|
| Status |
Public on Mar 21, 2014 |
| Title |
NI_0h_3 |
| Sample type |
RNA |
| |
|
| Source name |
U2OS_NI_0h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
cell type: osteosarcoma cells
transfected with: none (non-infected control)
treated with: dexamethasone (Dex) for 0h
|
| Treatment protocol |
On the next day the cells were transfected with 60 pmol of siRNA per well using Lipofectamine RNAiMAX (Invitrogen) using manufacturer’s protocol. After 2 days (24hr time point), or 3 days (2 hr and 4 hr timepoints) cells were treated with Dex for the indicated times. All treatment groups were harvested at the same time.
|
| Growth protocol |
A clonal line of U2OS cells that stably express wild-type rat GRα were plated in 6-well dishes with medium supplemented with 5% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 electrophoresis on an Agilent Bioanalyzer using the Experion RNA Stdsens analysis kit (Biorad). For each experimental condition 5 ug of high quality total RNA was submitted to the Southern California Genotyping Consortium at the University of California, Los Angeles.
|
| Label |
Cy3
|
| Label protocol |
Labeling, hybridization and scanning was performed by the Southern California Genotyping Consortium at UCLA as per their standard protocol.
|
| |
|
| Hybridization protocol |
standard Illumina protocol
|
| Scan protocol |
standard Illumina protocol
|
| Description |
rep 3
5645326020_I
|
| Data processing |
The data were normalized using neqc with limma (v.3.14.4) in R (v.2.15.3).
The non-normalized data matrix contains 48,210 data rows (with extra 887 rows for control probes). Control probes do not have Illumina IDs but have Probe IDs, were used in normalization, and thus removed in the dataset after normalization.
|
| |
|
| Submission date |
Apr 28, 2013 |
| Last update date |
Mar 21, 2014 |
| Contact name |
Dai-Ying Wu |
| Organization name |
University of Southern California
|
| Department |
Biochemistry
|
| Lab |
Stallcup
|
| Street address |
1441 Eastlake Ave, NOR 6314
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE46448 |
Selective enhancement and repression of glucocorticoid receptor signaling by coregulator Hic-5 |
|
