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Sample GSM389522 Query DataSets for GSM389522
Status Public on Jan 23, 2010
Title fESC-B rep1
Sample type RNA
Source name female ESC OG2
Organism Mus musculus
Characteristics gender: female
cell type: embryonic stem cell OG2
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 fESC: Mouse female ESC (Embryonic Stem Cell) OG2.
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
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 2.441348
ILMN_1212612 1.759262
ILMN_1212619 2.482799
ILMN_1212628 4.112996
ILMN_1212632 5.052915
ILMN_1212636 11.830342
ILMN_1212637 9.401391
ILMN_1212645 4.556080
ILMN_1212648 8.803590
ILMN_1212653 2.745455
ILMN_1212672 8.364638
ILMN_1212682 4.705237
ILMN_1212683 2.568070
ILMN_1212685 2.270172
ILMN_1212692 6.105972
ILMN_1212693 1.619286
ILMN_1212695 2.092541
ILMN_1212698 2.251484
ILMN_1212702 3.098084
ILMN_1212703 4.373001

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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