{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T06:29:47Z","timestamp":1784874587821,"version":"3.55.0"},"reference-count":30,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2024,4,5]],"date-time":"2024-04-05T00:00:00Z","timestamp":1712275200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HD078641"],"award-info":[{"award-number":["R01HD078641"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["P50HD096723"],"award-info":[{"award-number":["P50HD096723"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Andrology"],"published-print":{"date-parts":[[2025,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Single\u2010cell RNA\u2010seq (scRNA\u2010Seq) has been widely adopted to study gene expression of the human testis. Several datasets of scRNA\u2010Seq from human testis have been generated from different groups processed with different informatics pipelines. An integrated atlas of scRNA\u2010Seq expression constructed from multiple donors, developmental ages, and fertility states would be widely useful for the testis research community.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Objective<\/jats:title>\n                    <jats:p>To describe the generation and use of the human infertility single\u2010cell testis atlas (HISTA), an interactive web tool for understanding human spermatogenesis through scRNA\u2010Seq analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We obtained scRNA\u2010Seq datasets derived from 12 donors, including healthy adult controls, juveniles, and several infertility cases, and reprocessed these data using methods to remove batch effects. Using Shiny, an open\u2010source environment for data visualization, we created numerous interactive tools for exploring the data, some of which support simple statistical hypothesis testing. We used the resulting HISTA browser and its underlying data to demonstrate HISTA's value for testis researchers.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>A primary application of HISTA is to search by a single gene or a set of genes; thus, we present various analyses that quantify and visualize gene expression across the testis cells and pathology. HISTA also contains machine\u2010learning\u2010derived gene modules (\u201ccomponents\u201d) that capture the entire transcriptional landscape of the testis tissue. We show how the use of these components can simplify the highly complex data in HISTA and assist with the interpretation of genes with unknown functions. Finally, we demonstrate the diverse ways HISTA can be used for new data analysis, including hypothesis testing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion and conclusions<\/jats:title>\n                    <jats:p>HISTA is a research environment that can help scientists organize and understand the high\u2010dimensional transcriptional landscape of the human testis. HISTA has already contributed to published testis research and can be updated as needed with input from the research community or downloaded and modified for individual needs.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1111\/andr.13637","type":"journal-article","created":{"date-parts":[[2024,4,5]],"date-time":"2024-04-05T05:08:55Z","timestamp":1712293735000},"page":"1190-1200","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["The human infertility single\u2010cell testis atlas (HISTA): an interactive molecular scRNA\u2010Seq reference of the human testis"],"prefix":"10.1111","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5613-3131","authenticated-orcid":false,"given":"Eisa","family":"Mahyari","sequence":"first","affiliation":[{"name":"Division of Genetics Oregon National Primate Research Center Oregon Health &amp; Science University  Portland Oregon USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katinka A.","family":"Vigh\u2010Conrad","sequence":"additional","affiliation":[{"name":"Division of Genetics Oregon National Primate Research Center Oregon Health &amp; Science University  Portland Oregon USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cl\u00e9ment","family":"Daube","sequence":"additional","affiliation":[{"name":"Division of Genetics Oregon National Primate Research Center Oregon Health &amp; Science University  Portland Oregon USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana C.","family":"Lima","sequence":"additional","affiliation":[{"name":"Division of Genetics Oregon National Primate Research Center Oregon Health &amp; Science University  Portland Oregon USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingtao","family":"Guo","sequence":"additional","affiliation":[{"name":"Andrology and IVF Laboratory Division of Urology Department of Surgery University of Utah School of Medicine  Salt Lake City Utah USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douglas T.","family":"Carrell","sequence":"additional","affiliation":[{"name":"Andrology and IVF Laboratory Division of Urology Department of Surgery University of Utah School of Medicine  Salt Lake City Utah USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James M.","family":"Hotaling","sequence":"additional","affiliation":[{"name":"Andrology and IVF Laboratory Division of Urology Department of Surgery University of Utah School of Medicine  Salt Lake City Utah USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6459-2103","authenticated-orcid":false,"given":"Kenneth I.","family":"Aston","sequence":"additional","affiliation":[{"name":"Andrology and IVF Laboratory Division of Urology Department of Surgery University of Utah School of Medicine  Salt Lake City Utah USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3828-8970","authenticated-orcid":false,"given":"Donald F.","family":"Conrad","sequence":"additional","affiliation":[{"name":"Division of Genetics Oregon National Primate Research Center Oregon Health &amp; 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