QuestionsCategory: ChIP-Seq Data AnalysisLibrary/ChIP preparation: What if my antibody has low binding affinity and there isn’t a better option available?
stonelakeak@nih.gov Staff asked 10 months ago

What if my antibody has low binding affinity and there isn’t a better option available?

1 Answers
stonelakeak@nih.gov Staff answered 10 months ago

If when talking about low binding affinity you mean that the interaction between your protein of interest and its antibody is poor, you can try to make a library and sequence it but it is possible that the ChIP method is not appropriate for your protein/antibody pair. If you are worried about having a high background, you can test this and theoretically control for it by doing ChIP-seq in a cell where there should no binding. Please keep in mind that sometimes the inability to make a library is the result of a lack of antibody targets rather than an issue in library construction. – answered by Tovah Markowitz, Paul Schaughency, Vishal Koparde.