|
| Status |
Public on May 19, 2015 |
| Title |
AOCS_163_ICGC_DBDE_20130904_017 |
| Sample type |
genomic |
| |
|
| Source name |
Primarytumour
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tissue: Primarytumour
cell type: high grade serous ovarian cancer
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from fresh frozen tissues using AllPrep DNA/RNA Mini Kit (Qiagen). Genomic DNA (500ng) was bisulfite converted using EZ DNA methylation Kit (Zimo Research) following the manufacturer’s protocol with modification for Illumina Infinium Methyaltion arrays
|
| Label |
cy3/cy5
|
| Label protocol |
Bisulfite converted genomic DNAwas whole genome amplified and labeled using Illumina protocol
|
| |
|
| Hybridization protocol |
Samples were hybridized to Infinium Human Methylation 450K BeadChips (Illumina) according to the manufacturer’s protocol.
|
| Scan protocol |
Arrays were scanned on Iscan (Illumina)
|
| Description |
Raw data for arrays used for methylation analysis
|
| Data processing |
Data was background corrected, normalized to internal controls and QC was performed at the probe and sample level. COMBAT was used to remove batch effects (Johnson et al., 2007)
|
| |
|
| Submission date |
Feb 10, 2015 |
| Last update date |
Aug 19, 2022 |
| 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 |
GPL13534 |
| Series (2) |
| GSE65820 |
Whole genome characterisation of chemoresistant ovarian cancer [Illumina_450K_Methylation] |
| GSE65821 |
Whole genome characterisation of chemoresistant ovarian cancer |
|
| Relations |
| Reanalyzed by |
GSM6483135 |
