|
| Status |
Public on May 28, 2008 |
| Title |
Fusion: Yes, Deletion: No (prostate_42994) |
| Sample type |
RNA |
| |
|
| Source name |
primary prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
FUSION: YES
DELETION: NO
|
| Treatment protocol |
na
|
| Growth protocol |
na
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Using 3 biopsy cores (0.6µm each) taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using Trizol LS reagent (Invitrogen).
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Refer to the Illumina DASL Assay System Manual
|
| |
|
| Hybridization protocol |
Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays.
|
| Scan protocol |
Refer to the Illumina DASL Assay System Manual
|
| Description |
no additional
|
| Data processing |
For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were median-centered by subtraction of median (log2 scale) within sample and within DAP, and median set to a target value computed as the overall within DAP median. Data were then normalized using the qspline algorithm (on the log2 intensity scale) with reference distribution computed as the marginal (always within DAP) mean of every gene.
|
| |
|
| Submission date |
Jul 06, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Mark A. Rubin |
| E-mail(s) |
rubinma@med.cornell.edu
|
| Phone |
212-746-6313
|
| Organization name |
Weill Cornell Medical Center
|
| Department |
Pathology and Laboratory Medicine
|
| Lab |
Rubin
|
| Street address |
1300 York Avenue Room C 410-A
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL5474 |
| Series (1) |
| GSE8402 |
TMPRSS2-ERG fusion prostate cancer is a molecularly distinct estrogen-sensitive subclass of aggressive prostate cancer |
|
