|
| Status |
Public on May 19, 2015 |
| Title |
AOCS_056_ICGC_DBPC_20130205_013 |
| Sample type |
genomic |
| |
|
| Source name |
PrimaryTumour
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tissue: Primary Tumour
cell type: high grade serous ovarian cancer
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nucleic acids were extracted from frozen tissue sections were incubated in Buffer AL and proteinase K at 56°C overnight, while ascites cells were only incubated in Buffer AL and proteinase K at 56°C for 10min. Ethanol was added to sample which was applied to a DNeasy Mini spin column. Captured DNA was washed and eluted in Buffer AE. DNA was quantitated using the NanoDrop1000 (Thermo Scientific) and the Qubit® dsDNA BR assay.
|
| Label |
cy3/cy5
|
| Label protocol |
DNA was assayed using Illumina SNP BeadChips as per manufacturer’s instructions (Illumina, San Diego CA) (HumanOmni2.5-8 BeadChips).
|
| |
|
| Hybridization protocol |
As per manufacturer’s instructions (Illumina, San Diego CA)
|
| Scan protocol |
Arrays were scanned on iScan
|
| Description |
Raw data for arrays used for copy number analysis using GAP (Popova, et al 2009)
|
| Data processing |
Data was extracted using Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina, San Diego CA) to calculate B-allele frequencies (BAF) and LogR ratios.
|
| |
|
| Submission date |
Sep 19, 2014 |
| Last update date |
May 19, 2015 |
| Contact name |
Ann-Marie Patch |
| E-mail(s) |
ann-marie.patch@qimrberghofer.edu.au
|
| Organization name |
QIMR Berghofer Medical Research Institute
|
| Street address |
300 Herston Road
|
| City |
Herston |
| State/province |
QLD |
| ZIP/Postal code |
4006 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16104 |
| Series (2) |
| GSE61568 |
Whole genome characterisation of chemoresistant ovarian cancer [Illumina_Omini 2.5-8_SNP] |
| GSE65821 |
Whole genome characterisation of chemoresistant ovarian cancer |
|
