RT Journal Article SR Electronic T1 BayesSpace enables the robust characterization of spatial gene expression architecture in tissue sections at increased resolution JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.09.04.283812 DO 10.1101/2020.09.04.283812 A1 Edward Zhao A1 Matthew R. Stone A1 Xing Ren A1 Thomas Pulliam A1 Paul Nghiem A1 Jason H. Bielas A1 Raphael Gottardo YR 2020 UL http://biorxiv.org/content/early/2020/09/05/2020.09.04.283812.abstract AB Recently developed spatial gene expression technologies such as the Spatial Transcriptomics and Visium platforms allow for comprehensive measurement of transcriptomic profiles while retaining spatial context. However, existing methods for analyzing spatial gene expression data often do not efficiently leverage the spatial information and fail to address the limited resolution of the technology. Here, we introduce BayesSpace, a fully Bayesian statistical method for clustering analysis and resolution enhancement of spatial transcriptomics data that seamlessly integrates into current transcriptomics analysis workflows. We show that BayesSpace improves the identification of transcriptionally distinct tissues from spatial transcriptomics samples of the brain, of melanoma, and of squamous cell carcinoma. In particular, BayesSpace’s improved resolution allows the identification of tissue structure that is not detectable at the original resolution and thus not recovered by other methods. Using an in silico dataset constructed from scRNA-seq, we demonstrate that BayesSpace can spatially resolve expression patterns to near single-cell resolution without the need for external single-cell sequencing data. In all, our results illustrate the utility BayesSpace has in facilitating the discovery of biological insights from a variety of spatial transcriptomics datasets.Competing Interest StatementR.G. has received consulting income from Juno Therapeutics, Takeda, Infotech Soft, Celgene, Merck and has received research support from Janssen Pharmaceuticals and Juno Therapeutics, and declares ownership in CellSpace Biosciences.