|
| Status |
Public on Jan 16, 2007 |
| Title |
Tumor samples from patient No.56 PT56U95B |
| Sample type |
RNA |
| |
|
| Source name |
PT56, tumor samples from patient No.56
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: primary prostate tumor
Tumor stage: T3a
Gleason Grade: 7
|
| Treatment protocol |
Fresh prostate tissues were recovered immediately after surgical removal. Tissues were dissected/trimmed to obtain pure tumor then snap frozen in liquid nitrogen within 30 mintues of excision and stored in -80C untill RNA extraction. An H&E stained frozen section of each sample was evaluated by a pathologist, to determine epithelial and stromal content and verify the presence of tumor in the sample. Only tumor tissues with less than 30% of tromal components were selected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Qiagen Rneasy kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U95B array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Gene expression data from primary prostate cancer
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.
|
| |
|
| Submission date |
Dec 22, 2006 |
| Last update date |
Jan 16, 2007 |
| Contact name |
Federico Alberto Monzon |
| E-mail(s) |
famonzon@tmhs.org
|
| Organization name |
The Methodist Hospital
|
| Department |
Pathology
|
| Lab |
Molecular Diagnostics
|
| Street address |
6565 Fannin St, MS205
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL92 |
| Series (2) |
| GSE6606 |
Expression data from Primary Prostate Tumor |
| GSE6919 |
Expression Data from Normal and Prostate Tumor Tissues |
|
