|
| Status |
Public on Apr 30, 2010 |
| Title |
CWR_ctrl#1 |
| Sample type |
RNA |
| |
|
| Source name |
CWR22Rv1 cells, control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CWR22Rv1
cell type: prostrate cancer
|
| Treatment protocol |
DU145 and CWR22Rv1 cells were transfected with scrambled siRNA or siRNAs targeted to human Stat3 or Stat5a and Stat5b using Lipofectamine 2000. The cells were harvested 48 h after the transfections.
|
| Growth protocol |
DU145 and CWR22Rv1 cells were cultured in PRMI 1640 medium supplemented with 10% FBS, 2mM L-glutamine, 50IU/ml penicillin and 50mg/ml streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the Qiagen Rneasy Mini Kit according to the manufacturer's instructions. A Dnase I digestion step was included to eliminate DNA contamination. Each group (control-siRNA, Stat5a/b-siRNA and Stat3-siRNA) was done in triplicate and RNA samples from each group were not pooled. RNA was quantified on a Nanodrop ND-100 spectrophotometer, followed by RNA quality assessment on an Agilent 2100 Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr on Human Genome 133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 using the GeneChip Operating Software version 3.0.
|
| Description |
Gene expression data from CWR22Rv1 cells transfected with scramble siRNA(control)
|
| Data processing |
The data was processed using R/Bioconductor. The raw data was pre-processed using RMA with the default settings of the Bioconductor library “affy”. The transcripts were filtered based on availability of EntrezID and GO annotation for each transcript. We also chose a single representative transcript for each Entrez ID based on the maximum variation in the expression within each cell line type (DU and CWR). Analysis was carried out separately for the DU and CWR chips, by fitting a linear model to each transcript using the Bioconductor library “limma”, with the dependent variables being dummy variables indicating type (ctrl, stat3 or stat5).
|
| |
|
| Submission date |
Aug 03, 2009 |
| Last update date |
Aug 03, 2009 |
| Contact name |
Marja Nevalainen |
| E-mail(s) |
Marja.Nevalainen@jefferson.edu
|
| Phone |
215-503-9250
|
| Fax |
215-503-9245
|
| Organization name |
Thomas Jefferson University
|
| Department |
Cancer Biology
|
| Lab |
Nevalainen
|
| Street address |
233 S. 10th St
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19107 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE17482 |
Gene expression profiles regulated by Stat5a/b vs. Stat3 in human prostate cancer cells. |
|
