Xenium Analyzer from 10x Genomics

The most intuitive, high-throughput in situ analyzer

Service Overview

The advancements of targeted high-plex in situ analysis provided by Xenium gives scientists the capability to view their samples with subcellular resolution and at a depth like never before, by profiling up to 1,000s of targets, each in the context of their spatial localization patterns. This type of analysis enables studies to not only locate and type cells within their biological context, but also address questions about cell–cell communication, profile cellular microenvironments, and identify rare cell infiltration.

Therefore, Xenium In Situ provides another powerful tool that can be used alongside insights gained from Chromium Single Cell and Visium Spatial. The Xenium platform is a complete end-to-end solution that enables scientists to visualize, quantify, and analyze gene expression and protein in FF and FFPE-preserved tissue sections immobilized onto a Xenium slide. A diverse menu of validated, customizable fit-for-purpose gene panels, as well as fully custom and multi-tissue panels, are available for highly sensitive profiling of genes of interest.

The platform includes the Xenium Analyzer, a robust, versatile instrument for high-throughput analysis, that comes with onboard analysis capabilities to process image data, localize RNA and protein signals, and perform secondary analysis. You can also easily transfer data off the instrument to perform visualization and further analysis with 10x Genomics–provided software or third-party tools of your choice.

Additionally, researchers have access to 10x Genomics technical experts who can provide support through scientific and technical consultations, workflow optimization, and methodology troubleshooting.

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Xenium In Situ

Xenium is an end-to-end spatial platform from 10x Genomics that enables high-throughput subcellular mapping of 100s to 1,000s of RNA targets alongside multiplexed protein in the same tissue section. 

Compatible with fresh frozen (FF) and formalin-fixed, paraffin-embedded (FFPE) tissues, the platform includes the Xenium Analyzer, a versatile and easy-to-use spatial instrument; sensitive and specific chemistry; a diverse menu of customizable panels; and software. Data can be visualized with the intuitive Xenium Explorer or community-developed analysis tools. 

As with other 10x Genomics products, the Xenium platform has a robust roadmap to enhance the core platform with more capabilities and analytes. 

Xenium In Situ platform

Sample preparation

The Xenium workflow starts with sectioning tissues onto a Xenium slide (Figure 1). The sections are then treated to preserve and access the RNA with circularizable DNA probes. The DNA probes are flanked by two regions that independently hybridize to the target RNA and also contain a gene-specific barcode sequence. Ligation of the probe ends to each other then generates a circular DNA probe which is enzymatically amplified.

In the event that one part of the probe experiences off-target binding, ligation will not occur, thus suppressing off-target signals and ensuring high specificity. Multiplexed protein detection, a proven capability that will be enabled on the platform in the future, will leverage DNA-barcoded antibodies for labeling of protein targets in each tissue section.

The Xenium workflow is also non-destructive. With the sample morphology intact at the end of the workflow, both hematoxylin & eosin (H&E) and immunofluorescence (IF) staining are possible on the same tissue section, enabling the direct comparison of Xenium transcriptional data to morphological data.

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