The DNA yield for my CUT&RUN experiment seems a bit low compared to what I was getting in my ChIP experiments. How can I improve the yield?

A ChIP experiment uses 4M cells per reaction while a CUT&RUN assay only uses 5K to 100K starting cells, so it is expected to see a lower DNA yield from a CUT&RUN assay than from ChIP experiments. We have found that digestion at 4C can increase not only the signal strength but also the DNA yield. DNA purification with phenol/chloroform can also increase the DNA yield but it also can increase the background, so we do not recommend it. Always start with more cells if you can, and make sure that your cells are healthy. Please note that a high specificity of the DNA sample and not a high DNA yield is what you need to pursue for a good result.
 

Last updated: February 27, 2024