|
| Status |
Public on Mar 01, 2020 |
| Title |
IC467G_OncoScan |
| Sample type |
genomic |
| |
|
| Source name |
Lymphocyte DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral Blood Lymphocytes
tumor histology: Serous cystadenofibroma
diagnosis: Benign serous cystadenofibroma
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from tissues (epithelium and stroma) microdissected mucinous ovarian tumors 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 |
Sample name: 0004625_D03
|
| 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.
OncoScan MIP arrays were analyzed using Nexus
CEL and CHP files are provided for each sample in the study (Affymetrix SNP 6); normalized data is provided for OncoScan MIP arrays (Each sample has 5 columns: Copy A, Copy B, Copy number, Allele ratio and Allelic difference).
|
| |
|
| Submission date |
Mar 23, 2015 |
| Last update date |
Mar 01, 2020 |
| Contact name |
Kylie L Gorringe |
| E-mail(s) |
kylie.gorringe@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Research Division
|
| Lab |
Cancer Genetics Laboratory
|
| Street address |
St Andrew's Pl
|
| City |
East Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3002 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13270 |
| Series (2) |
| GSE67189 |
Molecular characterization of ovarian serous cystadenomas and fibromas [Copy number] |
| GSE67224 |
Molecular characterization of ovarian serous cystadenomas and fibromas |
|
