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To understand the roles for the epididymis in reproductive biology, we generated a single-cell atlas of the murine epididymis and vas deferens. We recovered key epithelial cell types including principal cells, clear cells, and basal cells, along with associated support cells that include fibroblasts, smooth muscle, macrophages and other immune cells. Moreover, our data illuminate extensive regional specialization of principal cell populations across the length of the epididymis. In addition to region-specific specialization of principal cells, we find evidence for functionally specialized subpopulations of stromal cells, and, most notably, two distinct populations of clear cells. Our dataset extends on existing knowledge of epididymal biology, and provides a wealth of information on potential regulatory and signaling factors that bear future investigation.<\/jats:p>","DOI":"10.7554\/elife.55474","type":"journal-article","created":{"date-parts":[[2020,7,30]],"date-time":"2020-07-30T08:00:16Z","timestamp":1596096016000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.55474","source":"Crossref","is-referenced-by-count":89,"title":["An atlas of cell types in the mouse epididymis and vas deferens"],"prefix":"10.7554","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0051-1754","authenticated-orcid":true,"given":"Vera D","family":"Rinaldi","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United 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