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Sample GSM389517 Query DataSets for GSM389517
Status Public on Jan 23, 2010
Title pNSC rep2
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 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 Apr 06, 2009
Last update date Jan 23, 2010
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)
GSE15561 Generation of parthenogenetic iPS cells from parthenogenetic neural stem cell

Data table header descriptions
VALUE quantile-normalized signal intensities

Data table
ILMN_1212607 2.613002
ILMN_1212612 3.846561
ILMN_1212619 6.877273
ILMN_1212628 1.930869
ILMN_1212632 6.203278
ILMN_1212636 11.784194
ILMN_1212637 9.460540
ILMN_1212645 3.200785
ILMN_1212648 7.352248
ILMN_1212653 9.784884
ILMN_1212672 8.374981
ILMN_1212682 4.157935
ILMN_1212683 2.610615
ILMN_1212685 2.178274
ILMN_1212692 1.947793
ILMN_1212693 7.231367
ILMN_1212695 2.250765
ILMN_1212698 3.134111
ILMN_1212702 2.163772
ILMN_1212703 6.695741

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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