Methodology study demonstrates an optimized MCSeEd protocol for partially degraded plant DNA, suggesting improved epigenomic profiling across diverse plant samples.
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.
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Herrero-González et al. (2026) studied this question.
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