|
| Status |
Public on Sep 26, 2011 |
| Title |
A17 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Mesothelioma tumor, epi
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: malignant pleural mesothelioma (MPM)
subtype: epi
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Standard Agilent Cy5/Cy3 labeling protocols were used with 3ug of DNA.
|
| |
|
| Channel 2 |
| Source name |
Promega normal reference
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: normal
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Standard Agilent Cy5/Cy3 labeling protocols were used with 3ug of DNA.
|
| |
|
| |
| Hybridization protocol |
Labelled cDNA was hybridized to the arrays at 20rpm at 65C for 40 hours following Agilent instructions.
|
| Scan protocol |
Slides were scanned using the Agilent Scanner with the standard protocols.
|
| Description |
Genomic DNA from an MPM tumor for aCGH analysis.
|
| Data processing |
The normalization is done through gcNormalization developed at MSKCC (http://cbio.mskcc.org/CGCC/methods_091022.pdf). The 'methods_091022.pdf' file is also linked to the Series record as a supplementary file.
|
| |
|
| Submission date |
Jun 10, 2011 |
| Last update date |
Sep 26, 2011 |
| Contact name |
Yupu Liang |
| E-mail(s) |
liangy@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Street address |
1230 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL9128 |
| Series (2) |
| GSE29211 |
The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma |
| GSE29902 |
Mesothelioma tumor aCGH profiles |
|
