My antibody works for ChIP but when I tried it in CUT&RUN, the results were variable. Why?

Both ChIP and CUT&RUN are looking at protein-DNA interactions, but they are very different assays. For example, the microenvironment of the reaction is different. In ChIP, the chromatin is fragmented and released into ChIP buffer for IP, while in CUT&RUN, the digestion happens in the intact nuclei. ChIP often uses fixed cells while CUT&RUN often uses live cells. Our internal validation tests show that only around 70% of ChIP or ChIP-seq validated antibodies work well in CUT&RUN. On the other hand, some antibodies that failed ChIP or ChIP-seq validation work well in CUT&RUN. Therefore, we strongly recommend using a CUT&RUN validated antibody for your assay. If you cannot find one for your target of interest, we suggest using a ChIP/ChIP-seq or IF validated antibody, as they have a higher chance of working in the CUT&RUN assay.
 

Last updated: March 15, 2023