I am working on standardizing my ChIP assay using a cancer cell line, but I am not seeing improvement in my results. The problem is that after PCR, the band intensity for the IgG control is same as the band intensity for the experimental IP (Antibody IP). However, the input sample shows a strong, clear band, as expected. I’ve tried increasing the number of washes from 5 to 8 and then to 10 with both low and high salt buffers, and I’ve also changed the promoter region and used new sets of primers. I do get proper results with positive control sets where the transcription factor I am studying is known to bind. My issue lies in getting reliable binding data for my selected transcription factor on the specific gene promoter region I am interested in.