Protocol for genome-wide differential methylation using long-read DNA sequencing in the cortex of a mouse model of Alzheimer’s disease
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.
Authors
- Dervis A. M. Salih (ORCID: https://orcid.org/0000-0001-7651-8998)
- Ümran Yaman (ORCID: https://orcid.org/0000-0003-4469-8407)
- Hannah L. Macpherson (ORCID: https://orcid.org/0000-0002-9535-4025)
- Hermione Ugolini
- Frances Wiseman
- Paige Mumford
- Emil Gustavsson
- Jasmaine Lee
- John Hardy
Institutions
- University of Cambridge (GB)
- Istanbul University-Cerrahpaşa (TR)
- UK Dementia Research Institute (GB)
- UCL Biomedical Research Centre (GB)
- NIHR Great Ormond Street Hospital Biomedical Research Centre (GB)
- UCL Queen Square Institute of Neurology (GB)
- University College London (GB)
- Istanbul University (TR)
Publication Details
- Journal
- STAR Protocols
- Published
- 2026-10-09
- DOI
- https://doi.org/10.1016/j.xpro.2026.104827
- Primary Topic
- Epigenetics and DNA Methylation
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Institute for Health and Care Research
- University College London
- UK Dementia Research Institute
- Medical Research Council