For new targets and cell types, optimize CUT&RUN workflows as described in Figure 1. CUT&RUN success depends on many factors, including cell type, cell number, target abundance, and antibody quality.
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 1. Development and optimization guides for successful CUT&RUN workflows.