Journal article
Cell2location maps fine-grained cell types in spatial transcriptomics
V Kleshchevnikov, A Shmatko, E Dann, A Aivazidis, HW King, T Li, R Elmentaite, A Lomakin, V Kedlian, A Gayoso, MS Jain, JS Park, L Ramona, E Tuck, A Arutyunyan, R Vento-Tormo, M Gerstung, L James, O Stegle, OA Bayraktar
Nature Biotechnology | Published : 2022
Abstract
Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in health and disease, but comprehensive mapping of cell types in situ remains a challenge. Here we present сell2location, a Bayesian model that can resolve fine-grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. Cell2location accounts for technical sources of variation and borrows statistical strength across locations, thereby enabling the integration of single-cell and spatial transcriptomics with higher sensitivity and resolution than existing tools. We assessed cell2location in three different tissues and show improved mapping of fine-graine..
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Funding Acknowledgements
We thank B. Velten, Y. Huang and L. Marconato for feedback on the cell2location model; M. Prete and V. Kiselev for dockerizing the cell2location tool and creating the web portals for sharing our data; N. Kumasaka for helpful comments on single-cell analysis; S. Leonard and K. Polanski for help with spatial and single-nucleus data processing; K. James for advice on gut immune cell types; K. Roberts for advice on smFISH; J. E. Kwa for advice on snRNA-seq; J. Eliasova for illustrations and logo design; K. James advice on human gut immune cells; A. Antanaviciute, H. Koohy and A. Simmons for sharing gut Visium data; F. Obermeyer and M. Jankowiak for help with advanced use of pyro code base; and D. Rowitch and S. Teichmann for comments on the manuscript. H.W.K. was funded by a Sir Henry Wellcome Postdoctoral Fellowship (213555/Z/18/Z). This study was supported by Wellcome Trust Core Funding to O.A.B.