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To have a comprehensive map of the cellular anatomy of bladder urothelial cells, we performed single\u2010cell RNA sequencing to thoroughly characterize mouse bladder urothelium.<\/jats:p><\/jats:sec><jats:sec><jats:title>Materials and methods<\/jats:title><jats:p>A total of 18,917 single cells from mouse bladder urothelium were analysed by unbiased single\u2010cell RNA sequencing. The expression of the novel cell marker was confirmed by immunofluorescence using urinary tract infection models.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Unsupervised clustering analysis identified 8 transcriptionally distinct cell subpopulations from mouse bladder urothelial cells. We discovered a novel type of bladder urothelial cells marked by Plxna4 that may be involved with host response and wound healing. We also found a group of basal\u2010like cells labelled by ASPM that could be the progenitor cells of adult bladder urothelium. ASPM<jats:sup>+<\/jats:sup> urothelial cells are significantly increased after injury by UPEC. In addition, specific transcription factors were found to be associated with urothelial cell differentiation. At the last, a number of interstitial cystitis\/bladder pain syndrome\u2013regulating genes were found differentially expressed among different urothelial cell subpopulations.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our study provides a comprehensive characterization of bladder urothelial cells, which is fundamental to understanding the biology of bladder urothelium and associated bladder disease.<\/jats:p><\/jats:sec>","DOI":"10.1111\/cpr.13007","type":"journal-article","created":{"date-parts":[[2021,2,6]],"date-time":"2021-02-06T16:30:35Z","timestamp":1612629035000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Single\u2010cell transcriptomes of mouse bladder urothelium uncover novel cell type markers and urothelial differentiation characteristics"],"prefix":"10.1111","volume":"54","author":[{"given":"Yan","family":"Li","sequence":"first","affiliation":[{"name":"Department 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