{
  "abstract": "Developing tissues comprise heterogeneous cell populations exhibiting stage-dependent transcriptional dynamics. We present a protocol to identify candidate Sox9 target genes in specific murine cell populations by integrating single-cell RNA sequencing (scRNA-seq) with Ty1-tag-based CUT&RUN. We describe steps for embryonic forelimb bud dissection, scRNA-seq and CUT&RUN sample and library preparation, and data processing. We then detail procedures for integrative analysis of stage- and cluster-specific Sox9 targets. The framework may be adaptable to other Sox9-expressing tissues and developmental stages with appropriate optimization. For complete details on the use and execution of this protocol, please refer to Sega et al.¹.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.",
    "Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Comprehensive Reproductive Medicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.",
    "Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Molecular and Cellular Biology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA.",
    "Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Department of Molecular and Cellular Biology, The Scripps Research Institute, La Jolla, San Diego, CA 92037, USA. Electronic address: asahara.syst@tmd.ac.jp."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Kohei Kita"
    },
    {
      "affs": [
        1
      ],
      "name": "Masayasu Sega"
    },
    {
      "affs": [
        2
      ],
      "name": "Yutaro Uchida"
    },
    {
      "affs": [
        0
      ],
      "name": "Tomoki Chiba"
    },
    {
      "affs": [
        0
      ],
      "name": "Takahide Matsushima"
    },
    {
      "affs": [
        3
      ],
      "name": "Hiroshi Asahara"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/ehntby8v2yv92.bib",
  "cited_by": 0,
  "doi": "10.1016/j.xpro.2026.104889",
  "fulltext_url": "https://europepmc.org/articles/PMC13675712",
  "id": "ehntby8v2yv92",
  "issns": [
    "2666-1667"
  ],
  "landing_url": "https://europepmc.org/article/MED/42853678",
  "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/PMC13675712?pdf=render",
  "pmcid": "PMC13675712",
  "pmid": "42853678",
  "published": "2026-10-08",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/ehntby8v2yv92.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:12Z",
      "native_id": "MED:42853678",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42853678"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "journal-openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Protocol to define Sox9 target programs during mouse limb chondrogenesis using scRNA-seq and CUT&RUN integration.",
  "title_text": "Protocol to define Sox9 target programs during mouse limb chondrogenesis using scRNA-seq and CUT&RUN integration.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:18:12Z",
  "url": "https://research.draconitic.com/paper/ehntby8v2yv92",
  "venue": "STAR protocols",
  "versions": []
}