|
| Status |
Public on Feb 28, 2011 |
| Title |
LNCaP EtOH rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
LNCaP cells, treated with EtOH, biological rep 1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP androgen-sensitive human prostate adenocarcinoma cell line
sirna transfection protocol: control siRNA
agent (treatment): EtOH vehicle
|
| Treatment protocol |
42 hours post-transfection, cells were treated for 48 hours with 5nM R1881 or ethanol vehicle
|
| Growth protocol |
LNCaP cells were cultured under androgen deprived conditions for 48 hours, and transfected with control siRNA or siRNA directed against SRF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction followed by Rneasy column purification
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix 1-Cycle protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
Gene expression data from LNCaP cells treated with EtOH
|
| Data processing |
The software R was used along with bioconductor. The GC corrections steps were used from GCRMA, then the PM probes were normalized using fastlo, and then the median-polish portion of rma was used to summarize the expression values into probesets.
|
| |
|
| Submission date |
Jun 28, 2010 |
| Last update date |
Feb 28, 2011 |
| Contact name |
Keith Anderson |
| E-mail(s) |
anderson.s@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Street address |
200 First Street SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55906 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE22606 |
Identification of an SRF- and androgen-dependent gene signature in prostate cancer |
|
