|
| Status |
Public on May 03, 2012 |
| Title |
untreated_NT2 cells_control2 |
| Sample type |
genomic |
| |
|
| Source name |
untreated_NT2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
cell line: NT2
cell type: embryocarcinoma
|
| Treatment protocol |
NT2 cells were induced to differentiate with 10 µM all-trans retinoic acid (Sigma). Medium containing RA was changed every 2 days.
|
| Growth protocol |
NT2 cells were maintained in Dulbecco's Modified Eagle Medium (D-MEM, with l-glutamine, 4500 mg/l d-glucose, without sodium pyruvat; Gibco) supplemented with 10% fetal bovine serum and 200 U/ml penicillin and 200 µg/ml streptomycin (all from Gibco) in a humidified atmosphere of 5% CO2 in air.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from RA-induced and untreated NT2 tissue culture cells was prepared using the DNeasy Blood & Tissue Kit (Invitrogen) according the manufacturer's specifications. Genomic DNA (500 ng) from each sample was bisulfite converted using the EZ-96 DNA Methylation Kit (Zymo Research Corporation, Irvine, CA, USA) according to the manufacturer's recommendations.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Data processing |
GenomeStudio V2010.3 [(Unmethylated and methylated) signal_intensities.txt is provided as a Series supplementary file]
|
| |
|
| Submission date |
Sep 24, 2011 |
| Last update date |
May 03, 2012 |
| Contact name |
michael thomas bocker |
| Organization name |
DKFZ Heidelberg
|
| Street address |
Im Neuenheimer Feld
|
| City |
heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE32362 |
Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster (Infinium HumanMethylation450 Beadchip) |
| GSE33130 |
Hydroxylation of 5-methylcytosine by TET2 maintains the active state of the mammalian HOXA cluster |
|
