|
| Status |
Public on Dec 31, 2014 |
| Title |
6 Hr DMSO (D5) |
| Sample type |
RNA |
| |
|
| Source name |
HEPG2 cells no treatment (control)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEPG2
compound: control (DMSO)
dose: 0
timepoint (hours): 6
|
| Treatment protocol |
The cells (6-wells each treatment) were treated with BRD-8518 (0.005uM-3.33 uM, two-fold dilution) for 6 hr at 37C. The cells were also treated with BRD-8518 (1 uM) or Oncostatin M (100 ng/mL) for 1 hr and 24 hr at 37C. DMSO controls were set up for each timepoint. Compounds were added to the cells to a final DMSO concentration of 0.25%. Oncostatin M was dissolved in PBS and DMSO was added to the wells to bring the final concentration to 0.25%.
|
| Growth protocol |
10000 HepG2 cells are plated in each well of a Corning, black 96-well, tissue culture plate (#3904) in 40μL of DMEM/10% FBS/1x Pen-Strep-Glutamine media. The cells are then incubated overnight in a tissue culture incubator at 37°C and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using RNeasy Minipreps (Qiagen) following the manufacture’s protocol.
|
| Label |
Biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Affymetrix GeneChip Human Gene ST 2.0 Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
6 Hr DMSO
Broad_D5_45
|
| Data processing |
Data were normalized using the Robust Multi-Array Average method as implemented in the R package oligo.
|
| |
|
| Submission date |
May 16, 2014 |
| Last update date |
Dec 31, 2014 |
| Contact name |
Marek M Nageic |
| Organization name |
Broad Institute
|
| Department |
Center for the Development of Therapeutics
|
| Street address |
7 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL16686 |
| Series (1) |
| GSE57753 |
Transcriptional profiling of HEPG2 cells after treatment with TRIB1-inducing compounds |
|
