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Sample GSM475157 Query DataSets for GSM475157
Status Public on Nov 25, 2009
Title iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3 clone 1
Sample type RNA
 
Source name iPS from MEFs with overexpression of Oct4, Sox2, Klf4 and Tbx3 clone 1
Organism Mus musculus
Characteristics cell type: iPS
Extracted molecule total RNA
Extraction protocol Cells from repective clones or cell cultures were harvested and then washed with PBS, trypsinised, resuspended in RNAlater and stored at -20°C. Total RNA extraction was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.
Label Biotin
Label protocol 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion).
 
Hybridization protocol 750ng of each labelled cRNA sample was hybridized to MouseRef-8 v2 Expression BeadChip microarrays (Illumina) according to manufacturer specifications.
Scan protocol Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.
Description Clone 1
Data processing The microarray data was subjected to background subtraction on the BeadStudio Data Analysis software (Illumina) and normalized using the Cross-correlation method (Chua et al., 2006).
Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.
 
Submission date Nov 24, 2009
Last update date Nov 24, 2009
Contact name Henry Yang
E-mail(s) henry_yang@immunol.a-star.edu.sg
Organization name SIgN
Department Bioinformatics Group
Street address 8A Biomedical Grove
City Singapore
ZIP/Postal code 138648
Country Singapore
 
Platform ID GPL6103
Series (1)
GSE19164 Tbx3 improves the germ-line competency of induced pluripotent stem cells

Data table header descriptions
ID_REF
VALUE Background subtracted cross-correlation method normalised intensity values generated using MATLAB scripts

Data table
ID_REF VALUE
ILMN_1212602 112.9
ILMN_1212605 570.1
ILMN_1212607 20.6
ILMN_1212612 79.6
ILMN_1212616 421.8
ILMN_1212619 109.7
ILMN_1212626 1255.3
ILMN_1212628 20.5
ILMN_1212632 131.6
ILMN_1212636 6209.6
ILMN_1212637 2807.5
ILMN_1212644 20.0
ILMN_1212645 100.4
ILMN_1212646 1215.1
ILMN_1212648 479.6
ILMN_1212672 420.3
ILMN_1212681 23.2
ILMN_1212682 23.2
ILMN_1212683 23.2
ILMN_1212685 23.2

Total number of rows: 24613

Table truncated, full table size 445 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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