Scientific data2026; 13(1); 1365; doi: 10.1038/s41597-026-08404-8

A single-cell RNA-seq dataset characterizing cellular diversity in healthy equine skin.

Akula, S
·
Zhang, B
·
Riihimäki, M
·
Wernersson, S
·
Raine, A

Abstract: The skin serves as the primary barrier tissue in horses and is frequently affected by immune-mediated dermatological conditions, most notably insect bite hypersensitivity (IBH). Yet, the cellular composition and transcriptional landscape of normal equine skin have never been characterized at single-cell resolution. Here, we present a single-cell RNA sequencing dataset of healthy equine skin comprising 85,574 high-quality transcriptomes from two horses, with one skin biopsy collected from each horse, divided into two portions for independent processing via manual or automated tissue dissociation. The dataset resolved 22 transcriptionally distinct cell populations, encompassing keratinocyte subpopulations that reflect discrete epidermal differentiation states, adnexal epithelial lineages, stromal and vascular compartments, and resident immune cell types. Cell-type identities are supported by marker gene expression, KEGG pathway enrichment analysis, and functional module scoring. This dataset constitutes the first single-cell transcriptomic reference of normal equine skin, enabling investigations into equine dermatological diseases, wound healing, immune responses and comparative skin biology.

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Publication Date: 2026-09-30 PubMed ID: 42816519PubMed Central: PMC13627664DOI: 10.1038/s41597-026-08404-8Google Scholar: Lookup

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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

Overview

This research presents a comprehensive single-cell RNA sequencing (scRNA-seq) dataset that profiles the cellular diversity of healthy horse skin.
The study provides a detailed map of different skin cell types and their gene expression patterns, establishing a foundational resource for studying equine skin biology and disease mechanisms.

Background and Motivation

The skin is the horse’s primary barrier tissue and plays a critical role in protecting against environmental insults and pathogens.
Equine skin is commonly affected by immune-related conditions, such as insect bite hypersensitivity (IBH), which significantly impacts horse health and welfare.
Despite the importance of skin, prior to this study, the cellular composition and gene expression profiles of normal (healthy) equine skin had not been characterized at the single-cell level.
Understanding the baseline cellular landscape is essential for comparative studies of disease states, wound healing, immune responses, and skin biology.

Study Design and Methods

Samples: Skin biopsies were obtained from two healthy horses, with one biopsy per horse.
Sample Processing: Each biopsy was split into two portions to compare processing methods — one portion underwent manual tissue dissociation and the other automated tissue dissociation.
Single-Cell RNA Sequencing: The study generated 85,574 high-quality single-cell transcriptomes (individual cell gene expression profiles), enabling in-depth analysis of cellular diversity.
Data Analysis involved:
- Clustering of cells based on transcriptomic profiles to identify distinct cell populations.
- Identification of marker genes uniquely or highly expressed in each cluster to assign cell identities.
- KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis to understand the functional roles of each cell population.
- Functional module scoring to assess specific gene sets related to epidermal differentiation, immune function, and other biological processes relevant to skin physiology.

Key Findings

The dataset identified 22 transcriptionally distinct cell populations in healthy equine skin.
These populations included:
- Keratinocyte subpopulations that reflect various stages of epidermal cell differentiation, crucial for skin barrier formation and maintenance.
- Adnexal epithelial lineages which contribute to skin appendages such as hair follicles and glands.
- Stromal cells that provide structural support.
- Vascular cells involved in blood vessel formation and function.
- Resident immune cells vital for skin immune surveillance and responses.
Marker gene expression validated the identities of these clusters, providing confidence in the annotations of each cell type.
KEGG enrichment helps interpret the biological pathways active in each population, offering insight into their function in healthy skin.

Significance and Applications

This is the first comprehensive single-cell transcriptomic reference specifically for normal equine skin.
The dataset provides a valuable resource for:
- Investigating pathogenesis and cellular dynamics in equine dermatological diseases such as IBH.
- Studying the mechanisms of wound healing processes in horses.
- Exploring immune responses in equine skin at a granular, cellular level.
- Facilitating comparative biology studies by comparing equine skin with that of other species.
The availability of both manual and automated tissue dissociation processed samples also allows future researchers to evaluate technical impacts on single-cell data quality.

Conclusion

This study establishes a foundational single-cell gene expression atlas of healthy horse skin, revealing cellular heterogeneity and providing essential tools for future skin biology and disease research in equine species.

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APA

Akula S, Zhang B, Riihimäki M, Wernersson S, Raine A. (2026). A single-cell RNA-seq dataset characterizing cellular diversity in healthy equine skin. Sci Data, 13(1), 1365. https://doi.org/10.1038/s41597-026-08404-8

Publication

Scientific data

ISSN: 2052-4463

NlmUniqueID: 101640192

Country: England

Language: English

Volume: 13

Issue: 1

PII: 1365

Researcher Affiliations

Akula, Srinivas

Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden. srinivas.akula@slu.se.

Zhang, Birong

Department of Medical Sciences, Uppsala University, Uppsala, Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.

Riihimäki, Miia

Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Wernersson, Sara

Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Raine, Amanda

Department of Medical Sciences, Uppsala University, Uppsala, Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. amanda.raine@medsci.uu.se.

MeSH Terms

Animals
Horses / genetics
Skin / cytology
Transcriptome
RNA-Seq
Single-Cell Analysis
Single-Cell Gene Expression Analysis
Sequence Analysis, RNA

Grant Funding

2023-01000 / Svenska Forskningsrådet Formas
2023-01377 / Svenska Forskningsrådet Formas

Conflict of Interest Statement

Competing interests: The authors declare no competing interests.

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