What should I do if I have low CUT&RUN yields (below 5ng)?
Low CUT&RUN DNA yields are common for low abundance targets (e.g. H3K4me3), but also depend on the number/quality of starting cells, cell type, and antibody performance. If you are consistently generating low yields for experimental targets:
- Review Basic CUT&RUN troubleshooting guidelines and be sure to always include all QC checks outlined in the Figure below. Pay careful attention to the quality and count of your cells during sample prep and avoid ConA bead dry out, which causes sample loss.
- Include H3K4me3 and IgG control reactions. If these controls work but experimental targets fail, confirm that your target is correctly localized to chromatin (e.g. stimulation conditions) and test additional antibodies and/or cross-linking conditions.
- If the experiment cannot be repeated, use the total amount of CUT&RUN-enriched DNA for library prep. See the CUTANA™ CUT&RUN Library Prep Kit manual for guidance.
NOTE: For some targets and cell types, low CUT&RUN yields are unavoidable. For guidance on these situations, see this article.
Figure. Quality control metrics for each step of the CUTANA CUT&RUN kit.