|
| Status |
Public on Jun 24, 2010 |
| Title |
Prostate tumor PCA0171 (aCGH) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
tumor DNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: PCA0171
tissue: prostate
disease status: prostate cancer
tumor type: Primary tumor
biopsy_gleason_grade: 6
clint_stage: T2A
pathological_stage: T3A
|
| 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 |
|
