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Sample GSM389521 Query DataSets for GSM389521
Status Public on Jan 23, 2010
Title pESC-B rep2
Sample type RNA
Source name parthenogenetic ESC SSEA-1 sorted
Organism Mus musculus
Characteristics gender: parthenogenetic
cell type: embryonic stem cell, SSEA-1 sorted
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 pESC-B: Mouse parthenogenetic ESC (Embryonic Stem Cell) SSEA-1 sorted.
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 2.307680
ILMN_1212612 2.533533
ILMN_1212619 3.682510
ILMN_1212628 2.947751
ILMN_1212632 5.866726
ILMN_1212636 11.889480
ILMN_1212637 8.938121
ILMN_1212645 3.002651
ILMN_1212648 8.575877
ILMN_1212653 3.500015
ILMN_1212672 8.660469
ILMN_1212682 3.292520
ILMN_1212683 2.283295
ILMN_1212685 2.651892
ILMN_1212692 7.922916
ILMN_1212693 2.885576
ILMN_1212695 2.905154
ILMN_1212698 2.545009
ILMN_1212702 2.340560
ILMN_1212703 3.129016

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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