{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T01:06:59Z","timestamp":1789780019483,"version":"4.0.1"},"reference-count":202,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T00:00:00Z","timestamp":1784332800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Beijing High-Level Innovation and Entrepreneurship Talent Support Program"},{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"publisher","award":["82271332"],"award-info":[{"award-number":["82271332"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science and Technology Plan of Beijing Tongzhou District","award":["KJ2023CX022"],"award-info":[{"award-number":["KJ2023CX022"]}]},{"name":"Beijing Tong Zhou District Financial Fund","award":["2026"],"award-info":[{"award-number":["2026"]}]},{"name":"Yunhe talent Program of Beijing Tongzhou District","award":["2026"],"award-info":[{"award-number":["2026"]}]},{"name":"Tongzhou District Medical Research and Achievement Transformation Special Project","award":["WS2025064"],"award-info":[{"award-number":["WS2025064"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Background: Ischemic stroke remains a leading cause of mortality and long-term disability worldwide, with complex and heterogeneous pathophysiological processes. Single-cell and single-nucleus RNA sequencing (sc\/snRNA-seq) has been increasingly applied to investigate cellular heterogeneity at high resolutions. Methods: We systematically searched PubMed, Web of Science, and Embase to identify studies that applied sc\/snRNA-seq in ischemic stroke research. Based on the retrieved literature, we summarized the bioinformatic analytical methods and application strategies reported in these studies, focusing on how sc\/snRNA-seq has been utilized across different research contexts. Results: The application of sc\/snRNA-seq in ischemic stroke has expanded rapidly across species and sample types. A wide range of downstream bioinformatic analyses have been employed, including clustering, differential expression analysis, trajectory inference, gene regulatory network analysis, and cell\u2013cell communication analysis. These approaches have been applied to investigate diverse biological processes in ischemic stroke. In addition, these analytical strategies have been extended to multiple biological contexts, including extracerebral tissues, stroke-related modifiers, and their associated complications. Furthermore, integrative analytical approaches that combine multiple datasets, bulk transcriptomics, and other omics data have been increasingly utilized. Advances in temporal and spatial resolutions have enabled analyses across different stages and anatomical regions. Conclusions: This review systematically summarizes the analytical methods and application strategies of sc\/snRNA-seq in ischemic stroke. These approaches provide a structured perspective for understanding the application of single-cell technologies in this field. Future studies may benefit from standardized designs and coordinated analytical strategies to facilitate more systematic investigations.<\/jats:p>","DOI":"10.3390\/biom16071054","type":"journal-article","created":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T00:47:32Z","timestamp":1784508452000},"page":"1054","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Analytical Methods and Application of Single-Cell and Single-Nucleus Transcriptomics in the Study of Ischemic Stroke"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-4771-8406","authenticated-orcid":false,"given":"Changqing","family":"Mu","sequence":"first","affiliation":[{"name":"Luhe Institute of Neuroscience, Capital Medical University, Beijing 101149, China"},{"name":"Department of Neurology, Beijing Luhe Hospital, Capital Medical University, Beijing 101149, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuchuan","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander","family":"Weiss","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-6448-9202","authenticated-orcid":false,"given":"Sydni","family":"Rosenfeld","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, Wayne State University School of Medicine, Detroit, MI 48201, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fengwu","family":"Li","sequence":"additional","affiliation":[{"name":"Luhe Institute of Neuroscience, Capital Medical University, Beijing 101149, China"},{"name":"Department of Neurology, Beijing Luhe Hospital, Capital Medical University, Beijing 101149, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8918-8748","authenticated-orcid":false,"given":"Xiaokun","family":"Geng","sequence":"additional","affiliation":[{"name":"Luhe Institute of Neuroscience, Capital Medical University, Beijing 101149, China"},{"name":"Department of Neurology, Beijing Luhe Hospital, Capital Medical University, Beijing 101149, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2820","DOI":"10.1016\/S0140-6736(24)00642-1","article-title":"Stroke","volume":"403","author":"Hilkens","year":"2024","journal-title":"Lancet"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"187","DOI":"10.4103\/bc.bc_161_24","article-title":"A narrative review of reperfusion therapy in acute ischemic stroke: Emerging advances, current challenges, and future directions","volume":"11","author":"Wang","year":"2025","journal-title":"Brain Circ."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1161\/STROKEAHA.122.040073","article-title":"Projected Global Trends in Ischemic Stroke Incidence, Deaths and Disability-Adjusted Life Years From 2020 to 2030","volume":"54","author":"Pu","year":"2023","journal-title":"Stroke"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1177\/17474930241308142","article-title":"World Stroke Organization: Global Stroke Fact Sheet 2025","volume":"20","author":"Feigin","year":"2025","journal-title":"Int. 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