Xenium In Situ Panels

Target biology that matters. In situ.

Select pre-designed panels customizable with add-on genes, or design a custom panel for single cell spatial profiling of fresh frozen or FFPE tissue sections.

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Graphic showing a comparison of the time it takes to process 30,000 cells using Cell Ranger on various infastructures
Preorder Xenium Prime 5K assays now
An ultra-high-plex assay with exceptional data quality
  • Explore your tissue with 5,000 genes to deeply characterize cell types, pathways, cell-cell interactions & more
  • Get greater confidence in your results with an optimized assay, multimodal cell segmentation & high spatial fidelity
  • Obtain results faster with up to 472 mm² of tissue analyzed in 6 days or less
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Pre-designed Panels

Curated & validated biological content

Get started quickly with ready-to-use panels targeting major cell types and states.

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A menu of carefully validated pre-designed panels
Select a panel with up to 5,000 genes curated from published single cell tissue-specific atlases and customer input to meet your research goals.
Custom Panels

Complete flexibility for your research

Target unique gene markers, expression signatures, and cell types. Advanced customization allows for probes designed to target isoforms, gene , and more.

Which option is right for you?

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Panel Type

Pre-designed Panels

Add-on Custom Panels

Standalone Custom Panels

Use case

Pilot experiments or projects targeting cell types and states relevant to specific tissues or applications

Supplement pre-designed panels with additional markers important for your research

Recommended when gene expression signatures differ from content in the pre-designed panels

Number of genes

Depends on the selected panel

Up to 100 genes not covered by pre-designed panel

Up to 480 genes

Compatible organism

Human, mouse

Human, mouse

Diploid eukaryotic species, xenografts and most species with well-annotated transcriptomes

Turnaround time

Available for immediate shipping

4-6 weeks including design, building, and shipping

4-6 weeks including design, building, and shipping

Advanced customization

-

Include application-specific probes to target isoforms, gene fusions, viral or bacterial sequences, protein tags, and fluorescent reporters

View tech note

Include application-specific probes to target isoforms, gene fusions, viral or bacterial sequences, protein tags, and fluorescent reporters

View tech note
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Frequently asked questions

The majority of RNA species are detectable since this is a probe-based assay and does not use 3’ poly(A) capture. In the future, Xenium will have the capacity to analyze thousands of targets.

Several panel options are available to help you target genes of interest. Our Pre-designed Panels, which can be customized with up to 100 genes using a Custom Add-on Panel, are available for several human and mouse tissues. You also have the option to request a Standalone Custom Panel of up to 300 genes for mammalian or most other species with well-annotated transcriptomes.

Both the add-on and standalone custom panels can include advanced custom designs for targeting isoforms, gene fusions, viral or bacterial sequences, protein tags, fluorescent reporters, and transgenes. To learn more about the custom panels for species currently not offered by 10x Genomics and advanced customization options, please refer to the following Tech Note.

Xenium panels consist of a unified assay compatible with both fresh frozen and FFPE tissue. Furthermore, the gentle chemistry utilized allows for tissues to be processed for H&E or IF staining post-Xenium processing.

Xenium is a non-destructive analysis and the same tissue sections analyzed with Xenium can be transferred off-instrument and stained for H&E or IF imaging.

The Xenium assay can take as few as 2 days with 4–6hrs of hands on time before loading on the Xenium Analyzer.

Yes, you can add up to 100 custom targets to each off-the-shelf panel. Standalone custom panels of up to 480 genes can also be designed for mammalian and most other species with well-annotated genomes.

Additionally, advanced customization probes designed for special applications (e.g. isoforms, gene fusions, viral or bacterial sequences, protein tags, fluorescent reporters, and transgenes) can be requested for both Add-on Custom and Standalone Custom Panels.

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The Xenium In Situ platform consists of an automated analyzer, curated and/or custom panels, and intuitive visualization and analysis software.

Xenium In Situ Platform

Building on our years of innovation in single cell and spatial technologies, Xenium was designed to transform the way researchers can characterize RNA, protein, and cells in their native tissue environment.

Start your Xenium journey