Protocol for genome-wide differential methylation using long-read DNA sequencing in the cortex of a mouse model of Alzheimer's disease

STAR Protoc. 2026 Oct 8;7(4):104827. doi: 10.1016/j.xpro.2026.104827. Online ahead of print.

ABSTRACT

Third-generation sequencing enables direct detection of genome-wide 5-methylcytosine without bisulfite conversion. Here, we present a protocol for generating long-read DNA sequencing from mouse cortex and performing genome-wide differential methylation analysis. We describe steps for high-molecular-weight DNA extraction, data generation, and downstream analysis. We demonstrate the workflow in the App^NL-G-F mouse model of amyloid pathology and provide a reproducible pipeline that links modified-base BAM (modBAM) files to annotated differentially methylated regions and functional enrichment results.

PMID:42853677 | DOI:10.1016/j.xpro.2026.104827