|
| Status |
Public on Mar 01, 2014 |
| Title |
Gene expression in KOPT-K1 persister, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
KOPT-K1 persister cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KOPT-K1
cell type: T-cell acute lymphoblastic leukemia
treated with: 1 uM gamma Secretase inhibitor over 7 weeks
|
| Treatment protocol |
Persister cells were established by treating DND-41 or KOPT-K1 cells with 1 microM GSI for at least 7 weeks, replenishing the inhibitor every 3 - 4 days (Compound E, EMD4 Biosciences).
|
| Growth protocol |
The human T-cell leukemia cell lines DND-41 and KOPT-K1 were grown in RPMI 1640 containing 10% FCS at 37°C with 5% CO2. Cells were maintained between a density of 5 x 105 cells/ml and 2 x 106 cells/ml.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA was hybridized according to the standard Affymetrix protocol.
|
| Scan protocol |
GeneChips were scanned according to the standard Affymetrix protocol.
|
| Description |
KOPT-K1_p_r2
|
| Data processing |
Data were processed using GenePattern GC-RMA (v.2.30.0) with standard parameters for normalization and scaling.
|
| |
|
| Submission date |
Jan 24, 2014 |
| Last update date |
Mar 01, 2014 |
| Contact name |
Jiang Zhu |
| E-mail(s) |
jzhu@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital, Harvard Medical School and Broad Institute
|
| Lab |
Bradley Bernstein Lab
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE54378 |
Gene expression profiles of T-cell acute lymphoblastic leukemia cell lines with and without chronic GSI-treatment |
| GSE54380 |
Genome-wide chromatin maps of T-cell acute lymphoblastic leukemia (T-ALL) |
|
