Tips for wide-scale epigenetic detection

Every assay has strengths and weaknesses, so it's a good idea to try more than one, if possible. ChIP-on-chip is significantly cheaper than ChIP-Seq, but unless you tile the entire genome, you will miss any region not represented on your chip. HELP probes only a fraction of the genome, but a genome's worth of testable HpaII fragments will fit on a single array, making analysis relatively inexpensive. (Greally now uses a 1.32-million element Nimblegen array.) You can use other assays (not described here) to double-check your results (see #2).