Department

Computer Science

Document Type

Article

Publication Title

eLife

ISSN

2050-084X

DOI

10.7554/eLife.87211.1

Publication Date

Spring 1-1-2023

Abstract

Technical advances have led to an explosion in the amount of biological data available in recent years, especially in the field of RNA sequencing. Specifically, spatial transcriptomics (ST) datasets, which allow each RNA molecule to be mapped to the 2D location it originated from within a tissue, have become readily available. Due to computational challenges, ST data has rarely been used to study RNA processing such as splicing or differential UTR usage. We apply the ReadZS and the SpliZ, methods developed to analyze RNA process in scRNA-seq data, to analyze spatial localization of RNA processing directly from ST data for the first time. Using Moran’s I metric for spatial autocorrelation, we identify genes with spatially regulated RNA processing in the mouse brain and kidney, re-discovering known spatial regulation in Myl6 and identifying previously-unknown spatial regulation in genes such as Rps24, Gng13, Slc8a1, Gpm6a, Gpx3, ActB, Rps8 , and S100A9 . The rich set of discoveries made here from commonly used reference datasets provides a small taste of what can be learned by applying this technique more broadly to the large quantity of Visium data currently being created.

Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

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