|
| Status |
Public on Mar 01, 2015 |
| Title |
4836T |
| Sample type |
genomic |
| |
|
| Source name |
Serous ovarian tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Tumor epithelium
tumour histology: SEROUS
diagnosis: BORDERLINE
somatic ras/raf mutations: BRAF p.V600E
age at diagnosis: 42
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from tissues (epithelium and stroma) microdissected mucinous ovarian tumours stained with haematoxylin and eosin, and from lymphcoytes obtained from peripheral blood (for matched normal DNA) using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Qubit.
|
| Label |
BIOTIN
|
| Label protocol |
As per manufacturer's recommendations (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
HYBRIDISED TO SNP6
|
| Data processing |
CHP files were generated using the Affymetrix Genotyping Console algorithm Birdseed v2. Total and allele-specific copy number analysis was performed using Partek Genomics Suite 6.5, using both paired copy number generation.
|
| |
|
| Submission date |
Jun 17, 2014 |
| Last update date |
Mar 01, 2015 |
| Contact name |
Sally Hunter |
| E-mail(s) |
Sally.Hunter@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Research
|
| Lab |
Cancer Genetics
|
| Street address |
7 St Andrew's Pl
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3002 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE58579 |
High-resolution genome-wide copy number analysis of low grade serous ovarian tumours |
|
