|
| Status |
Public on Dec 10, 2013 |
| Title |
Ly1_0h_nothing_A_1_10 |
| Sample type |
RNA |
| |
|
| Source name |
Cell line Ly1 treated with nothing at 0h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Ly1
cell type: diffuse large B-cell lymphoma (DLBCL)
time: 0h
treatment: nothing
replicate: A
|
| Treatment protocol |
Each lymphoma cell line was profiled in triplicate at baseline (0h) and at four additional time points (2h, 6h, 24h and 48h) after treatment with 500nM of JQ1 or vehcile (DMSO) control.
|
| Growth protocol |
Five lymphoma cell lines, SU-DHL6, OCI-Ly1, OCI-Ly4, Toledo and HBL-1, were propagated in their appropriate growth media under standard conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA, cells were homogenized in Trizol and RNA was extracted according to standard protocols.
|
| Label |
Biotin
|
| Label protocol |
cRNA was biotinylated according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA was hybridized overnight according to the Affymetrix protocol.
|
| Scan protocol |
GCS3000 (Affymetrix)
|
| Description |
Cell line Ly1 treated with nothing at 0h (replicateA)
|
| Data processing |
The raw cel files were converted into probeset-specific expression values using Affymetrix RMA summarization method and alternative probe set definitions (HuGene10stv1_Hs_ENTREZ, Brainarray v15) as implemented in the BioConductor package simpleaffy (Gentleman et al., 2004). All samples were scaled to have a mean expression level of 100.
|
| |
|
| Submission date |
Mar 29, 2013 |
| Last update date |
Dec 10, 2013 |
| Contact name |
Björn Chapuy |
| E-mail(s) |
Bjoern_Chapuy@dfci.harvard.edu
|
| Phone |
+1-617-632-3881
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Onology
|
| Lab |
Shipp Lab
|
| Street address |
450 Brookline Ave.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL16522 |
| Series (1) |
| GSE45630 |
Time course gene expression profiling of five diffuse large B-cell lymphoma cell lines following JQ1 treatment |
|
