Depending on your target, you may need to consider modifications to the CUTANA™ CUT&RUN DNA Purification protocol.
The current CUTANA™ CUT&RUN DNA Purification protocol uses a 1.4X SPRI bead ratio to capture mononucleosome-sized chromatin fragments (~140-180 bp). In EpiCypher’s experience, the majority of transcription factors, modifying enzymes, and other chromatin-associated proteins generate predominantly mononucleosome-sized fragments in CUT&RUN, and are successfully profiled using the current protocol.
However, some transcription factors and nuclear hormone receptors generate both mononucleosome- and subnucleosome-sized fragments (<120 bp). In these cases, a 1.8X volume of SPRI beads can be used to help enhance capture of smaller fragments. Additional SPRI beads are available via purchase of our CUTANA™ Quick Cleanup DNA Purification Kit (EpiCypher 14-0052). Perform Ethanol washes and elution as described in the CUT&RUN protocol.
If you routinely profile transcription factors in CUT&RUN, you may consider using our validated CTCF antibody (EpiCypher 13-2014) as a positive control, in addition to the H3K4me3 and H3K27me3 positive controls provided with the CUTANA CUT&RUN Kit.
If you are unsure what to expect for your target, reach out to EpiCypher Tech Support for guidance.