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Peer-reviewedCC BYSTAR protocols

Protocol to define Sox9 target programs during mouse limb chondrogenesis using scRNA-seq and CUT&RUN integration.

  • Kohei Kita1
  • Masayasu Sega2
  • Yutaro Uchida3
  • Tomoki Chiba1
  • Takahide Matsushima1
  • Hiroshi Asahara4
4 affiliations
  1. 1Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
  2. 2Department 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.
  3. 3Department 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.
  4. 4Department 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: [email protected].
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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.

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Cite

BibTeXRIS
BibTeX
@article{kita2026protocol,
  title = {{Protocol to define Sox9 target programs during mouse limb chondrogenesis using scRNA-seq and CUT&RUN integration.}},
  author = {Kohei Kita and Masayasu Sega and Yutaro Uchida and Tomoki Chiba and Takahide Matsushima and Hiroshi Asahara},
  journal = {STAR protocols},
  year = {2026},
  month = oct,
  doi = {10.1016/j.xpro.2026.104889},
  url = {https://europepmc.org/article/MED/42853678},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Protocol to define Sox9 target programs during mouse limb chondrogenesis using scRNA-seq and CUT&RUN integration.
AU  - Kohei Kita
AU  - Masayasu Sega
AU  - Yutaro Uchida
AU  - Tomoki Chiba
AU  - Takahide Matsushima
AU  - Hiroshi Asahara
PY  - 2026
DA  - 2026/10/08
JO  - STAR protocols
DO  - 10.1016/j.xpro.2026.104889
UR  - https://europepmc.org/article/MED/42853678
AB  - 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.
SN  - 2666-1667
ER  -