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{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,1,18]],"date-time":"2024-01-18T13:02:57Z","timestamp":1705582977996},"reference-count":79,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2023,3,18]],"date-time":"2023-03-18T00:00:00Z","timestamp":1679097600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2023,3,18]],"date-time":"2023-03-18T00:00:00Z","timestamp":1679097600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Spatially resolved transcriptomics of tissue sections enables advances in fundamental and applied biomedical research. Here, we present Multiplexed Deterministic Barcoding in Tissue (xDBiT) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17\u2009cm<jats:sup>2<\/jats:sup> with a 50\u2009\u00b5m resolution. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared to previous reports. Furthermore, the introduction of alignment markers allowed seamless registration of images and spatial transcriptomic spots. Together with technological advances, we provide an open-source computational pipeline to prepare raw sequencing data for downstream analysis. The functionality of xDBiT was demonstrated by acquiring 16 spatially resolved transcriptomic datasets from five different murine organs, including the cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of spatial transcriptomes allowed for in-depth characterization of the murine kidney.<\/jats:p>","DOI":"10.1038\/s41467-023-37111-w","type":"journal-article","created":{"date-parts":[[2023,3,26]],"date-time":"2023-03-26T20:03:17Z","timestamp":1679860997000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Spatial transcriptomics using multiplexed deterministic barcoding in tissue"],"prefix":"10.1038","volume":"14","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-2216-3332","authenticated-orcid":false,"given":"Johannes","family":"Wirth","sequence":"first","affiliation":[]},{"given":"Nina","family":"Huber","sequence":"additional","affiliation":[]},{"given":"Kelvin","family":"Yin","sequence":"additional","affiliation":[]},{"given":"Sophie","family":"Brood","sequence":"additional","affiliation":[]},{"given":"Simon","family":"Chang","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-9534-6201","authenticated-orcid":false,"given":"Celia P.","family":"Martinez-Jimenez","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0001-9455-4538","authenticated-orcid":false,"given":"Matthias","family":"Meier","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,3,18]]},"reference":[{"key":"37111_CR1","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","volume":"161","author":"EZ Macosko","year":"2015","unstructured":"Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202\u20131214 (2015).","journal-title":"Cell"},{"key":"37111_CR2","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1038\/nmeth.4154","volume":"14","author":"SA Vitak","year":"2017","unstructured":"Vitak, S. A. et al. Sequencing thousands of single-cell genomes with combinatorial indexing. Nat. Methods 14, 302\u2013308 (2017).","journal-title":"Nat. Methods"},{"key":"37111_CR3","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1126\/science.aam8999","volume":"360","author":"AB Rosenberg","
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