This method is modified from that described by\u00a0Nakatani Y, Ogryzko V. Immunoaffinity purification of mammalian protein complexes. Methods Enzymol. 2003;370:430-44. Epub 2004\/01\/10. doi: 10.1016\/S0076-6879(03)70037-8\u00a0S0076687903700378 [pii]. PubMed PMID: 14712665. It can be used to immunopurify proteins from nuclear extract through 2 sequential rounds of immunoprecipitation. Non-specific interactions are largely eliminated. This protocol is described for Flag, then HA immunoaffinity, but can be adapted for use with other epitopes.