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Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes

Author(s)
Genshaft, Alex S; Ziegler, Carly GK; Tzouanas, Constantine N; Mead, Benjamin E; Jaeger, Alex M; Navia, Andrew W; King, Ryan P; Mana, Miyeko D; Huang, Siyi; Mitsialis, Vanessa; Snapper, Scott B; Yilmaz, Ömer H; Jacks, Tyler; Van Humbeck, Jeffrey F; Shalek, Alex K; ... Show more Show less
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Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/
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Abstract
<jats:title>Abstract</jats:title><jats:p>A cell’s phenotype and function are influenced by dynamic interactions with its microenvironment. To examine cellular spatiotemporal activity, we developed SPACECAT—Spatially PhotoActivatable Color Encoded Cell Address Tags—to annotate, track, and isolate cells while preserving viability. In SPACECAT, samples are stained with photocaged fluorescent molecules, and cells are labeled by uncaging those molecules with user-patterned near-UV light. SPACECAT offers single-cell precision and temporal stability across diverse cell and tissue types. Illustratively, we target crypt-like regions in patient-derived intestinal organoids to enrich for stem-like and actively mitotic cells, matching literature expectations. Moreover, we apply SPACECAT to ex vivo tissue sections from four healthy organs and an autochthonous lung tumor model. Lastly, we provide a computational framework to identify spatially-biased transcriptome patterns and enriched phenotypes. This minimally perturbative and broadly applicable method links cellular spatiotemporal and/or behavioral phenotypes with diverse downstream assays, enabling insights into the connections between tissue microenvironments and (dys)function.</jats:p>
Date issued
2021
URI
https://hdl.handle.net/1721.1/141279
Journal
Nature Communications
Publisher
Springer Science and Business Media LLC
Citation
Genshaft, Alex S, Ziegler, Carly GK, Tzouanas, Constantine N, Mead, Benjamin E, Jaeger, Alex M et al. 2021. "Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes." Nature Communications, 12 (1).
Version: Final published version

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