|
| Status |
Public on Aug 07, 2015 |
| Title |
AA_tumor_51 [reanalysis Affymetrix] |
| Sample type |
RNA |
| |
|
| Source name |
prostate biopsy from prostate cancer patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate
|
| Treatment protocol |
No treatment was performed on the collected tissue samples.
|
| Growth protocol |
Samples were collected from patients, so there was no growth protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All RNA samples were purified by using Qiagen RNeasy micro kit (Qiagen). Samples were then treated with the RiobMinus, rRNA reduction kit (Invitrogen), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute. Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix GeneChIP Scanner 3000
|
| Description |
needle biopsy specimen from prostate
|
| Data processing |
Data were processed using Partek Genomics Suite software. Quantile normalization and GC-RMA background correction were applied to probe intensities, gene level expression were summarized from the corrected/normalized intensities. Only core probe sets were used for data analysis.
HuEx-1_0-st-v2.r2.pgf
|
| |
|
| Submission date |
Aug 06, 2015 |
| Last update date |
Aug 07, 2015 |
| Contact name |
Bi-Dar Wang |
| E-mail(s) |
wangbi@gwu.edu
|
| Phone |
202-994-3543
|
| Fax |
202-994-2870
|
| Organization name |
The George Washington University Medical Center
|
| Department |
Pharmacology and Physiology
|
| Street address |
2300 I street, NW
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20037 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE64333 |
MicroRNA and Gene expression profiling of the prostate biopsy samples from African American and European American prostate cancer patients |
| GSE71781 |
Gene expression profiling of the prostate biopsy samples (cancer and adjacent normal tissues) from African American prostate cancer patients |
|
| Relations |
| Reanalysis of |
GSM1568987 |
