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Series GSE86831 Query DataSets for GSE86831
Status Public on Sep 12, 2016
Title Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [MethylationEPIC]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary We performed a critical evaluation of the new Infinium MethylationEPIC BeadChip microarray. EPIC covers over 850,000 CpG sites, including >90% of the CpGs from the HumanMethylation450 (HM450) BeadChip and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58% of FANTOM5 enhancers, only 7% distal and 27% proximal ENCODE regulatory elements are represented. Detailed comparisons of regulatory elements from EPIC and whole-genome bisulphite sequencing data (WGBS) show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region. However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform.
 
Overall design To assess the performance of the EPIC array we ran a series of technical analyses using DNA from different samples types (cell lines, clinical samples and blood) commonly profiled in array-based methylation studies: a transformed prostate cancer cell line (LNCaP); primary cell cultures of prostate epithelial cells (PrEC); patient-matched cancer associated fibroblasts (CAF) and non-malignant tissue associated fibroblasts (NAF); and infant blood from archival Guthrie cards. We first profiled the DNA on both the HM450 and EPIC arrays. LNCaP and PrEC samples were also profiled with WGBS.
 
Contributor(s) Zotenko E, Pidsley R, Peters TJ, Clark SJ
Citation(s) 27717381
Submission date Sep 12, 2016
Last update date Jan 20, 2019
Contact name Ruth Pidsley
E-mail r.pidsley@garvan.org.au
Organization name Garvan Institute of Medical Research
Street address 384 Victoria Street
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (15)
GSM2309170 LNCaP Rep1
GSM2309171 LNCaP Rep2
GSM2309172 PrEC Rep1
This SubSeries is part of SuperSeries:
GSE86833 Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling
Relations
BioProject PRJNA342658

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE86831_RAW.tar 372.7 Mb (http)(custom) TAR (of IDAT)
GSE86831_epic_processed.txt.gz 57.1 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table
Processed data is available on Series record

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