- Xenium In Situ is 10x Genomics’ advanced spatial transcriptomics platform that enables high-resolution, single-cell analysis of gene expression directly in tissue samples. This technology provides researchers with detailed insights into cellular organization and gene expression patterns while preserving spatial context within the tissue architecture.
- The platform utilizes a novel approach to in situ analysis, combining high-sensitivity molecular detection with advanced imaging capabilities. It employs gene-specific probes and sequential chemistry to detect individual RNA molecules at subcellular resolution. The system can analyze hundreds of genes simultaneously in both fresh-frozen and FFPE (Formalin-Fixed Paraffin-Embedded) tissue samples, making it compatible with standard clinical specimen preservation methods.
- The workflow consists of several key steps. Initially, tissue sections are prepared and mounted on specialized slides. The platform then uses a cyclic detection method where specific probes hybridize to target RNA molecules. Each cycle involves hybridization, imaging, and signal removal, allowing for the detection of multiple genes. The system’s automated fluidics and imaging components ensure consistent and reliable data collection across the entire tissue section.
- Data processing and analysis are integral components of the Xenium workflow. The platform generates high-resolution images that capture both spatial information and molecular data. Advanced computational algorithms process these images to identify individual cells, quantify gene expression, and map spatial relationships. The analysis pipeline can identify cell types, analyze expression patterns, and reveal tissue organization at unprecedented resolution.
- A key feature of Xenium is its ability to detect and quantify individual RNA molecules with high specificity and sensitivity. This single-molecule resolution, combined with spatial context, provides researchers with detailed insights into gene expression heterogeneity within tissues. The technology can reveal subtle variations in gene expression between neighboring cells and identify rare cell populations within complex tissues.
- Applications of Xenium span various research areas. In cancer research, it helps understand tumor heterogeneity, immune cell interactions, and treatment responses. In developmental biology, it enables tracking of gene expression changes during tissue formation. The technology is also valuable in neuroscience, immunology, and other fields where understanding spatial context is crucial for biological interpretation.
- The platform offers several technical advantages. Its high sensitivity allows detection of low-abundance transcripts, while the multiplex capability enables comprehensive profiling of cellular states. The automated workflow reduces technical variability and increases reproducibility. The system also provides tools for data visualization and analysis, making complex spatial transcriptomics data more accessible to researchers.
- Technical considerations include sample preparation quality, probe design, and data management. Proper tissue handling and preservation are crucial for optimal results. The selection of target genes requires careful consideration of biological relevance and technical feasibility. The large datasets generated necessitate robust computational infrastructure and expertise in data analysis.
- Recent developments continue to enhance the platform’s capabilities. These include expanded gene panels, improved detection sensitivity, and advanced analysis tools. Integration with other single-cell and spatial analysis methods provides complementary approaches for comprehensive tissue analysis. The technology continues to evolve, offering new possibilities for understanding tissue organization and function.
