Xenium In Situ Gene Expression

Expertly curated, easily customizable in situ panels

Xenium In Situ is the next-level in situ solution for subcellular profiling of 100s of RNA targets, in fresh frozen or FFPE tissue. Our diverse panel menu of biologically relevant content can also be customized for your specific research questions.

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In Situ Gene Expression
  • Expertly curated. Biologically relevant

    Each panel is carefully designed using a data-driven approach and the input of subject matter experts.

  • Flexible compatibility

    Panels work on fresh frozen or FFPE tissues, and the assay maintains tissue integrity, making H&E or IF staining post-Xenium runs possible.

  • Easy to implement

    Validated panels need no optimization, saving time and precious samples, so you can focus on your science.

  • Diverse panel menu

    Focused panels capture relevant foundational biology across different tissue types for streamlined data analysis and faster answers.

  • Customizable

    Easily add up to 100 custom targets to any panel, letting you address your specific research objectives.

  • High performance

    Have confidence in your results thanks to the proprietary chemistry and probe design, which deliver high sensitivity and specificity.

Learn the story of each cell

Explore the unique gene signatures of the cells in your fresh frozen (FF) and FFPE tissues with single cell and subcellular resolution.

Reveal cell relationships from development to health to disease

Uncover the cell–cell interactions and relationships that influence cellular function in the context of health and disease.

Lock and preserve rapidly changing cell states

Perform studies with short timescales, where samples change rapidly in response to a treatment or perturbation.

Validate discoveries from Chromium and Visium experiments

Build gene expression maps of key targets with subcellular resolution to refine and validate biological mechanisms discovered with whole transcriptome technologies.

Targeted, customizable panels

Human Breast Gene Expression Panel

Optimal for high-resolution cell typing of breast tissues and characterization of breast cancer disease states, including tumor microenvironments.
  • ~280 genes chosen to target cell types and cell states for human breast tissue
  • Customize up to 100 genes for a total of 380 genes
  • Designed using a wealth of public single cell datasets with direct input from customers
Human Breast Gene Expression Panel

Mouse Brain Gene Expression Panel

Optimal for high-resolution cell typing of mouse brain tissue.
  • ~248 genes chosen to target cell types and cell states for mouse brain research
  • Customize up to 100 genes for total of 348 genes
  • Designed using single cell datasets with direct customer input
Mouse Brain Gene Expression Panel

Extensive panel roadmap

Stay tuned for an expanded menu of tissue and application panels.
  • Human Brain
  • Lung
  • Skin
  • Kidney
  • Pancreas
  • More to come!

Our end-to-end solution

Xenium Analyzer

Simple design and interface plus fast run times and on-instrument analysis combine for world-class in situ profiling.

Xenium In Situ reagents

Choose from a diverse menu of curated panels, customizable to fit your research needs.

Data visualization

Xenium Explorer provides off-instrument interactive visualization, simplified data QC, and exploration of subcellular readouts.

Dedicated team of spatial experts

Get the help you need from our expert support team, reachable by phone or email.

Xenium resources

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High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue

High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue

Janesick A, et al. bioRxiv (2022).

Janesick A, et al. bioRxiv (2022).

Interactive dataset

Interactive dataset

Interactive data visualization for human breast panel

Interactive data visualization for human breast panel

Xenium resources

Resources

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Frequently asked questions

Xenium has pre-validated RNA panels for analyzing 100s of RNA targets in human and mouse tissue. 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.

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 imaging or other downstream assays, including whole transcriptome analysis using Visium. This compatibility has been demonstrated for a limited number of samples and is not currently formally supported.

The Xenium assay can take as few as 2 days with ~3 hours of hands-on time before loading on the Xenium Analyzer.

Yes, you can add up to 100 custom targets to each panel. The same design process used for our off-shelf assays will be used to help you design probes for the custom targets.

Single Cell Gene Expression

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