|
| Status |
Public on Dec 02, 2013 |
| Title |
D556 cell line, treated by JQ1 (form active) |
| Sample type |
RNA |
| |
|
| Source name |
patient-derived cell line D556
|
| Organism |
Homo sapiens |
| Characteristics |
tissue origin: pediatric medulloblastoma
treatment: JQS 1 uM for 24 hours
|
| Treatment protocol |
Cell lines were treated with JQ1R or JQ1S, 1ÎĽM for 24 hours
|
| Growth protocol |
MB002 and MB004 cells were maintained in culture media with 1:1 Dulbecco modified Eagle medium (Gibco) and neural stem cell media (Gibco) supplemented with B27 (Gibco) EGF (02653, Stem Cell), FGF (GF003, Millipore), Heparin (07980, Stem Cell) and LIF (LIF1010, Millipore). D283, D458, D556 were maintained in Dulbecco modified Eagle medium (Gibco) supplemented with 10% FBS (100106, Benchmark) and 1% penicillin–streptomycin with 1% glutamine (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed according to the QIAGEN manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)
|
| |
|
| Hybridization protocol |
Following fragmentation, 1.4ug ug of cDNA were hybridized for 16 hr at 45C on Human Gene 1.0 st Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
|
| Scan protocol |
Affymetrix GeneChip Scanner 3000
|
| Description |
Gene expression data from patient-derived medulloblastoma cell line D556, treated by JQ1S
|
| Data processing |
The data were analyzed using GenePattern (The Broad Institute) using Affymetrix default analysis settings and RMA as normalization method.
|
| |
|
| Submission date |
Sep 19, 2013 |
| Last update date |
Dec 02, 2013 |
| Contact name |
Rameen Beroukhim |
| E-mail(s) |
[email protected]
|
| Organization name |
DANA-FARBER CANCER INSTITUTE
|
| Department |
Cancer Biology
|
| Street address |
450 Brookline Av
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE51020 |
Gene expression profiling of MYC-amplified medulloblastoma cell lines treated by JQ1, a BET bromodomain inhibitor |
|
