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Status |
Public on Feb 15, 2011 |
Title |
OCI-Ly1 panobinostat 48h_methlyation data |
Sample type |
genomic |
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Source name |
DLBCL patient
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Organism |
Homo sapiens |
Characteristics |
cell type: Diffuse large B-cell lymphoma cell line: OCI-Ly1 agent: panobinostat
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Treatment protocol |
Cells were treated with panobinostat alone, decitabine alone or their combination. Following 48h of incubation with the drugs total DNA was isolated.
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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.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Total DNA was isolated using phenol chloroform method
|
Label |
biotin
|
Label protocol |
standard Illumina protocol
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Hybridization protocol |
standard Illumina protocol
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Scan protocol |
standard Illumina protocol
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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).
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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
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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 |
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Platform ID |
GPL8490 |
Series (1) |
GSE27226 |
HDACI and DAC induce specific epigenetic profile in DLBCL |
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