Spatial Transcriptomics
method
spatial-omics
Definition
Spatial transcriptomics measures gene expression while preserving information about where transcripts, cells, or spots are located in tissue.
What It Gives
- Gene expression with spatial coordinates
- Tissue-region-specific expression programs
- Spatial gradients from tumour core to stroma
- Input data for spatial domain and spatial ecotype analysis
Common Platforms
- 10x Genomics Visium
- Visium HD
- MERSCOPE
- Xenium
- Legacy ST platforms
Main Limitation
Platforms trade off spatial resolution, gene coverage, throughput, cost, and sensitivity. Some assays capture transcriptome-wide data at spot-level resolution; others provide single-cell resolution with targeted gene panels.
In Papers
- Zhang et al. 2026 integrates multiple spatial transcriptomics platforms to identify and validate spatial ecotypes.