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

Gillespie, J.; Xie, J.; Jung, K. J.; Hardiman, G.; Pietrzak, M.; Chung, D.

doi:10.1101/2025.05.01.651786

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bioRxiv · 10.1101/2025.05.01.651786

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

Gillespie, J.·Xie, J.·Jung, K. J.·Hardiman, G.·Pietrzak, M.·Chung, D.

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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

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Gillespie, J., Xie, J., Jung, K. J., Hardiman, G., Pietrzak, M., Chung, D.. 2025-05-07. A Gentle Introduction to Spatial Transcriptomic Analysis with 10X Visium Data. https://doi.org/10.1101/2025.05.01.651786

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