|
| Status |
Public on Jul 15, 2014 |
| Title |
U2OS_GRgamma-2hr-replicate3 |
| Sample type |
RNA |
| |
|
| Source name |
U2OS_2 hours_100 nM dexamethasone_GRgamma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
time: 2 hours
treatment: 100 nM dexamethasone
expressed allele: GRgamma
|
| Treatment protocol |
Dexamethasone (Sigma) at a final concentration of 100 nM was added to the medium for 2, 4, or 24 hours (hr); for the “0 hr” time point, cells were treated with vehicle (ethanol) only for 4 hr.
|
| Growth protocol |
Cells were plated in 6-well plates using DMEM supplemented with 5% v/v fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed and total RNA was isolated using QIAshredder and RNeasy mini columns (Qiagen). The quality of RNA samples was evaluated by A260/A280 ratio which was at least 1.9 and the integrity was analyzed using the Bioanalyzer 2100
(Agilent) with the Experion RNA Stdsens analysis kit (Biorad). For each experimental condition 2 μg of high quality total RNA was submitted to the University of Southern California Epigenome Center.
|
| Label |
biotin
|
| Label protocol |
Labeling was done by the University of Southern California Epigenome Center.
|
| |
|
| Hybridization protocol |
Hybridization was done by the University of Southern California Epigenome Center.
|
| Scan protocol |
Scanning and image acquisition was done by the University of Southern California Epigenome Center.
|
| Description |
4858944020_G
replicate 3
|
| Data processing |
Bead-level data outputted from Illumina’s BeadScan software were read using the beadarray package from Bioconductor. BASH was used to correct for compact and diffuse spatial artifacts on the arrays. Bead-level data were summarized using
beadarray, filtering out beads that were > 3 MADs from the median (this is the raw data). Probe annotations were retrieved using the illuminaHumanv3.db package from Bioconductor; bad quality probes and probes not corresponding to known
HUGO gene symbols were removed from the data before further processing. Bead summary data were log2 transformed and quantile normalized. We then used the non-parametric empirical Bayes method described by Johnson and Rabinovic to
correct for chip-to-chip batch effects. Detection pvalues were not available after batch correction.
|
| |
|
| Submission date |
Mar 21, 2013 |
| Last update date |
Jul 15, 2014 |
| Contact name |
Benjamin J Schiller |
| Organization name |
University of California, San Francisco
|
| Lab |
Keith Yamamoto
|
| Street address |
600 16th St
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL6883 |
| Series (1) |
| GSE45407 |
Gene expression of hormone-treated U2OS cells expressing GR alleles |
|
