What is the most suitable control DNA sample for my CUT&RUN NG-seq experiment?

When performing CUT&RUN with downstream NG-seq analysis, one can use a normal IgG antibody enriched sample as the negative control. However, we have seen and heard from other scientists that normal IgG antibodies generate very low diversity DNA libraries and can generate what looks to be specific enrichment of genomic regions in the CUT&RUN assay, complicating your NG-seq data analysis. Instead, we recommend generating and using an input chromatin DNA sample as described in the protocol of our CUT&RUN Assay Kit #86652. This input DNA sample generates a more diverse DNA library and works better as a negative control for analysis by NG-seq.

Last updated: October 6, 2025