|
| Status |
Public on Jun 10, 2008 |
| Title |
Patient 025 Core Set (custom panel) |
| Sample type |
RNA |
| |
|
| Source name |
primary prostate cancer
|
| Organism |
Homo sapiens |
| Characteristics |
Case-Control Group: Systemic
Training or Validation: val
Age (yrs) at RRP: 71
PSA (ng/ml) at RRP: 8.4
Revised Gleason Score: 8
Stage: T2N0
Ploidy: tetraploid
First Rising PSA (ng/ml): 0.2
Time (yrs) from RRP to first rising PSA: 0.213552361396304
Second Rising PSA (ng/ml): 0.9
Time (yrs) from RRP to second rising PSA: 0.479123887748118
PSA Slope (ng/ml/yr): 2.63582474226804
Time (yrs) from PSA recurrence to systemic disease: 2.12183436002738
Years of Followup after RRP: 4.93908281998631
patient's status: Deceased
Prostate cancer specific death: No
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Four freshly cut 10 micron sections of FFPE tissue were deparaffinized and the Gleason dominant cancer focus was macrodissected. RNA was extracted using the High Pure RNA Paraffin Kit from Roche (Indianapolis, IN).
|
| Label |
cy3, cy5
|
| Label protocol |
cy3, cy5 labeling was performed in accordance with the manufacturer's instructions
|
| |
|
| Hybridization protocol |
hybridization was performed in accordance with the manufacturer's instructions
|
| Scan protocol |
Arrays were scanned using Illumina's BeadArray Reader
|
| Description |
TNPr-025
|
| Data processing |
Illumina's Bead Studio Software using no normalization was used to process the image files. The raw data was then normalized using cyclic loess (fastlo). The normalized value for the probes was averaged to determine the expression level for the gene. The DASL method labels each sample with a mixture of CY3 and Cy5. Only a single sample is applied to each array. The scanner measures fluorescence of both Cy3 and Cy5. This data is contained in the red and grn files for each sample. The bead studio software averages the red and green signals to provide a single value for the expression of a particular probe.
|
| |
|
| Submission date |
Feb 26, 2008 |
| Last update date |
Jun 10, 2008 |
| Contact name |
Robert B. Jenkins |
| E-mail(s) |
rjenkins@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Department |
Laboratory Medicine and Pathology
|
| Street address |
200 First Street SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL5873 |
| Series (1) |
| GSE10645 |
Focused gene expression microarray of tumors from 596 men with prostate cancer using RNA from archival FFPE tissue |
|
