CUT&RUN Assays

CUT&RUN reagents for genome-wide protein-DNA binding maps from low cell input

When you need ChIP-seq-style genome-wide protein-DNA binding maps from low cell input with cleaner background and shorter protocol, CUT&RUN uses a protein-A-MNase fusion targeted by primary antibody to release short DNA fragments around binding sites. Works from as few as 5,000 cells.

Pick by enzyme and input.

1. Enzyme platform. pA-MNase is original CUT&RUN. pAG-MNase recognises broader IgG species range.
2. Cell input. CUT&RUN works from 5,000 cells. Optimised kits go lower.
3. Antibody validation. Poor antibody quality is the main failure mode. Use SNAP-CUTANA spike-in controls before scaling.
4. Bridge antibodies. For uncommon IgG species improve pA-MNase binding.
5. Bioinformatics. Standard ChIP-seq pipelines work; minor parameter adjustments for shorter fragments.

EpiCypher dominates with CUTANA kits, SNAP-CUTANA spike-in controls, and validated antibody panels.