|
Status |
Public on Dec 19, 2011 |
Title |
Prostate tumor 2 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Prostate cancer tissue
|
Organism |
Homo sapiens |
Characteristics |
pre-psa: 8.4 tumor stage: T3a gleason grade: 4+4 psa recurrence-free survival event: 0 psa recurrence-free survival months: 0.033 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 648T
|
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 |
|