{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "UK 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.",
    "Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK.",
    "Department 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.",
    "UK Dementia Research Institute at UCL, Gower Street, London WC1E 6BT, UK.",
    "UK 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.",
    "UK 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: dervis.salih@ucl.ac.uk."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 9,
  "authors": [
    {
      "name": "Ümran Yaman",
      "orcid": "0000-0003-4469-8407"
    },
    {
      "affs": [
        0
      ],
      "name": "Emil Gustavsson"
    },
    {
      "affs": [
        1
      ],
      "name": "Jasmaine Lee"
    },
    {
      "affs": [
        1
      ],
      "name": "Hermione Ugolini"
    },
    {
      "affs": [
        2
      ],
      "name": "Hannah Macpherson"
    },
    {
      "affs": [
        3
      ],
      "name": "Paige Mumford"
    },
    {
      "affs": [
        3
      ],
      "name": "Frances Wiseman"
    },
    {
      "affs": [
        4
      ],
      "name": "John Hardy"
    },
    {
      "affs": [
        5
      ],
      "name": "Dervis A Salih",
      "orcid": "0000-0001-7651-8998"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8vybbetmbk038.bib",
  "cited_by": 0,
  "doi": "10.1016/j.xpro.2026.104827",
  "fulltext_url": "https://europepmc.org/articles/PMC13675703",
  "id": "8vybbetmbk038",
  "issns": [
    "2666-1667"
  ],
  "landing_url": "https://europepmc.org/article/MED/42853677",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [],
  "openalex": null,
  "pdf_url": "https://europepmc.org/articles/PMC13675703?pdf=render",
  "pmcid": "PMC13675703",
  "pmid": "42853677",
  "published": "2026-10-08",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/8vybbetmbk038.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:12Z",
      "native_id": "MED:42853677",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42853677"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "journal-openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Protocol for genome-wide differential methylation using long-read DNA sequencing in the cortex of a mouse model of Alzheimer's disease.",
  "title_text": "Protocol for genome-wide differential methylation using long-read DNA sequencing in the cortex of a mouse model of Alzheimer's disease.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:12Z",
  "url": "https://research.draconitic.com/paper/8vybbetmbk038",
  "venue": "STAR protocols",
  "versions": []
}