Schematic of the ChIP-chip method. Cells are first cross-linked with formaldehyde prior to lysis and DNA fragmentation. Following fragmentation, chromatin is incubated with antibodies and subsequently immunoprecipitated with Protein A or Protein G beads, which bind to the F_c segment of the antibodies. Following elution from the beads, reversal of cross-links, and proteinase K digestion, ChIP samples are typically phenol-chloroform extracted, ethanol precipitated, and then treated with RNase A to eliminate RNA that has carried over from the immunoprecipitation. The ChIP samples and the unenriched input material are then amplified and labeled with fluorescent dyes. The ChIP sample is subsequently hybridized, along with the unenriched input, on a spotted microarray. (Reprinted with permission, © 2005 Scion Publishing Ltd.)