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Detection of allele-specific expression in spatial transcriptomics with spASE
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Detection of allele-specific expression in spatial transcriptomics with spASE
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Journal Article
Detection of allele-specific expression in spatial transcriptomics with spASE
2024
Overview
Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framework for detecting and estimating spatial ASE. To tackle the challenges presented by cell type mixtures and a low signal to noise ratio, we implement a hierarchical model involving additive mixtures of spatial smoothing splines. We apply our method to allele-resolved Visium and Slide-seq from the mouse cerebellum and hippocampus and report new insight into the landscape of spatial and cell type-specific ASE therein.
Publisher
BioMed Central,Springer Nature B.V,BMC
