What types of beads should I use to capture the immunoprecipitated DNA?
There are two competing platforms for ChIP based on what type of beads one uses for immunoprecipitation: agarose protein-A/protein-G beads or magnetic latex immunoglobulin beads. Due to the inherent porosity of the agarose beads, a significant amount of nonspecific DNA binding is observed and consequently a much higher ChIP DNA yield than with magnetic latex beads. Some researchers have claimed that they observe good ChIP results without amplification using agarose beads. However, we recommend magnetic beads because we believe these beads will give much cleaner results.
