RNA
 
Source name Embryonic Stem Cells
Organism Mus musculus
Characteristics cell type: Embryonic Stem Cells
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 400 ng of total DNA-free RNA was used as input for cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions (IVT: 12h).
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol. Quality-checked cRNA samples were hybridized as biological or technical duplicates for 18 h onto mouse-8 v2 expression BeadChips (Illumina), washed, and stained following guidelines and using materials / instrumentation supplied / suggested by the manufacturer.
Scan protocol Standard Illumina scanning protocol. Scanned following guidelines and using materials / instrumentation supplied / suggested by the manufacturer.
Description replicate 1
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 May 20, 2009
Last update date Jul 29, 2009
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)
GSE16178 Induction of Pluripotency in Adult Unipotent Germline Stem Cells

Data table header descriptions
ID_REF
VALUE log2, quantile-normalized signal intensities

Data table
ID_REF VALUE
ILMN_1212607 1.330486
ILMN_1212612 2.043674
ILMN_1212619 2.411736
ILMN_1212628 1.664374
ILMN_1212632 6.081083
ILMN_1212636 11.726976
ILMN_1212637 7.880883
ILMN_1212645 1.993609
ILMN_1212648 7.466449
ILMN_1212653 2.887248
ILMN_1212672 7.724944
ILMN_1212682 3.600071
ILMN_1212683 0.922447
ILMN_1212685 1.860782
ILMN_1212692 6.567058
ILMN_1212693 3.08684
ILMN_1212695 1.451346
ILMN_1212698 1.344508
ILMN_1212702 1.443442
ILMN_1212703 4.625658

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