3 Introduction to 10x Genomics Xenium
Xenium In Situ is 10x Genomics’ high-resolution spatial transcriptomics platform that enables the detection of RNA molecules directly within intact tissue sections, preserving cellular and subcellular spatial context. Unlike sequencing-based spatial platforms like Visium, Xenium is an imaging-based technology that uses fluorescent detection of barcoded probes to measure RNA expression at near-single-cell or even subcellular resolution.
3.1 🔧 How Xenium Works
- Uses padlock probes and rolling circle amplification to label RNA molecules in situ.
- Targets a panel of genes (up to ~400–1000 genes, depending on panel design).
- Detection is done via fluorescence microscopy, capturing multiple imaging cycles.
- The result is spatially resolved gene expression data, with high sensitivity and specificity.
3.2 📦 Xenium Data Output
Xenium produces several types of output files, typically including:
- RNA molecule coordinates (per gene, per spot)
- Cell segmentation and assignments
- Gene counts per cell
- Morphology and fluorescence images
These files allow detailed analysis of gene expression within and across individual cells while preserving their spatial relationships.
3.3 🧠 Applications of Xenium
- Single-cell spatial profiling in tissue sections
- Identifying cell types and states based on spatial markers
- Analyzing cellular neighborhoods and microenvironments
- Studying spatial regulation of gene expression in disease
✅ In this workshop, we’ll go through how to process and visualize Xenium data, including quality control, data import into analysis tools (like Seurat or Squidpy), and downstream interpretation.