A method of analyzing DNA which, in a cell, is bound to a DNA binding moiety, the method comprising: (a) obtaining at least two samples of complexes of DNA bound to a DNA binding moiety; (b) isolating the complexes on a solid support; (c) labeling the DNA of the complexes, wherein the labeling distinguishes between the complexes of the first of the at least two samples and the complexes of the second of the at least two samples; (d) pooling the at least two samples of complexes; and (e) isolating the complexes using an agent which specifically binds to the DNA binding moiety; and (f) analyzing the DNA of the complexes.