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Sample GSM406304 Query DataSets for GSM406304
Status Public on Jul 29, 2009
Title GSC line 1
Sample type RNA
 
Source name Germ stem cells
Organism Mus musculus
Characteristics cell type: Germ stem cells
potency: Unipotent
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 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 2.140695
ILMN_1212612 2.889443
ILMN_1212619 4.588164
ILMN_1212628 1.370515
ILMN_1212632 4.27864
ILMN_1212636 11.167413
ILMN_1212637 8.63689
ILMN_1212645 1.671607
ILMN_1212648 8.01191
ILMN_1212653 3.622604
ILMN_1212672 6.30208
ILMN_1212682 2.777463
ILMN_1212683 0.89401
ILMN_1212685 1.570625
ILMN_1212692 6.945982
ILMN_1212693 7.232525
ILMN_1212695 2.093586
ILMN_1212698 0.661656
ILMN_1212702 1.805201
ILMN_1212703 3.580811

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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