How should I optimize my workflow for reduced cell inputs?
See the Figure below for optimization guidelines. Note that using low cell numbers may result in lower signal and increased background, including for control antibodies.
Lower yields may be partly due to antibody quality and target abundance, as well as reduced cell numbers. Furthermore, an antibody that works well with 500,000 cells may fail at lower inputs.
Library prep can be optimized for low yields. Deeper sequencing is often recommended.
Figure. Development and optimization guidelines for successful CUT&RUN experiments.