I was tring to check the differential binding/association of my protein to genes using mutant S. pombe. For this, I used a Flag tagged normal strain and a Flag tagged mutant strain. I did culture, sonicatiion, ChIP and qPCR of these strains in parallel, but I found variation in enrichment in terms of percentage input. For example, the mutant strain is expected to increase signal in binding site but I get different result (sometimes increase/sometimes decrease) while I am repeating experiment. I rather expect a constant trend compared to normal tagged strain.

Which parameters/aporoaches could help me to get consistent result?