Evidence map›Paper›PMID 42853678›Full record

ArticleSTAR protocols2026

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

Kohei Kita, Masayasu Sega, Yutaro Uchida, Tomoki Chiba, Takahide Matsushima, Hiroshi Asahara

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Kohei KitaDepartment of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
Masayasu SegaDepartment 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.
Yutaro UchidaDepartment 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.
Tomoki ChibaDepartment of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
Takahide MatsushimaDepartment of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.
Hiroshi AsaharaDepartment 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.

Funding

Mechano signals regulating tendon and ligament homeostasisR01AR080127 · NIAMS · SCRIPPS RESEARCH INSTITUTE, THE · PI Hiroshi Asahara · 2022 to 2026
$1.9M
NIAMS NIH HHS R01 AR080127
6 · The paper itself

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.

Indexed as

Cell BiologyDevelopmental biologyGenomics

Identifiers

PMID42853678
PMCPMC13675712

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.