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Sample GSM6483085 Query DataSets for GSM6483085
Status Public on Aug 26, 2022
Title AOCS_080_1_9
Sample type genomic
 
Source name Primary Tumor
Organism Homo sapiens
Characteristics gender: Female
tissue: Primary Tumor
case id: AOCS-080
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 GSM1606877
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 GSM1606877

Supplementary file Size Download File type/resource
GSM6483085_9298768174_R06C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM6483085_9298768174_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data are available on Series record

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