|
| Status |
Public on Apr 25, 2018 |
| Title |
4h replicate veh |
| Sample type |
RNA |
| |
|
| Source name |
triple-negative breast cancer cell line MDA-MB-231 treated for 4 hours with vehicle
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
|
| Treatment protocol |
Treatments include either Vehicle, 100 nM Dex +/- 100 nM C297 or 100 nM Mif for 4, 8, and 12h. )
|
| Growth protocol |
MDA-MB-231 cells were grown to 80% confluence in 15-cm dishes in DMEM with 10% FBS. After culturing cells for 48h in DMEM with 2.5% charcoal-stripped FBS, 2 x 10^7 cells (per condition) were treated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following compound exposure, cells were washed in PBS, and lysed in RNA lysis buffer (Qiagen overnight at -80°C. RNA extraction, with accompanying DNase treatment, was performed using the RNeasy kit (Qiagen) following the manufacturer’s protocol
|
| Label |
biotin
|
| Label protocol |
The University of Chicago Genomics Core facility carried out the reverse transcription on the samples, followed by hybridization and microarray analysis using the Affymetrix Human U133 Plus 2.0 platform
|
| |
|
| Hybridization protocol |
The University of Chicago Genomics Core facility carried out the reverse transcription on the samples, followed by hybridization and microarray analysis using the Affymetrix Human U133 Plus 2.0 platform
|
| Scan protocol |
The University of Chicago Genomics Core facility carried out the reverse transcription on the samples, followed by hybridization and microarray analysis using the Affymetrix Human U133 Plus 2.0 platform
|
| Description |
RMA-normalized by the BiocLite(Affy) package in R
|
| Data processing |
RMA normalization and expression fold-change over vehicle control was calculated.
Application of a cut-off of at least +/- 1.3-fold change difference in expression for each treatment group versus vehicle, the genes became candidates for further analysis when their expression was altered significantly by Dex, and inhibited commonly by Mif and C297 (within the same time point as Dex) by at least 25%, in any treatment group.
|
| |
|
| Submission date |
Apr 24, 2018 |
| Last update date |
Apr 25, 2018 |
| Contact name |
Suzanne D Conzen |
| Organization name |
The University of Chicago
|
| Department |
Medicine
|
| Lab |
Conzen Lab
|
| Street address |
KCBD 8th Floor Conzen Lab, 900 E 57th Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE113571 |
Microarray: Discovery of a glucocorticoid receptor (GR) activity signature using selective GR antagonism in ER-negative breast cancer |
|
