|
| Status |
Public on Feb 12, 2013 |
| Title |
ko_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Dnmt1-/- mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
background strain: unknown [Lande-Diner et al 2007 (PMID:17311920)]
tissue: Mouse embryonic fibroblasts
genotype: Trp53-/- Dnmt1-/-
|
| Treatment protocol |
Not applicable
|
| 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; 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 |
GPL6887 |
| Series (2) |
| GSE44277 |
Comparison of gene expression in Dnmt1+/+ and Dnmt1-/- MEFs |
| GSE44278 |
Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of polycomb-target genes |
|
