Peer-reviewedCC BYSTAR protocols
Protocol for genome-wide differential methylation using long-read DNA sequencing in the cortex of a mouse model of Alzheimer's disease.
6 affiliations
- 1UK Dementia Research Institute at University of Cambridge, Cambridge CB2 0AH, UK; Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.
- 2Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK.
- 3Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK; Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK.
- 4UK Dementia Research Institute at UCL, Gower Street, London WC1E 6BT, UK.
- 5UK Dementia Research Institute at UCL, Gower Street, London WC1E 6BT, UK; Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK.
- 6UK Dementia Research Institute at UCL, Gower Street, London WC1E 6BT, UK; Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK. Electronic address: [email protected].
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 AppNL-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.
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BibTeX
@article{yaman2026protocol,
title = {{Protocol for genome-wide differential methylation using long-read DNA sequencing in the cortex of a mouse model of Alzheimer's disease.}},
author = {Ümran Yaman and Emil Gustavsson and Jasmaine Lee and Hermione Ugolini and Hannah Macpherson and Paige Mumford and Frances Wiseman and John Hardy and Dervis A Salih},
journal = {STAR protocols},
year = {2026},
month = oct,
doi = {10.1016/j.xpro.2026.104827},
url = {https://europepmc.org/article/MED/42853677},
note = {CC BY},
}
RIS
TY - JOUR
TI - Protocol for genome-wide differential methylation using long-read DNA sequencing in the cortex of a mouse model of Alzheimer's disease.
AU - Ümran Yaman
AU - Emil Gustavsson
AU - Jasmaine Lee
AU - Hermione Ugolini
AU - Hannah Macpherson
AU - Paige Mumford
AU - Frances Wiseman
AU - John Hardy
AU - Dervis A Salih
PY - 2026
DA - 2026/10/08
JO - STAR protocols
DO - 10.1016/j.xpro.2026.104827
UR - https://europepmc.org/article/MED/42853677
AB - 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 AppNL-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.
SN - 2666-1667
ER -