Protocol for optimized methylation context-sensitive enzyme ddRAD library preparation from partially degraded genomic plant DNA.

Here, we present an optimized methylation context-sensitive enzyme ddRAD (MCSeEd) library-preparation protocol for methylation analysis in CG, CHG, and CHH sequence contexts from plant samples that yield low-quality or partially degraded genomic DNA. We describe steps for quadruple restriction-enzyme digestion and adapter ligation, double size selection, freeze-and-squeeze gel purification, and bead-based cleanup. We then detail a two-step PCR enrichment procedure to generate Illumina-compatible epigenomic libraries.