|
| Status |
Public on Feb 20, 2007 |
| Title |
Prostate tumor metastases in para tracheal lymph node EB667LNPT3_Uniset20K |
| Sample type |
RNA |
| |
|
| Source name |
EB667LNPT3, metastatic prostate tumor samples in para tracheal lymph node from patient EB667
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: prostate tumor metastases in para tracheal lymph node
|
| Treatment protocol |
Specimens were received directly from the operating room. Samples (>500 mg) were excised and snap frozen in liquid nitrogen within 30 min of excision and stored at -80°C until extraction of RNA. Metastatic tumor samples were obtained from a warm autopsy program and processed similarly to primary tumors. 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. Dissection of the frozen tissue block was performed with the guidance of a marked H & E slide to minimize the presence of host tissue in the metastatic samples. All samples used in the study contained >80% tumor. Metastatic tumor samples were minced and divided into two equal portions to be extracted with the sample protocol used for each set of primary tumors.
|
| 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 CodeLink protocol from 1 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 18 hr at 37C on Human Uniset 20K arrays (GE Healthcare, Piscataway, NJ). Arrays were washed and stained according to the standard CodeLink manual.
|
| Scan protocol |
CodeLink arrays were scanned with the GenePix 4000B scanner using GenePix Pro 4.1 software.
|
| Description |
CodeLink gene expression data from metastatic prostate tumor samples
|
| Data processing |
For CodeLink arrays, image files were analyzed with the CodeLink Expression Analysis Software version 4.1 (GE HealthCare) with use of the normalized intensity values in downstream analysis.
|
| |
|
| Submission date |
Jan 16, 2007 |
| Last update date |
Feb 20, 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 |
GPL2891 |
| Series (1) |
| GSE6752 |
CodeLink Expression Data from primary prostate tumor and prostate tumor metastases |
|
