|
| Status |
Public on Nov 30, 2012 |
| Title |
abl control at VEH rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
abl cells transfected with control siRNA under hormone depleted conditions
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP-abl (abl) prostate cancer cells
genotype/variation: transfected with control siRNA
treatment protocol: under hormone depleted conditions
|
| Treatment protocol |
Cells were transfected with either control siRNA (siCtrl) or siRNAs targeting EZH2 (siEZH2), and maintained in androgen-depleted medium for 24 hours, and then treated with either 10 nM 5α-dihydrotestosterone (DHT, for LNCaP cells) or with ethanol only (for abl cells) for another 24 hours before the RNA was extracted.
|
| Growth protocol |
LNCaP cells were routinely maintained in RPMI-1640 with 10% fetal bovine serum (FBS) plus 1% antibiotics (penicillin and streptomycin). LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI with 10% charcoal-stripped FBS plus 1% antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by additional purification using RNeasy Kit (Qiagen, Cat#74104).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8-15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized overnight at 45ºC on Affymetrix human U133 plus 2.0 expression array. The chips were transferred to a fluidics instrument that performs washes and then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE).
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G.
|
| Description |
Gene expression data from abl cells after transfection with control siRNA
abl-VEH-siCtrl-2
|
| Data processing |
The data is processed by RMA with quantile normalization.
Probes are converted to genes by averaging values of probes mapped to the same gene. Combat is used to remove the batch effect. The Combat-Matrix.txt files are linked as supplementary files on the Series record.
|
| |
|
| Submission date |
Jul 18, 2012 |
| Last update date |
May 31, 2013 |
| Contact name |
Kexin Xu |
| E-mail(s) |
kxuthscsa@gmail.com
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Molecular Medicine
|
| Street address |
7703 Floyd Curl, MC 8257
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE39452 |
Expression data of EZH2-dependent genes in prostate cancer cell lines |
| GSE39461 |
Role of PRC2 complex components in prostate cancer cell lines |
|
