| Temperature | Time | Cycles |
| 98 °C | 30 sec | 1 |
| 98 °C | 10 sec | 10–16* |
| 65 °C | 45 sec | |
| 65 °C | 5 min | 1 |
| 4 °C | Hold | |
*
Cycle number should be adjusted
based on experimental results, including quantity
of library obtained and CUT&RUN profile
generated. We typically use 14 cycles for
3–15 ng input DNA. Increasing cycles may
result in excessive PCR duplicates, which show up
as duplicated sequences in the data analysis, and
may decrease data quality. Too few cycles would
result in insufficient DNA quantities to sequence
at the end of the protocol. In general, the fewer
cycles the better, but enough cycles must be run
to produce enough DNA for sequencing.