|
| Status |
Public on Feb 15, 2011 |
| Title |
OCI-Ly1 decitabine 48h_methlyation data |
| Sample type |
genomic |
| |
|
| Source name |
DLBCL patient
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Diffuse large B-cell lymphoma
cell line: OCI-Ly1
agent: decitabine
|
| Treatment protocol |
Cells were treated with panobinostat alone, decitabine alone or their combination. Following 48h of incubation with the drugs total DNA was isolated.
|
| Growth protocol |
cells were grown in IMDM (Ly1 and Ly10) or RPMI (Su-DHL6) medium with 10% fetal bovine serum. Fresh medium was added every 2-3 days and the cells were kept at a cell concentration of 0.5-1 x 106/mL.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was isolated using phenol chloroform method
|
| Label |
biotin
|
| Label protocol |
standard Illumina protocol
|
| |
|
| Hybridization protocol |
standard Illumina protocol
|
| Scan protocol |
standard Illumina protocol
|
| Data processing |
Methylation scores represented as â values are generated for each site using BeadStudio 3.2 software (© Illumina, Inc. 2003-2008) and are computed based on the ratio of methylated to methylated plus unmethylated signal outputs. Thus the â values range from 0 (unmethylated) to 1 (fully methylated) on a continuous scale. Intra-array normalisation was performed by the Illumina BeadStudio3.2 software. The resulting â-valued data matrix was normalised further using a quantile-normalization strategy, designed to reduce unwanted inter-array variation using CLCBio Genomics Workbench 3 software package (version 3.7.1).
|
| |
|
| Submission date |
Feb 10, 2011 |
| Last update date |
Feb 15, 2011 |
| Contact name |
Matko Kalac |
| E-mail(s) |
matko.kalac@nyumc.org
|
| Phone |
212 263 9124
|
| Organization name |
NYU Medical Center
|
| Department |
NYU Cancer Institute
|
| Lab |
O'Connor-Smilow 1207
|
| Street address |
522 1st Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL8490 |
| Series (1) |
| GSE27226 |
HDACI and DAC induce specific epigenetic profile in DLBCL |
|
