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Here, we present a paired whole-genome sequencing (WGS) dataset from 53 Han Chinese men, comprising matched blood WGS per participant (target ~10\u00d7) and 3\u20135 low-coverage single-sperm WGS libraries per participant (target ~1\u00d7). The dataset includes 263 single-sperm libraries (79 from 16 asthenozoospermic participants and 184 from 37 normozoospermic participants) and is accompanied by rich participant-level metadata, including baseline characteristics, endocrine measurements, and semen parameters such as sperm motility and vitality. Raw reads underwent standardized quality-control filtering, and key sequencing metrics (Q20 and GC content) met commonly used thresholds; the achieved mean depth was approximately 10\u00d7 for blood and ~1.7\u00d7 for single sperm. By integrating sperm motility\/vitality phenotypes with individual-matched genomic information, this resource provides a foundation for male reproductive genomics and for developing and benchmarking algorithms for gamete-genome dissection, and may support future translational research on male infertility evaluation.<\/jats:p>","DOI":"10.1038\/s41597-026-06808-0","type":"journal-article","created":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T05:12:17Z","timestamp":1770700337000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Matched whole-genome sequencing of blood (10\u00d7) and five single sperm cells (1\u00d7) per individual in 53 men"],"prefix":"10.1038","volume":"13","author":[{"given":"Weiming","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruidong","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Su","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zongyu","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhixu","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hui","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaolan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yani","family":"Ding","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feifei","family":"Gou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu","family":"Lu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ye","family":"Pan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yong","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"He","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chaojun","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zongjian","family":"Tan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1428-904X","authenticated-orcid":false,"given":"Zhenyu","family":"Jia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1171-0126","authenticated-orcid":false,"given":"Jianguo","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,2,10]]},"reference":[{"issue":"2","key":"6808_CR1","doi-asserted-by":"publisher","first-page":"237","DOI":"10.5534\/wjmh.220213","volume":"41","author":"AE Calogero","year":"2023","unstructured":"Calogero, A. E. et al. The Renaissance of Male Infertility Management in the Golden Age of Andrology. The world journal of men\u2019s health 41(2), 237\u2013254, https:\/\/doi.org\/10.5534\/wjmh.220213 (2023).","journal-title":"The world journal of men\u2019s health"},{"key":"6808_CR2","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1007\/978-3-030-25905-1_16","volume":"111","author":"C Krausz","year":"2019","unstructured":"Krausz, C. & Riera-Escamilla, A. Monogenic Forms of Male Infertility. Experientia supplementum (2012) 111, 341\u2013366, https:\/\/doi.org\/10.1007\/978-3-030-25905-1_16 (2019).","journal-title":"Experientia supplementum (2012)"},{"issue":"6","key":"6808_CR3","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1016\/j.fertnstert.2025.03.006","volume":"123","author":"C Krausz","year":"2025","unstructured":"Krausz, C. & Abrardo, C. The Y chromosome: male reproduction and beyond. 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