Detection of Allele-specific Expression in Spatial Transcriptomics with SpASE

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2024 Jul 8

PMID 38978101

Authors

Luli S Zou

Dylan M Cable

Irving A Barrera-Lopez

Tongtong Zhao

Evan Murray

Martin J Aryee

Fei Chen

Rafael A Irizarry

Affiliations

Soon will be listed here.

Abstract

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.

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