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Status |
Public on May 19, 2015 |
Title |
AOCS_139_ICGC_DBDE_20130729_001 |
Sample type |
genomic |
|
|
Source name |
TumourMetastasisToDistantLocation
|
Organism |
Homo sapiens |
Characteristics |
gender: Female tissue: Tumour Metastasis To Distant Location 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).
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|
|
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.
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|
|
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 |
GPL18952 |
Series (2) |
GSE61568 |
Whole genome characterisation of chemoresistant ovarian cancer [Illumina_Omini 2.5-8_SNP] |
GSE65821 |
Whole genome characterisation of chemoresistant ovarian cancer |
|