Quantitative real time PCR analyses of ChIP experiments. ChIP experiments were performed using antibodies targeted to H3 trimethyl-K9 (condensed/inactive chromatin: mid columns), H3 trimethyl-K4 (open/active chromatin: right handed columns) or using a control IgG (left handed columns). The percentage of either pEPI-1 (gray columns) or the linearized control vector (striped columns) precipitated from input was quantified using real time PCR. Since no significant amount of the vector molecules was pulled down with the control IgG, it could be clearly demonstrated that about 30 times more vector molecules were precipitated using the anti-H3 trimethyl-K9 antibody in a precipitate from cells containing the integrated vector compared to cells containing the vector in its episomal form. When the same chromatin preparations were precipitated with an antibody directed against H3 trimethyl-K4 over 20 times more vector molecules were obtained from cells containing the episome compared to cells containing the integrated vector.