|
Status |
Public on Jun 24, 2010 |
Title |
Prostate tumor PCA0042 (aCGH) |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
tumor DNA
|
Organism |
Homo sapiens |
Characteristics |
sample id: PCA0042 tissue: prostate disease status: prostate cancer tumor type: Primary tumor biopsy_gleason_grade: 6 clint_stage: T2C pathological_stage: T4
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genome DNA was extracted from all samples with standard proteinase K digestion and phenol/chloroform extraction.
|
Label |
Cy5
|
Label protocol |
Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5
|
|
|
Channel 2 |
Source name |
adjacent normal prostate DNA
|
Organism |
Homo sapiens |
Characteristics |
tissue: prostate disease status: normal
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genome DNA was extracted from all samples with standard proteinase K digestion and phenol/chloroform extraction.
|
Label |
Cy3
|
Label protocol |
Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5
|
|
|
|
Hybridization protocol |
Per manufacturer's instructions
|
Scan protocol |
Per manufacturer's instructions
|
Description |
DNA copy number
|
Data processing |
Images quantified with Agilent Feature Extraction ver9.1. Probe sequences were re-mapped to the hg18 build of the human genome and merged. Probe-level data was subsequently normalized for local GC content with a two-stage LOESS fit. Probe-level data is the log2 ratio of tumor-to-normal.
|
|
|
Submission date |
Mar 24, 2010 |
Last update date |
Jun 15, 2010 |
Contact name |
Barry Stephen Taylor |
Organization name |
Memorial Sloan-Kettering Cancer Center
|
Street address |
1275 York Avenue, Box #460
|
City |
New York |
State/province |
NY |
ZIP/Postal code |
10065 |
Country |
USA |
|
|
Platform ID |
GPL4091 |
Series (2) |
GSE21032 |
Integrative genomic profiling of human prostate cancer |
GSE21035 |
Agilent 244K aCGH data for human primary and metastatic prostate cancer samples |
|