{
  "abstract": "The assay for transposase-accessible chromatin using sequencing (ATAC-seq) on formalin-fixed paraffin-embedded (FFPE) samples maps accessible chromatin in archival tissues, but DNA degradation and crosslinking remain significant challenges when processing these samples. Here, we present a protocol for Omni-ATAC-seq on degraded human small-cell lung cancer (SCLC) FFPE-derived samples. We detail steps for successful nuclei isolation, efficient tagmentation, and optimal library amplification to overcome the low signal-to-noise ratio. This protocol enables high-quality epigenetic profiling, turning archived SCLC samples into valuable resources for studying disease progression.\n\nFor complete details on the use and execution of this protocol, please refer to Kawasaki et al.1",
  "abstract_shown": true,
  "affiliations": [
    "Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA",
    "Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan",
    "Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA",
    "Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Eralda Salataj"
    },
    {
      "affs": [
        1
      ],
      "name": "Kenta Kawasaki"
    },
    {
      "affs": [
        2
      ],
      "name": "Joan Massagué"
    },
    {
      "affs": [
        3
      ],
      "name": "Charles M. Rudin"
    },
    {
      "affs": [
        0
      ],
      "name": "Iestyn Whitehouse"
    },
    {
      "affs": [
        0
      ],
      "name": "Richard Koche"
    },
    {
      "affs": [
        0
      ],
      "name": "Pierre-Jacques Hamard"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/f443hrd77a22b.bib",
  "cited_by": 0,
  "doi": "10.1016/j.xpro.2026.104916",
  "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13718845/?tool=EBI",
  "id": "f443hrd77a22b",
  "issns": [
    "2666-1667"
  ],
  "landing_url": "https://europepmc.org/article/PMC/PMC13718845",
  "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": [
    [
      "heading",
      "Protocol"
    ],
    [
      "openalex",
      "1312|Genomics and Chromatin Dynamics"
    ]
  ],
  "openalex": "W7223356184",
  "pdf_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13718845/pdf/?tool=EBI",
  "pmcid": "PMC13718845",
  "pmid": "42912498",
  "published": "2026-10-23",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/f443hrd77a22b.ris",
  "sources": [
    {
      "first_seen": "2026-10-31T00:20:37Z",
      "native_id": "PMC:PMC13718845",
      "source": "europepmc",
      "url": "https://europepmc.org/article/PMC/PMC13718845"
    },
    {
      "first_seen": "2026-11-02T12:22:47Z",
      "native_id": "PMC13718845",
      "source": "pmc",
      "url": "https://doi.org/10.1016/j.xpro.2026.104916"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Chromatin Dynamics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Protocol for profiling chromatin accessibility in human small-cell lung cancer FFPE-derived samples using Omni-ATAC-seq",
  "title_text": "Protocol for profiling chromatin accessibility in human small-cell lung cancer FFPE-derived samples using Omni-ATAC-seq",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:22:47Z",
  "url": "https://research.draconitic.com/paper/f443hrd77a22b",
  "venue": "STAR protocols",
  "versions": []
}