We assayed chromosomal locations for up to 12 histone modifications and variants in 46 cell types, including a complete matrix of eight modifications across Tier 1 and Tier 2. Because modification states may span multiple nucleosomes, which themselves can vary in position across cell populations, we used a continuous signal measure of histone modifications in downstream analysis, rather than calling regions (M.M. Hoffman et al., manuscript in preparation, http://code.google.com/p/align2rawsignal/). For the strongest, “peak-like” histone modifications, we used MACS 35 to characterize enriched sites. Table 2 describes the different histone modifications, their peak characteristics, and a summary of their known roles (reviewed in refs36–39).
