I have been performing ChIP assays for a few years and I have always used input and IgG as controls for my experiments. I am actually collaborating with some people who would like to study if their protein of interest (which is not a transcription factor) is recruited onto consensus sequences specific for some TFs. I will have to preform ChIP experiments (we'll evaluate if re-ChIP is needed later on) on bone marrow cells derived from mice. According to our calculations, they will have to sacrifice about 20 mice for each antibody I'm using. They have both wild-type and complete knockout mice for our protein of interest. Now my question is: Do you think I need to perform IgG immunoprecipitation as a negative control or could I immunoprecipitate with my antibody of interest in complete knockout cells and use it as a negative control instead of IgG?
If I think about it, the two strategies should in theory be equivalent but would reviewers accept these experiments? What do you think about it?
Thanks in advance,