|
| Status |
Public on May 23, 2012 |
| Title |
N11 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
normal human male DNA (Promega)
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was isolated using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
1.5 - 3 ug of gDNA from prostate specimens (test channel) or Human Male Genomic DNA (Promega, reference channel), was restriction digested with AluI and RsaI, and labeled with Cy-5 (test channel) or Cy-3 (reference channel).
|
| |
|
| Channel 2 |
| Source name |
prostate tissue (radical prostatectomy specimen)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: benign prostate tissue (N)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was isolated using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions.
|
| Label |
Cy5
|
| Label protocol |
1.5 - 3 ug of gDNA from prostate specimens (test channel) or Human Male Genomic DNA (Promega, reference channel), was restriction digested with AluI and RsaI, and labeled with Cy-5 (test channel) or Cy-3 (reference channel).
|
| |
|
| |
| Hybridization protocol |
Cy-5 (test channel) and Cy-3 (reference channel) labeled DNA was purified using Microcon YM-30 columns and hybridized for 40 hours at 65o C. Post-hybridization wash was performed with acetonitrile wash and Agilent Stabilization and Drying Solution wash.
|
| Scan protocol |
Scanning was performed on an Agilent scanner Model G2505B (5 micron scan with software v7.0).
|
| Data processing |
Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (v9.5) using protocol CGH-v4_95_Feb07. For data analysis, probes on all arrays were limited to those on the 105K array. Log(2) ratios for each probe were determined as rProcessedSignal/gProcessedSignal. To remove copy number variants, all probes with log(2) values >1 or <-1 in any of the 28 benign prostate samples were excluded. The final dataset (consisting of localized prostate cancer and castrate resistant metastatic samples) was uploaded into a custom instance of Oncomine for automated copy number analysis. In Oncomine, circular binary segmentation was performed on the dataset using the DNACopy package (v1.18) available via the Bioconductor project. Agilent Probe IDs are mapped to segments and reporter values are used to generate segment values (mean of reporters). Resulting segments are mapped to hg18 (NCBI 36.1) RefSeq coordinates (UCSC refGene) as provided by UCSC (UCSC refGene, July 2009, hg18, NCBI 36.1, March 2006) and segment values are assigned to each gene. Copy number profiles were visualized using Oncomine Power Tools.
|
| |
|
| Submission date |
Feb 21, 2012 |
| Last update date |
May 23, 2012 |
| Contact name |
Scott Tomlins |
| E-mail(s) |
[email protected]
|
| Phone |
734-615-1417
|
| Organization name |
University of Michigan
|
| Department |
Pathology
|
| Lab |
Chinnaiyan Lab
|
| Street address |
1400 E. Medical Center Dr., 5410 CCGC
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL9075 |
| Series (1) |
| GSE35988 |
The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer |
|
