|
| Status |
Public on Aug 26, 2022 |
| Title |
AOCS_095_1_4 |
| Sample type |
genomic |
| |
|
| Source name |
Primary Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tissue: Primary Tumor
case id: AOCS-095
cell type: high grade serous ovarian cancer
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated from frozen tissue sections using either the Gentra Puregene Tissue Kit (Qiagen), DNeasy Blood and Tissue Kit (Qiagen), or AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Illumina Infinium HD Methylation Assay
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina Infinium HD Methylation protocol
|
| Scan protocol |
Arrays were imaged using Illumina iScan using standard recommended Illumina scanner settings.
|
| Description |
Re-analysis of GSM1606897
|
| Data processing |
Methylation data quality control assessment and processing were performed using the R package minfi (v1.32.0). Probes failing detection (P > 0.01), SNP positions, and cross reactive probes (as collected in https://github.com/sirselim/illumina450k_filtering) were excluded. Data was normalized using the minfi function "preprocessFunnorm" and beta values were generated for each EPIC and 450k arrays separately. The beta values for each array were then merged by the probe ID into file "betaVals.all.txt.gz" file (i.e., union of the two arrays). To generate file "betaVals.platform_corrected_by_combat.txt.gz" (i.e., intersection of the two arrays), first only probes present in both arrays were kept and then batch corrected for platform differences using the "ComBat" function in the R package sva (v3.34.0).
|
| |
|
| Submission date |
Aug 19, 2022 |
| Last update date |
Nov 08, 2022 |
| Contact name |
Dale W Garsed |
| E-mail(s) |
dale.garsed@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan St
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE211686 |
The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer [Methylation array] |
| GSE211687 |
The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer |
|
| Relations |
| Reanalysis of |
GSM1606897 |
