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Related Experiment Video

Updated: Aug 5, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

Published on: July 6, 2022

SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data.

Souvik Seal¹, Benjamin G Bitler², Debashis Ghosh³

¹Department of Public Health Sciences, School of Medicine, Medical University of South Carolina, Charleston, USA.

Biorxiv : the Preprint Server for Biology

|March 30, 2023

Summary

Identifying spatially variable genes (SVGs) is key in spatial transcriptomics. SMASH is a new method that efficiently detects SVGs with high statistical power, offering biological insights into tissue structure and function.

Keywords:

10X Visium Covariance Modelling MERFISH Non-paramteric method Single cell imaging datasets Slide-seq V2 Spatial transcriptomics Spatially variable genes

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

High-throughput spatial transcriptomics (ST) enables gene expression analysis within tissue context.
Identifying spatially variable genes (SVGs) is crucial for understanding tissue structure and function.
Current SVG detection methods face challenges with computational demand or statistical power.

Approach:

Propose SMASH, a novel non-parametric method for detecting SVGs.
SMASH balances computational efficiency with high statistical power.
Validate SMASH through simulations and application to diverse ST datasets.

Key Points:

SMASH demonstrates superior statistical power and robustness compared to existing methods in simulations.
The method effectively identifies biologically relevant SVGs across different ST platforms.
SMASH provides valuable insights into the spatial organization of gene expression in complex tissues.

Conclusions:

SMASH offers an effective and efficient solution for SVG detection in ST studies.
The method enhances biological discovery by revealing spatially organized gene expression patterns.
SMASH is a valuable tool for researchers in transcriptomics and computational biology.