Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: ReducedRepresentation : Focussing reduced representation CpG sequencing through judicious restriction enzyme choice      
keywords:
Other
ID:
PRJEB12622
description:
Current restriction enzyme based reduced representation methylation analyses aim for limited, but unbiased, methylome coverage. Since only ~20% of CpGs are dynamically regulated, we characterised the CpG and genomic context surrounding all suitable restriction enzyme sites to identify those that were located in regions rich in dynamically methylated CpGs. The restriction-site distributions for MspI, BstUI, and HhaI were non-random. CpGs in CGI and shelf+shore could be enriched, particularly in gene bodies for all genomic regions, promoters (TSS1500, TSS200), intra- (1st exon, gene body, 3’UTR, 5’UTR) and inter-genic regions. HpyCH4IV enriched CpG elements in the open sea for all genomic elements. Judicious restriction enzyme choice improves the focus of reduced representation approaches by avoiding the monopolization of read coverage by genomic regions that are irrelevant, unwanted or difficult to map, and only sequencing the most informative fraction of CpGs.
accesstypes:
download
landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJEB12622
authentication:
none
authorization:
none
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject