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.
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Protein co-detection
Combine whole transcriptome spatial analysis with immunofluorescence protein detection.
Profile entire tissue sections
No need to select regions of interest—analyze the whole transcriptome from an entire section.
High resolution
1–10 cell resolution on average per spot depending on tissue type.
Streamlined data analysis
Combine histological and gene expression data with easy-to-use software.
One-day lab workflow
From tissue section to sequencing-ready library in one day.
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 (Coming soon)
Choose from pre-designed cancer, immunology, neuroscience and gene signature panels with the ability to add up to 200 custom genes, or design fully custom panels. Optimized protocol, support, and software for targeted panels with Visium Spatial Gene Expression coming September 2020.
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
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
Our End-to-End Solution
Visium Spatial Tissue Optimization Slides
Easily adoptable within existing lab infrastructure, no need for a new instrument.
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
Our analysis pipelines
Our visualization software
World-Class Technical and Customer Support
Our expert support team can be contacted by phone or email.
Workflow
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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.
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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.
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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.
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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.
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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.
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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.
While Visium Spatial Gene Expression is compatible with the targeted gene panels offered by 10x Genomics, it is not supported at this time. A supported protocol, along with software analysis for targeted panels used with Visium Spatial Gene Expression, will be coming in September 2020.
