What are the most suitable control DNA samples when performing CUT&RUN with downstream qPCR analysis?

When performing CUT&RUN with downstream qPCR analysis, one can use a normal IgG antibody enriched sample as the negative control and calculate the target-specific antibody enrichment as fold over IgG background. However, the IgG sample typically contains extremely small amounts of DNA and is not a good indicator for how well your target-specific antibody is working in the assay. Therefore, we recommend generating and using an input chromatin DNA sample as well, as described in the protocol of our CUT&RUN Assay Kit #86652. This way, you can express the target-specific antibody DNA enrichment as a percent of the total input DNA and directly determine how well the target-specific antibody is working in the assay.

Last updated: March 13, 2023