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Sample GSM389515 Query DataSets for GSM389515
Status Public on Jan 23, 2010
Title fNSC rep2
Sample type RNA
Source name female NSC
Organism Mus musculus
Characteristics gender: female
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 fNSC: Mouse female 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 3.780294
ILMN_1212612 3.341996
ILMN_1212619 6.569092
ILMN_1212628 2.276612
ILMN_1212632 4.502674
ILMN_1212636 11.499786
ILMN_1212637 9.232845
ILMN_1212645 3.259889
ILMN_1212648 7.600160
ILMN_1212653 9.285773
ILMN_1212672 7.628768
ILMN_1212682 4.226928
ILMN_1212683 2.419560
ILMN_1212685 2.269366
ILMN_1212692 2.839959
ILMN_1212693 6.849665
ILMN_1212695 2.466799
ILMN_1212698 2.526642
ILMN_1212702 2.743284
ILMN_1212703 7.685866

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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