If you have low CUT&RUN yields (below 5 ng), there are several steps you can take to help ensure high-quality library prep.
Tips for library prep from low CUT&RUN yields
Use the CUTANA™ CUT&RUN Library Prep Kit (EpiCypher 14-1001 & 14-1002), which is specifically optimized for CUT&RUN workflows.
For CUT&RUN yields < 5 ng, use as much CUT&RUN DNA as possible library prep.
Increase number of cycles for indexing PCR to improve library yields for Bioanalyzer/TapeStation analysis and sequencing.
Remove adapter dimers when they comprise >5% of your library (% Integrated area on TapeStation analysis). High levels of adapter dimers take up valuable sequencing bandwidth. To remove adapter dimers, see our optimized protocol in the CUTANA Quick Cleanup DNA Purification Kit Manual.
Deeper sequencing (>8 million reads) is recommended to capture full read diversity.
Read duplicates may be increased by some of these strategies, but can be filtered out with Picard (broadinstitute.github.io/picard).
Caveats when using low yields for library prep
Note that ideally, you would troubleshoot low CUT&RUN yields, repeat the experiment, and then perform library prep and sequence. This will result in higher quality sequencing data compared to using ultra-low CUT&RUN yields.
However, in some cases, repeating the experiment isn’t possible. In fact, for some targets and cell types, low CUT&RUN yields are unavoidable. Although useful sequencing data can be obtained, the resulting libraries often have low concentrations with elevated adapter dimers, reduced read diversity, and low signal over background, all of which impact data quality. The tips in