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Kleshchevnikov V, Shmatko A, Dann E, et al. Cell2location maps fine-grained cell types in spatial transcriptomics. Nat Biotechnol. 2022;doi: 10.1038/s41587-021-01139-4.
Kleshchevnikov, V., Shmatko, A., Dann, E., Aivazidis, A., King, H. W., Li, T., Elmentaite, R., Lomakin, A., Kedlian, V., Gayoso, A., Jain, M. S., Park, J. S., Ramona, L., Tuck, E., Arutyunyan, A., Vento-Tormo, R., Gerstung, M., James, L., Stegle, O., & Bayraktar, O. A. (2022). Cell2location maps fine-grained cell types in spatial transcriptomics. Nature biotechnology, . https://doi.org/10.1038/s41587-021-01139-4
Kleshchevnikov, Vitalii, et al. "Cell2location maps fine-grained cell types in spatial transcriptomics." Nature biotechnology vol. (2022). doi: https://doi.org/10.1038/s41587-021-01139-4
Kleshchevnikov V, Shmatko A, Dann E, Aivazidis A, King HW, Li T, Elmentaite R, Lomakin A, Kedlian V, Gayoso A, Jain MS, Park JS, Ramona L, Tuck E, Arutyunyan A, Vento-Tormo R, Gerstung M, James L, Stegle O, Bayraktar OA. Cell2location maps fine-grained cell types in spatial transcriptomics. Nat Biotechnol. 2022 Jan 13; doi: 10.1038/s41587-021-01139-4. Epub 2022 Jan 13. PMID: 35027729.
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Nat Biotechnol. 2022 Jan 13; doi: 10.1038/s41587-021-01139-4. Epub 2022 Jan 13.

Cell2location maps fine-grained cell types in spatial transcriptomics.

Nature biotechnology

Vitalii Kleshchevnikov, Artem Shmatko, Emma Dann, Alexander Aivazidis, Hamish W King, Tong Li, Rasa Elmentaite, Artem Lomakin, Veronika Kedlian, Adam Gayoso, Mika Sarkin Jain, Jun Sung Park, Lauma Ramona, Elizabeth Tuck, Anna Arutyunyan, Roser Vento-Tormo, Moritz Gerstung, Louisa James, Oliver Stegle, Omer Ali Bayraktar

Affiliations

  1. Wellcome Sanger Institute, Hinxton, Cambridge, UK.
  2. Moscow State University, Leninskie Gory, Moscow, Russia.
  3. Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK.
  4. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.
  5. European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
  6. Center for Computational Biology, University of California, Berkeley, Berkeley CA, USA.
  7. Theory of Condensed Matter, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
  8. Wellcome Sanger Institute, Hinxton, Cambridge, UK. [email protected].
  9. European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. [email protected].
  10. Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. [email protected].
  11. Wellcome Sanger Institute, Hinxton, Cambridge, UK. [email protected].

PMID: 35027729 DOI: 10.1038/s41587-021-01139-4

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-grained cell types. In the mouse brain, we discovered fine regional astrocyte subtypes across the thalamus and hypothalamus. In the human lymph node, we spatially mapped a rare pre-germinal center B cell population. In the human gut, we resolved fine immune cell populations in lymphoid follicles. Collectively, our results present сell2location as a versatile analysis tool for mapping tissue architectures in a comprehensive manner.

© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.

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