Protocol for in vivo DNA-RNA hybrid immunoprecipitation, sequencing, and analysis from frozen mouse tissues

DNA-RNA hybrids (R-loops) form transiently on the genome and regulate cellular homeostasis. They also influence genome-editing outcomes, highlighting their therapeutic potential. Here, we present a protocol for high-resolution mapping of DNA-RNA hybrids from frozen mouse tissues, including genomic DNA extraction and isolation of digested DNA-RNA hybrids using the hybrid-specific S9.6 antibody. We detail procedures for processing hybrids for whole-genome sequencing to generate R-loop profiles. For details on the use of this protocol, please refer to Puzzo et al. 1