Hello, I recently prepared CUT&RUN libraries using two different antibodies. I also performed ChIP with streptavidin beads as a control. I tested my CUT&RUN libraries and ChIP DNA using qPCR with primers I designed for certain regions of interest. While ChIP-qPCR showed enrichment in the loci of interest, the CUT&RUN libraries, regardless of the sample (IgG control, antibody treated, basically all controls and actual samples) or the primers (again all controls), all Ct values are almost the same, near 23-25. What do you think could be the reason here?

I did CUT&RUN using 500,000 nuclei, and used NEBNext® Ultra™ II DNA Library Prep Kit to prepare the libraries. I used EpiCypher's CUT&RUN kit and protocol.