{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:34:02Z","timestamp":1791387242588,"version":"4.3.3"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T00:00:00Z","timestamp":1699228800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["466168626"],"award-info":[{"award-number":["466168626"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000864","name":"Michael J. 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A growing number of single-cell studies have implicated various neural, glial, and immune cell subtypes to affect the mammalian central nervous system in many age-related disorders. Integrating this body of transcriptomic evidence into a comprehensive and reproducible framework poses several computational challenges. Here, we introduce ZEBRA, a large single-cell and single-nucleus RNA-seq database. ZEBRA integrates and normalizes gene expression and metadata from 33 studies, encompassing 4.2 million human and mouse brain cells sampled from 39 brain regions. It incorporates samples from patients with neurodegenerative diseases like Alzheimer\u2019s disease, Parkinson\u2019s disease, and Multiple sclerosis, as well as samples from relevant mouse models. We employed scVI, a deep probabilistic auto-encoder model, to integrate the samples and curated both cell and sample metadata for downstream analysis. ZEBRA allows for cell-type and disease-specific markers to be explored and compared between sample conditions and brain regions, a cell composition analysis, and gene-wise feature mappings. Our comprehensive molecular database facilitates the generation of data-driven hypotheses, enhancing our understanding of mammalian brain function during aging and disease. The data sets, along with an interactive database are freely available at https:\/\/www.ccb.uni-saarland.de\/zebra.<\/jats:p>","DOI":"10.1093\/nar\/gkad990","type":"journal-article","created":{"date-parts":[[2023,11,9]],"date-time":"2023-11-09T05:26:35Z","timestamp":1699507595000},"page":"D1089-D1096","source":"Crossref","is-referenced-by-count":18,"title":["ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution"],"prefix":"10.1093","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-4374-0801","authenticated-orcid":false,"given":"Matthias","family":"Flotho","sequence":"first","affiliation":[{"name":"Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus , 66123 Saarbr\u00fccken, Germany"},{"name":"Clinical Bioinformatics, Center for Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1354-5486","authenticated-orcid":false,"given":"J\u00e9r\u00e9my","family":"Amand","sequence":"additional","affiliation":[{"name":"Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus , 66123 Saarbr\u00fccken, Germany"},{"name":"Clinical Bioinformatics, Center for Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4152-9931","authenticated-orcid":false,"given":"Pascal","family":"Hirsch","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics, Center for Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Friederike","family":"Grandke","sequence":"additional","affiliation":[{"name":"Clinical Bioinformatics, Center for Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tony","family":"Wyss-Coray","sequence":"additional","affiliation":[{"name":"Department of Neurology and Neurological Sciences, Stanford University , Stanford, CA, USA"},{"name":"The Phil and Penny Knight Initiative for Brain Resilience, Stanford University , Stanford, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5361-0895","authenticated-orcid":false,"given":"Andreas","family":"Keller","sequence":"additional","affiliation":[{"name":"Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus , 66123 Saarbr\u00fccken, Germany"},{"name":"Clinical Bioinformatics, Center for Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8223-3750","authenticated-orcid":false,"given":"Fabian","family":"Kern","sequence":"additional","affiliation":[{"name":"Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus , 66123 Saarbr\u00fccken, Germany"},{"name":"Clinical Bioinformatics, Center for Bioinformatics, Saarland University , 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,11,6]]},"reference":[{"key":"2024010511443613900_B1","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/s41583-022-00641-1","article-title":"Astrocyte contribution to dysfunction, risk and progression in neurodegenerative disorders","volume":"24","author":"Brandebura","year":"2023","journal-title":"Nat. Rev. Neurosci."},{"key":"2024010511443613900_B2","doi-asserted-by":"crossref","first-page":"a008888","DOI":"10.1101\/cshperspect.a008888","article-title":"Genetics of Parkinson\u2019s disease","volume":"2","author":"Klein","year":"2012","journal-title":"Cold Spring Harbor Perspect. Med."},{"key":"2024010511443613900_B3","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1016\/j.jalz.2014.12.007","article-title":"Alzheimer\u2019s disease first symptoms are age dependent: evidence from the NACC dataset","volume":"11","author":"Barnes","year":"2015","journal-title":"Alzheimer Dement."},{"key":"2024010511443613900_B4","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/nprot.2017.149","article-title":"Exponential scaling of single-cell RNA-seq in the past decade","volume":"13","author":"Svensson","year":"2018","journal-title":"Nat. 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