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. 2012 Jun;4(3):317-24.
doi: 10.2217/epi.12.18.

The NIH Roadmap Epigenomics Program data resource

Lisa Helbling Chadwick  1
Affiliations

The NIH Roadmap Epigenomics Program data resource

Lisa Helbling Chadwick. Epigenomics. 2012 Jun.

Abstract

The NIH Roadmap Reference Epigenome Mapping Consortium is developing a community resource of genome-wide epigenetic maps in a broad range of human primary cells and tissues. There are large amounts of data already available, and a number of different options for viewing and analyzing the data. This report will describe key features of the websites where users will find data, protocols and analysis tools developed by the consortium, and provide a perspective on how this unique resource will facilitate and inform human disease research, both immediately and in the future.

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Figures

Figure 1
Figure 1. The NIH Roadmap Epigenomic Mapping Consortium homepage
Users interested in browsing data, protocols and other program resources should start here, at the consortium homepage. This site also links to additional program websites, which each offer unique features for data viewing or analysis [103].
See this image and copyright information in PMC

References

    1. Bernstein BE, Stamatoyannopoulos JA, Costello JF, et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol. 2010;28(10):1045–1048. - PMC - PubMed

    2. ■■White paper describing the scope and goals of the NIH Roadmap Epigenomic Mapping Consortium.

    1. Bock C, Tomazou EM, Brinkman AB, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol. 2010;28(10):1106–1114. - PMC - PubMed

    2. ■A comprehensive comparison of the data generated by four popular platforms for genome-wide DNA methylation analyses, highlighting the strengths and limitations of each technology. This will be of particular interest for investigators planning their own genome-wide DNA methylation studies.

    1. Meissner A, Gnirke A, Bell GW, Ramsahoye B, Lander ES, Jaenisch R. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res. 2005;33(18):5868–5877. - PMC - PubMed
    1. Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466(7303):253–257. - PMC - PubMed
    1. Lister R, Pelizzola M, Dowen RH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462(7271):315–322. - PMC - PubMed

    2. ■Describes the first human DNA methylomes.

Websites

    1. NIH Common Fund Epigenomics Program. http://commonfund.nih.gov/epigenomics.
    1. Protocols and Data Standards on the Consortium homepage. www.roadmapepigenomics.org/protocols.
    1. Reference Epigenome Mapping Consortium homepage. http://roadmapepigenomics.org.
    1. Epigenomics mirror of UCSC Genome Browser. www.epigenomebrowser.org.
    1. Roadmap Epigenomics Program data at GEO. www.ncbi.nlm.nih.gov/geo/roadmap/epigenomics. - PMC - PubMed