Should I be concerned that my Concanavalin A beads "clump together" in some of my CUT&RUN experiments?

The Concanavalin A beads can clump together rather easily, especially when the cells become lysed. To avoid this, make sure your cells are healthy and be sure to treat them very gently during the cell wash. We also recommend limiting the room temperature incubation time of the cell suspension with the Concanavalin A beads to 5 minutes. Instead of rotating or rocking the tubes during the incubations for cell-bead binding, antibody binding, and pAG-MNase enzyme binding, you may also let the tubes rest at the appropriate incubation temperatures. This seems to help to mitigate the beads from clumping and does not have any adverse effects on the final results. With all that being said, our internal testing has shown that bead clumping does not negatively affect the final results of CUT&RUN experiments.

Last updated: July 12, 2023