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Homo sapiens

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

PROVIDER: PRJNA342657 | 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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Homo sapiens

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

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

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

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Homo sapiens

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

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

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.

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

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Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis

Project description:We compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study's aims and the available resources in the laboratory

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Project description:DNA methylation data generated by the Illumina Mouse Methylation Beadchip for comparison to WGBS

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