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Sample GSM406307 Query DataSets for GSM406307
Status Public on Jul 29, 2009
Title GSC line 4
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 4
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
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
VALUE log2, quantile-normalized signal intensities

Data table
ILMN_1212607 1.507724
ILMN_1212612 0.849671
ILMN_1212619 4.85055
ILMN_1212628 1.555091
ILMN_1212632 4.595465
ILMN_1212636 10.789883
ILMN_1212637 8.134015
ILMN_1212645 1.832787
ILMN_1212648 8.063806
ILMN_1212653 3.540632
ILMN_1212672 7.009587
ILMN_1212682 3.130697
ILMN_1212683 1.413579
ILMN_1212685 1.315608
ILMN_1212692 6.369026
ILMN_1212693 7.189841
ILMN_1212695 1.779389
ILMN_1212698 0.979557
ILMN_1212702 1.218116
ILMN_1212703 3.825758

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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