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Sample GSM389516 Query DataSets for GSM389516
Status Public on Jan 23, 2010
Title pNSC rep1
Sample type RNA
 
Source name parthenogenetic NSC
Organism Mus musculus
Characteristics gender: parthenogenetic
cell type: neural stem cell
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 Specifically, 400 ng of total RNA per sample was used as input into a linear amplification protocol for labelled cRNA synthesis (Illumina TotalPrep RNA Amplification Kit - Ambion) following the manufacturer's instructions, which involved synthesis of T7-linked double-stranded cDNA and 10-12 hrs of in-vitro transcription (IVT) incorporating biotin-labelled nucleotides.
 
Hybridization protocol Standard Illumina hybridization protocol. Purified and labelled cRNA was then hybridized for 18 hrs onto MouseRef-8 v2 expression BeadChips (Illumina) according to the manufacturer's instructions. After washing, as recommended, chips were stained with streptavidin-Cy3 (GE Healthcare). Samples were exclusively hybridized as biological replicates.
Scan protocol Standard Illumina scanning protocol. Scanned using the iScan reader (Illumina) and accompanying software.
Description pNSC: Mouse parthenogenetic NSC (Neural Stem Cell).
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 Apr 06, 2009
Last update date Jan 23, 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)
GSE15561 Generation of parthenogenetic iPS cells from parthenogenetic neural stem cell

Data table header descriptions
ID_REF
VALUE quantile-normalized signal intensities

Data table
ID_REF VALUE
ILMN_1212607 3.426230
ILMN_1212612 3.934811
ILMN_1212619 6.960137
ILMN_1212628 1.985709
ILMN_1212632 5.328065
ILMN_1212636 11.637357
ILMN_1212637 9.519150
ILMN_1212645 3.210120
ILMN_1212648 7.305618
ILMN_1212653 9.701796
ILMN_1212672 8.065163
ILMN_1212682 3.930000
ILMN_1212683 2.255264
ILMN_1212685 2.641022
ILMN_1212692 1.995363
ILMN_1212693 7.203464
ILMN_1212695 2.024370
ILMN_1212698 2.600678
ILMN_1212702 2.125010
ILMN_1212703 6.823459

Total number of rows: 25697

Table truncated, full table size 554 Kbytes.




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

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