What other types of controls are used in a ChIP-chip experiment?
The most common experimental control used when performing ChIP is an isotope control, such as nonspecific IgG or antibodies against GST or GFP. A potential pitfall in using these controls is that since the antibodies do not immunoprecipitate the nonspecific DNA yield is often very low. The resulting hybridization also tends to be much noisier and can result in many false positives due to amplification of trace amount of nonspecific DNA. Another, yet rare, control that is sometimes performed is a ChIP using uncrosslinked chromatin. However, many researchers prefer to perform ChIP with an antibody against the protein of interest in a cell line where the protein has been depleted (by target genetic deletion or siRNA). Alternatively, a cell line that does not express the protein of interest could be used as a negative control.
