Protocol for Robust Genomic Mapping of Chromatin Targets Using High-Throughput CUT&RUN

The genomic distribution of proteins that define chromatin state including transcription factors, chromatin modifiers and histone modifications, is critical for understanding gene regulation, cellular identity, and disease development. CUT&RUN assay is a powerful tool for high-resolution genomic mapping of factors that define the epigenome. Here, we present a high-throughput CUT&RUN protocol performed in 96-well plate format, from targeted DNA enrichment to high-quality library preparation, enabling reproducible, efficient, and robust genomic mapping of protein of interests and epigenomic profiling.