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Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

ABSTRACT: Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

PROVIDER: PRJNA342654 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4238610_1.fastq.gz	Fastqsanger.gz
	SRR4238610_2.fastq.gz	Fastqsanger.gz
	SRR4238611_1.fastq.gz	Fastqsanger.gz
	SRR4238611_2.fastq.gz	Fastqsanger.gz
	SRR4238612_1.fastq.gz	Fastqsanger.gz

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Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [MethylationEPIC]

Project description: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.

2016-09-12 | GSE86831 | GEO

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [WGBS]

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Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [HumanMethylation450]

2016-09-12 | GSE86829 | GEO

Evaluating The Infinium Human MethylationEPIC v2 BeadChip

Project description:We conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility.

2023-07-04 | GSE228820 | GEO

Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of 12 different growing teratoma tissues. Samples were subgrouped based on growth speed into GTSslow to GTSrapid (see corresponding publication).

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Illumina Infinium MethylationEPIC BeadChip (850k) data of germ cell tumor-related somatic-type maligancies

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of germ cell tumor related somati-type malignancies (STM), i. e. adenocarcinomas and rhabdomyosarcomas. As controls, yolk-sac tumors and teratoma without STM population were included.

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Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-09-12 | GSE86833 | GEO

Distinguishing active versus passive DNA demethylation using Illumina MethylationEPIC BeadChip microarrays

Project description:Distinguishing active versus passive DNA demethylation using Illumina MethylationEPIC BeadChip microarrays

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Illumina Infinium MethylationEPIC BeadChip (850k) data of NCCIT / 2102EP cells deficient for CD24 and parental controls

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of embryonal carcinoma cell lines NCCIT and 2102EP deficient for CD24 and parental cells. CD24 deficiency was genereted by CRISPR/Cas9 method. Three different NCCIT and 2102EP knock out clones were analyzed.

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Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays.

Project description:The 5-carbon positions on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). DNA methylation removal can occur through both active and passive mechanisms. Ten-eleven translocation enzymes (TETs) oxidize 5mC in a stepwise manner to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC can also be removed passively through sequential cell divisions in the absence of DNA methylation maintenance. In this chapter, we describe approaches that couple TET-assisted bisulfite (TAB) and oxidative bisulfite (OxBS) conversion to the Illumina MethylationEPIC BeadChIP (EPIC array) and show how these technologies can be used to distinguish active versus passive DNA demethylation. We also describe integrative bioinformatics pipelines to facilitate this analysis.

| S-EPMC8265207 | biostudies-literature

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