What is the expected CUT&RUN DNA yield when starting with extremely low cell numbers, such as 5,000 - 10,000 cells?

If you start with 100,000 cells, you typically get 0.6-6ng DNA. However, if you start with 5,000 - 10,000 cells, the DNA yield can be as low as 0.1-0.2 ng or even undetectable by the picogreen assay. In this case, we suggest you directly proceed with library prep using 20 PCR amplification cycles, which will result in a library DNA with a concentration of around 10-30 ng/ul. QC of the CUT&RUN DNA by qPCR can be performed on the library DNA if you hope to save as much CUT&RUN DNA as possible for the library prep.
 

Last updated: October 6, 2025