Spatial gene expression profiling

Overview:

Spatial transcriptomics with the 10x Genomics Xenium platform enables high-plex in situ gene expression profiling directly within intact tissue sections, preserving the native spatial organization of cells and their microenvironment. The technology uses targeted RNA detection through highly specific probe sets, combined with iterative fluorescent imaging, to localize transcripts at single-cell and subcellular resolution. Xenium analysis is performed entirely on the instrument, producing spatially resolved gene expression maps without requiring sequencing. The assay is applicable to fresh-frozen or FFPE tissues, provided that sample integrity, fixation quality, and sectioning thickness (typically 5–10 µm) meet platform requirements. Xenium enables accurate detection and quantification of hundreds to thousands of selected transcripts, supporting detailed reconstruction of tissue architecture, cell-type composition, cell–cell interactions, and niche-level organization. It is particularly suited for characterizing tumor microenvironments, immune infiltration patterns, developmental processes, and biomarker distribution in both healthy and pathological tissues.

Workflow:

Tissue sectioning, fixation and permeabilization, probe hybridization, imaging, sequencing.