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Genome Biol. 2010;11(4):R36. doi: 10.1186/gb-2010-11-4-r36. Epub 2010 Apr 1.

Optimized design and data analysis of tag-based cytosine methylation assays.

Author information

  • 1Department of Genetics (Computational Genetics), Center for Epigenomics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA.

Abstract

Using the type III restriction-modification enzyme EcoP15I, we isolated sequences flanking sites digested by the methylation-sensitive HpaII enzyme or its methylation-insensitive MspI isoschizomer for massively parallel sequencing. A novel data transformation allows us to normalise HpaII by MspI counts, resulting in more accurate quantification of methylation at >1.8 million loci in the human genome. This HELP-tagging assay is not sensitive to sequence polymorphism or base composition and allows exploration of both CG-rich and depleted genomic contexts.

PMID:
20359321
[PubMed - indexed for MEDLINE]
PMCID:
PMC2884539
Free PMC Article

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