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Rheumatoid arthritis synovium has primarily been studied either by immunostaining or by molecular profiling after tissue homogenization. Here, we use Spatial Transcriptomics, where tissue-resident RNA is spatially labeled in situ with barcodes in a transcriptome-wide fashion, to study local tissue interactions at the site of chronic synovial inflammation. We report comprehensive spatial RNA-Seq data coupled to cell type-specific localization patterns at and around organized structures of infiltrating leukocyte cells in the synovium. Combining morphological features and high-throughput spatially resolved transcriptomics may be able to provide higher statistical power and more insights into monitoring disease severity and treatment-specific responses in seropositive and seronegative rheumatoid arthritis.<\/jats:p>","DOI":"10.1038\/s42003-022-03050-3","type":"journal-article","created":{"date-parts":[[2022,2,11]],"date-time":"2022-02-11T06:05:04Z","timestamp":1644559504000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":79,"title":["Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium"],"prefix":"10.1038","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0985-9885","authenticated-orcid":false,"given":"Sanja","family":"Vickovic","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9391-5722","authenticated-orcid":false,"given":"Denis","family":"Schapiro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1774-6058","authenticated-orcid":false,"given":"Konstantin","family":"Carlberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Britta","family":"L\u00f6tstedt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4209-2911","authenticated-orcid":false,"given":"Ludvig","family":"Larsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franziska","family":"Hildebrandt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Korotkova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aase H.","family":"Hensvold","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anca I.","family":"Catrina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3364-1838","authenticated-orcid":false,"given":"Peter K.","family":"Sorger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9251-8082","authenticated-orcid":false,"given":"Vivianne","family":"Malmstr\u00f6m","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3293-3158","authenticated-orcid":false,"given":"Aviv","family":"Regev","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2207-7370","authenticated-orcid":false,"given":"Patrik L.","family":"St\u00e5hl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,2,11]]},"reference":[{"key":"3050_CR1","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1038\/nri.2016.124","volume":"17","author":"V Malmstr\u00f6m","year":"2017","unstructured":"Malmstr\u00f6m, V., Catrina, A. 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D.S. is a scientific consultant to Roche Glycart AG. P.L.S. and K.C. are scientific consultants to 10\u00d7 Genomics Inc. P.K.S. is on the SAB or BOD of Rarecyte Inc., Applied Biomath LLC, Glencoe Software Inc. and Nanostring Inc.; none of these relationships are directly related to the topic of this study. A.R. is a founder and equity holder of Celsius Therapeutics, an equity holder in Immunitas Therapeutics and until August 31, 2020 was an SAB member of Syros Pharmaceuticals, Neogene Therapeutics, Asimov, and ThermoFisher Scientific. From August 1, 2020, A.R. is an employee of Genentech, a member of the Roche Group. S.V. and A.R. are co-inventors on PCT\/US2020\/015481 relating to this work. All other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"129"}}