Xenium – In Situ Sequencing
Xenium (Launching Q3 2025) enables high resolution through in situ sequencing with a predefined gene panel, offering cell segmentation. This cutting-edge approach allows for subcellular resolution, providing unparalleled insights into the spatial distribution of transcripts within specific cellular compartments. With Xenium, researchers can achieve precise cell segmentation and detailed analysis of gene expression patterns.
Capture: In situ sequencing (padlock probe-based)
Tissue: Fresh, FFPE
Resolution: Subcellular (0,3 µm)
Cell segmentation: Multimodal cell segmentation
Species: Human, mouse tissue and species-agnostic (custom panel)
Analyte: predesigned panels (up to 100 custom genes) and complete custom panels
Size ROI: 10.45 mm x 22.45 mm
Links to 10x Genomics: Xenium platform and Panel Designer
Sample Type: FFPE tissue
RNA Quality: DV200 >30% recommended for optimal data quality
Tissue Morphology: Optional but recommended (DAPI/H&E staining) to assess suitability. Avoid artifacts like necrosis or cracks.
Protocols:
Section Thickness: 5 µm (recommended)
Slide Type: Xenium-compatible slides (refer to 10x Genomics guidelines)
Sectioning: Ensure precise placement within the Xenium instrument’s capture area.
Replicates: Provide backup sections for troubleshooting or optimization.
Storage: Store the Xenium slide containing dry tissue sections at room temperature in a desiccator for up to 4 weeks
Imaging: Before delivery, send images of DAPI/H&E staining.
RNA Quality & Assessment
Researchers must extract RNA and assess transcript quality (DV200). Positive results help identify low-risk samples but do not guarantee success.
Variability & Outcome
Gene count, UMIs per spot, and overall success vary by tissue type, species, embedding date and protocol, as well as RNA quality.
Library Construction & Sequencing
qPCR confirms RNA capture. Investigators decide whether to proceed with sequencing:
- If a sample fails and sequencing is skipped, users cover reagent and user fees.
- If a suboptimal sample fails after sequencing, users cover reagent and labor costs.