SpotClean adjusts for spot swapping in spatial transcriptomics data

Zijian Ni; Aman Prasad; Shuyang Chen; Richard B. Halberg; Lisa M. Arkin; Beth A. Drolet; Michael A. Newton; Christina Kendziorski

doi:10.1038/s41467-022-30587-y

Nature Communications (May 2022)

SpotClean adjusts for spot swapping in spatial transcriptomics data

Zijian Ni,
Aman Prasad,
Shuyang Chen,
Richard B. Halberg,
Lisa M. Arkin,
Beth A. Drolet,
Michael A. Newton,
Christina Kendziorski

Affiliations

Zijian Ni: Department of Statistics, University of Wisconsin-Madison
Aman Prasad: Department of Dermatology, University of Wisconsin-Madison
Shuyang Chen: Department of Statistics, University of Wisconsin-Madison
Richard B. Halberg: Department of Medicine, University of Wisconsin-Madison
Lisa M. Arkin: Department of Dermatology, University of Wisconsin-Madison
Beth A. Drolet: Department of Dermatology, University of Wisconsin-Madison
Michael A. Newton: Department of Statistics, University of Wisconsin-Madison
Christina Kendziorski: Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison

DOI: https://doi.org/10.1038/s41467-022-30587-y
Journal volume & issue: Vol. 13, no. 1
pp. 1 – 11

Abstract

Read online

Spatial transcriptomics experiments profile genome-wide gene expression at localized spots across a tissue. Here, the authors identify spot swapping, an artifact where RNA expressed at one tissue spot binds probes at another, and they propose SpotClean to adjust for it.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

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