|
| Status |
Public on Dec 06, 2011 |
| Title |
Met28_5M [aCGH] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Soft Tissue Metastasis
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with a Wizard Genomic DNA Isolation kit (Promega) and purified by phenol/chloroform extraction
|
| Label |
Cy3
|
| Label protocol |
500 ng of tumor genomic DNA were labeled with Cy-3 and 500 ng normal reference DNA labelled with Cy-5 along with 5X Buffer, 10X dNTP and Exo-Klenow enzyme, incubated at 37C for 2 hr and 65C for 10 min. All reagents from the Agilent Genomic DNA Labeling Kit PLUS
|
| |
|
| Channel 2 |
| Source name |
Pooled genomic DNA from healthy anonymous donors
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with a Wizard Genomic DNA Isolation kit (Promega) and purified by phenol/chloroform extraction
|
| Label |
Cy5
|
| Label protocol |
500 ng of tumor genomic DNA were labeled with Cy-3 and 500 ng normal reference DNA labelled with Cy-5 along with 5X Buffer, 10X dNTP and Exo-Klenow enzyme, incubated at 37C for 2 hr and 65C for 10 min. All reagents from the Agilent Genomic DNA Labeling Kit PLUS
|
| |
|
| |
| Hybridization protocol |
Labelled tumor and normal DNA were combined together and with hybridization buffer (Agilent Oligo aCGH Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2505B scanner
Images were quantified using Agilent Feature Extraction Software (version 9.5.1.1)
|
| Description |
genomic DNA from metastatic prostate cancer
Cy3=Metastatic Prostate Tumor from Rapid Autopsy, Cy5=Pooled Male Genomic DNA
|
| Data processing |
CN data was mapped to the human genome sequence hg18 freeze and log2 intensity ratios were segmented using circular binary segmentation (CBS) to translate noisy intensity measurements into regions of equal CN (UCSF Biostatistic Core)
|
| |
|
| Submission date |
Dec 05, 2011 |
| Last update date |
Dec 06, 2011 |
| Contact name |
Terence Friedlander |
| E-mail(s) |
[email protected]
|
| Phone |
415-514-2559
|
| Organization name |
UCSF
|
| Department |
Hemotology-Oncology
|
| Lab |
Paris Lab
|
| Street address |
1450 3rd Street
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL4091 |
| Series (1) |
| GSE34174 |
Whole Genome Methylation Analysis of Metastatic Castration Resistant Prostate Cancer |
|
