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Sample GSM406309 Query DataSets for GSM406309
Status Public on Jul 29, 2009
Title gPS line 2
Sample type RNA
 
Source name germ Pluripotent Stem cells
Organism Mus musculus
Characteristics cell type: germ Pluripotent 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 cell line 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 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 3.645567
ILMN_1212612 0.982292
ILMN_1212619 5.107452
ILMN_1212628 2.021908
ILMN_1212632 4.637672
ILMN_1212636 11.663354
ILMN_1212637 7.67592
ILMN_1212645 3.103518
ILMN_1212648 6.89958
ILMN_1212653 2.235539
ILMN_1212672 7.706906
ILMN_1212682 2.94457
ILMN_1212683 1.180959
ILMN_1212685 2.645898
ILMN_1212692 7.316701
ILMN_1212693 2.702217
ILMN_1212695 1.249097
ILMN_1212698 1.187011
ILMN_1212702 2.35506
ILMN_1212703 4.145088

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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