A Gentle Introduction to Spatial Transcriptomic Analysis with 10X Visium Data

Abstract

Spatial transcriptomics (ST) combines single-cell RNA-seq gene expression data with spatial coordinates to provide an accurate, 2D picture of gene expression across a tissue sample. With this technology, we can discover detailed RNA localization, study development, investigate the tumor microenvironment, and create a tissue atlas. Full ST analysis requires several steps, however, as this protocol aims to be a simple introduction to the analysis process, only the foundational steps of clustering, spatially variable gene discovery, and cell-cell communication are presented, focusing on data obtained from the 10X Genomics Visium platform. An expanded protocol with full code is available at https://github.com/j-gillespie-dna/STanalysis.git