Visium Spatial Gene Expression

Map the Whole Transcriptome Within the Tissue Context

Visium Spatial Gene Expression is a next-generation molecular technology for classifying tissue based on total mRNA. Map the whole transcriptome with morphological context to discover novel insights into normal development, disease pathology, and clinical translational research.

Spatial Gene Expression
  • Protein co-detection

    Protein co-detection

    Combine whole transcriptome spatial analysis with immunofluorescence protein detection.

  • Profile entire tissue sections

    Profile entire tissue sections

    No need to select regions of interest—analyze the whole transcriptome from an entire section.

  • High resolution

    High resolution

    1–10 cell resolution on average per spot depending on tissue type.

  • Streamlined data analysis

    Streamlined data analysis

    Combine histological and gene expression data with easy-to-use software.

  • One-day lab workflow

    One-day lab workflow

    From tissue section to sequencing-ready library in one day.

  • Diverse sample compatibility

    Diverse sample compatibility

    Demonstrated on a diverse set of organs across species (human, mouse, rat, and more).

Explore what you can do

  • Gain a complete view of disease complexity

  • Discover new biomarkers and identify novel cell types and states

  • Map the spatial organization of cell atlases

  • Identify spatiotemporal gene expression patterns

Flexible Targeted and Whole Transcriptome Assays

Spatially map global gene expression with whole transcriptome analysis or focus on your genes of interest using targeted gene expression panels.

Targeted Gene Expression Panels

Choose from pre-designed cancer, immunology, neuroscience and gene signature panels with the ability to add up to 200 custom genes.

With our comprehensive Visium Spatial Gene Expression solutions you get:

Powerful discovery

Envision the spatial organization of newly discovered cell types, states, and biomarkers with whole transcriptome analysis.

Seamless integration

Transition seamlessly between whole transcriptome and targeted analysis from the same library preparation to validate discoveries and explore new hypotheses.

Focused expansion

Scale up from a few genes of interest to all relevant genes and pathways by combining high-throughput spatial gene expression with the efficiency of targeted panels.

Extendable for Protein Co-detection

Protein Co-Detection

Immunofluorescence

Protein Co-Detection

Enable discovery of novel cell types and their spatial organization by combining immunofluorescence and whole transcriptome spatial gene expression.

  • Explore transcriptome and protein relationships with simultaneous spatial detection
  • Discover new tissue biomarkers with cell type specificity

Proven Results

Proven Results

Videos

Watch how customers are using Spatial Gene Expression.

Publications

Search hundreds peer-reviewed publications using Spatial Gene Expression.

Resources

Find the latest app notes and other documentation Spatial Gene Expression.

Our End-to-End Solution

Visium Spatial Tissue Optimization Slides

Visium Spatial Tissue Optimization Slides

Easily adoptable within existing lab infrastructure, no need for a new instrument.

Visium Spatial Gene Expression Reagents

Visium Spatial Gene Expression Reagents

With our reagent kits, capture whole transcriptome gene expression with spatial resolution across an entire tissue section.

Analysis and Visualization Software

Analysis and Visualization Software

Our analysis pipelines

Our visualization software

World-Class Technical and Customer Support

World-Class Technical and Customer Support

Our expert support team can be contacted by phone or email.

Workflow

  1. 1Step 1

    Prepare your sample

    Embed, section, and place fresh-frozen tissue onto a capture area of the gene expression slide. Each capture area has thousands of barcoded spots, each containing millions of capture oligonucleotides with spatial barcodes unique to that spot.

    Resources
  2. 2Step 2

    Stain and image the tissue

    Utilize standard fixation and staining techniques, including Hematoxylin and Eosin (H&E) staining, to visualize tissue sections on slides using a brightfield microscope and immunofluorescence staining to visualize protein detection in tissue sections on slides using a fluorescent microscope.

    Resources
  3. 3Step 3

    Permeabilize tissue and construct library

    Permeabilize the tissue to release mRNA from the cells, which binds to the spatially barcoded oligonucleotides present on the spots. A reverse transcription reaction produces cDNA from the captured mRNA. The barcoded cDNA is then pooled for downstream processing to complete a sequencing-ready library.

    Resources
  4. 4Step 4

    Sequence

    The resulting 10x Barcoded library is compatible with standard NGS short-read sequencing on Illumina sequencers for massive transcriptional profiling of entire tissue sections.

    Resources
  5. 5Step 5

    Analyze and visualize your data

    Use our Space Ranger analysis software to process your Spatial Gene Expression data and interactively explore the results with our Loupe Browser visualization software.

    Do I need to be a bioinformatician to use Loupe?

    Loupe is a point-and-click software that’s easy for anyone to download and use.

    Resources

Frequently Asked Questions

It enables you to perform spatial transcriptomics, where histological spatial information is paired with whole transcriptome data or targeted gene expression profiles from panels in cancer, immunology, and gene signatures.

Visium is compatible with fresh-frozen tissues containing mRNA. Right now, Visium is not compatible with fixed sample types. However, it is something that we are actively working to enable in the future. A list of tissues successfully tested in-house can be found below.

Visium is based on Spatial Transcriptomics technology, which has been demonstrated by a number of published peer review articles. You can find them on our publications page. For external validation of Visium, beta testers, such as Sanger, SciLife, Broad, USC, and Garvan, have been able to generate spatial gene expression profiles for a number of different sample types. Internally, 30+ different tissues have been tested successfully.

10x Genomics provides two types of software to help you analyze your data: Space Ranger and Loupe Browser. Space Ranger is an analysis software which automatically overlays spatial gene expression information on your tissue image and identifies clusters of spots with similar transcription profiles. You can then use Loupe Browser, a visualization software, to interactively explore the results. You can download Space Ranger and Loupe Browser from the 10x Support site at no cost.

Visium Spatial Gene Expression is compatible with pre-designed targeted panels offered by 10x Genomics. Customizing the pre-designed panels with up to 200 genes or 10 endogenous sequences is supported using the Custom Panel Designer; however, fully custom panels are not supported at this time.

Single Cell Gene Expression

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