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Sample GSM1081735 Query DataSets for GSM1081735
Status Public on Feb 12, 2013
Title aza_rep1b
Sample type RNA
 
Source name Dnmt1+/+ mouse embryonic fibroblasts treated with 5-aza-2'-deoxycytidine
Organism Mus musculus
Characteristics background strain: unknown [Lande-Diner et al 2007 (PMID:17311920)]
cell type: Mouse embryonic fibroblasts
genotype: Trp53-/- Dnmt1+/+
Treatment protocol MEFs were treated for 72 hours with either DMSO control or 1uM 5-aza-2'-deoxycytidine (Sigma)
Growth protocol MEFs were cultured under standard conditions
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol reagent according to manufacturers instructions followed by DNase I treatment. Quality control was performed with Agilent Bioanalyser.
Label Biotin
Label protocol Biotinylated cRNA was prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description Dnmt1+/+ mouse embryonic fibroblasts treated with 5-aza-2'-deoxycytidine; biological replicate 1, technical replicate 2
Data processing Data was processed using the lumi R package. Background subtraction was performed using the 'forcePositive' option to ensure that only positive values were achieved. Data was normalised using Robust Spline Normalisation
 
Submission date Feb 12, 2013
Last update date Feb 12, 2013
Contact name James P Reddington
Organization name EMBL
Street address Meyerhofstrasse 1
City Heidelberg
ZIP/Postal code 69115 Heidelberg
Country Germany
 
Platform ID GPL6885
Series (2)
GSE44276 Comparison of gene expression in Dnmt1+/+ MEFs treated with 5-aza-2'-deoxycytidine or vector control
GSE44278 Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of polycomb-target genes

Data table header descriptions
ID_REF
VALUE normalised microarray intensities
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 46.7598833 0.2030075
ILMN_1212612 133.534242 0
ILMN_1212619 196.9837441 0
ILMN_1212628 40.35475172 0.8483709
ILMN_1212632 59.16202385 0.01503759
ILMN_1212636 4298.440701 0
ILMN_1212637 950.6910729 0
ILMN_1212645 43.89166606 0.4360902
ILMN_1212648 232.6472928 0
ILMN_1212653 159.866898 0
ILMN_1212672 254.3257369 0
ILMN_1212682 56.5372033 0.03007519
ILMN_1212683 39.01678257 0.9323308
ILMN_1212685 45.19189519 0.3120301
ILMN_1212692 44.93875641 0.3320802
ILMN_1212693 103.5012787 0
ILMN_1212695 40.86388744 0.8145363
ILMN_1212698 42.3513545 0.6478696
ILMN_1212702 44.50493275 0.3721805
ILMN_1212703 78.04397984 0

Total number of rows: 25697

Table truncated, full table size 794 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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