|
| Status |
Public on Dec 19, 2011 |
| Title |
Prostate tumor 29 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Prostate cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
pre-psa: 4.42
tumor stage: T3a
gleason grade: 4+5
psa recurrence-free survival event: 1
psa recurrence-free survival months: 19.13
Stage: T3a
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the Qiagen Allprep DNA/RNA minikit
|
| Label |
Cy5
|
| Label protocol |
1.5ug of genomic DNA was digested with DpnII for 1.5 hrs at 37C, then labeled with C5 (test) or Cy3 (reference) using the BioPrime array CGH Genomic Labeling Module
|
| |
|
| Channel 2 |
| Source name |
normal male reference DNA (pooled from eight donor leukocyte preps)
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the Qiagen Allprep DNA/RNA minikit
|
| Label |
Cy3
|
| Label protocol |
1.5ug of genomic DNA was digested with DpnII for 1.5 hrs at 37C, then labeled with C5 (test) or Cy3 (reference) using the BioPrime array CGH Genomic Labeling Module
|
| |
|
| |
| Hybridization protocol |
Oligo aCGH hybridization buffer (Agilent) were added along with 50ug Human Cot-1 DNA and 100ug Yeast tRNA, denatured by boiling for 2 mins, incubated at 37C for 30mins, and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.
|
| Scan protocol |
Scanned on an Agilent G2505C scanner.
|
| Description |
PC 19T
|
| Data processing |
Agilent Feature Extraction (v.9.5.3) was used to quantify and normalize the data.
|
| |
|
| Submission date |
May 11, 2011 |
| Last update date |
Dec 19, 2011 |
| Contact name |
Stephanie Huang |
| E-mail(s) |
shuang1@stanford.edu
|
| Phone |
6507361989
|
| Fax |
6507360073
|
| Organization name |
Stanford University
|
| Department |
Pathology
|
| Lab |
Pollack
|
| Street address |
269 Campus Drive, CCSR 3240
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL5477 |
| Series (2) |
| GSE29227 |
aCGH profiling of prostate tumors |
| GSE29229 |
Identification of the tumor suppressor gene at chromosome 5q21 |
|
