Are you familiar with the Epigenome's Protocols?
Bisulfite sequencing allows for precise identification of methylated cytosines within DNA. Petr Svoboda of the Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, has developed a protocol optimized for bisulfite sequencing of very small samples where the starting material is a small number of cells.
The Peter Jones lab, of the USC / Norris Comprehensive Cancer Center, has modified a histone nucleosomal footprinting strategy. Their methyltransferase-based single-promoter analysis assay allows the study the chromatin structure of individual molecules.
