|
| Status |
Public on Apr 10, 2017 |
| Title |
TPK409 |
| Sample type |
RNA |
| |
|
| Source name |
T47D-Y cells stably expressing empty pIRESneo3 plasmid, co-treated with ethanol and RU486, for 6 hours
|
| Organism |
Homo sapiens |
| Characteristics |
parental cell line: T47D-Y
tissue: Breast
stable vector integration: pIRESneo3-empty
treatment: ethanol and RU486
time point: 6 hr
|
| Treatment protocol |
Samples treated in IMEM medium, with or without progestin (10e-8 M) and/or antiprogestin (10e-7 M) for 6 hr.
|
| Growth protocol |
Samples grown in complete medium (MEM, 5% FBS, 1% NEAA, 1% pen/strep, 6ng/ml insulin, 200 ug/ml G418) before 1 day starvation in IMEM medium, then treated in IMEM medium for 6 hr.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
T47D_PR_null_ethanol_RU486_6h_expt_2_rep_3
|
| Data processing |
The data were filtered and any probes with a detection P value less than 0.05 were removed. The data was then normalized using log2 transformation and quantile normalization with R using the lumi bioconductor package
|
| |
|
| Submission date |
Feb 01, 2017 |
| Last update date |
Apr 10, 2017 |
| Contact name |
Todd P Knutson |
| E-mail(s) |
knut0297@umn.edu
|
| Phone |
612-626-8911
|
| Organization name |
University of Minnesota
|
| Department |
Minnesota Supercomputing Institute
|
| Street address |
117 Pleasant St SE
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE94363 |
Posttranslationally modified progesterone receptors direct ligand-specific expression of breast cancer stem cell-associated gene programs |
|
