|
| Status |
Public on Sep 01, 2010 |
| Title |
PPC1_non-target shRNA_replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
prostate cancer cell line, non-target control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: prostate cancer, PPC1
|
| Treatment protocol |
Asynchronously growing NT and CBFbeta knockdown cells were used for the RNA isolation.
|
| Growth protocol |
Lentiviral infected PPC1 cells were maintained in RPMI containing 10% fetal calf serum, pen/strep, L-glutamine and 1 microgram/ml puromycin. Cells were subcultured 1:2 every 3 to 4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified using Ribopure (Ambion) RNA isolation
|
| Label |
Alexa-555
|
| Label protocol |
First and second strand cDNA was prepared from the total RNA samples. cRNA target was prepared from the DNA template and verified on the Bioanalyzer. cRNA was fragmented to uniform size and verified on the Bioanalyzer.
|
| |
|
| Hybridization protocol |
1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Whole Human Genome microarrays (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, and washed at 37° C for 1 min.
|
| Scan protocol |
Rinsed and dried arrays were scanned with an Agilent G2565 Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.
|
| Description |
gene expression in non-target shRNA-expressing PPC1 cells
|
| Data processing |
Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).
|
| |
|
| Submission date |
Apr 28, 2010 |
| Last update date |
Apr 28, 2010 |
| Contact name |
Shari Meyers |
| E-mail(s) |
smeyer@lsuhsc.edu
|
| Phone |
318-675-4937
|
| Fax |
318-675-5180
|
| Organization name |
LSU Health Sciences Center-Shreveport
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Meyers Lab
|
| Street address |
1501 Kings Highway
|
| City |
Shreveport |
| State/province |
LA |
| ZIP/Postal code |
71130 |
| Country |
USA |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE21561 |
Gene expression analysis of CBFbeta knockdown PPC1 cells |
|
