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Sample GSM389518 Query DataSets for GSM389518
Status Public on Jan 23, 2010
Title piPS-2F rep1
Sample type RNA
 
Source name parthenogenetic iPS from NSC overexpressing Oct4 and Klf4
Organism Mus musculus
Characteristics gender: parthenogenetic
cell type: pluripotent cells, derived from NSC overexpressing Oct4 and Klf4
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 piPS-2F: Mouse parthenogenetic induced pluripotent cells derived from NSC overexpressing Oct4 and Klf4.
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 2.972043
ILMN_1212612 2.225907
ILMN_1212619 5.440108
ILMN_1212628 2.126860
ILMN_1212632 5.603572
ILMN_1212636 12.113984
ILMN_1212637 8.610554
ILMN_1212645 2.522556
ILMN_1212648 9.281788
ILMN_1212653 4.648575
ILMN_1212672 9.680639
ILMN_1212682 3.833443
ILMN_1212683 2.238971
ILMN_1212685 4.375457
ILMN_1212692 7.396203
ILMN_1212693 2.434622
ILMN_1212695 3.543397
ILMN_1212698 2.164979
ILMN_1212702 4.060933
ILMN_1212703 5.320166

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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