Visium Spatial Proteogenomics

Tissue profiling with transcriptomics and protein co-detection

Combine whole transcriptome spatial analysis with immunofluorescence protein detection in the same tissue section. Gain a deeper, more holistic understanding of tissue organization with co-localized protein detection and gene expression analysis.

Spatial Proteogenomics

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  • Maximize your insights

    Maximize your insights

    Gain a deeper, more complete assessment of your samples with protein, total mRNA, and morphology in one.

  • Profile entire tissue sections

    Profile entire tissue sections

    Visualize protein detection and whole transcriptome expression, without selecting regions of interest.

  • Accessible technology

    Accessible technology

    Use standard microscopy, immunofluorescence staining protocols, and antibodies.

  • Streamlined data analysis

    Streamlined data analysis

    Combine protein detection profiles with gene expression data in easy-to-use software.

  • Accelerate discovery

    Accelerate discovery

    Get to results faster with parallel processing of up four samples per run.

  • Access more sample types

    Access more sample types

    Compatible with either FFPE or fresh frozen tissue samples.

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

Rich insights

  • Go back in time—Apply new biomarkers to archived FFPE samples and uncover hidden biology from the past
  • Multiomic analysis—Characterize heterogeneity more completely with spatial multiomic analysis of protein and mRNA to a single tissue section
  • Powerful discovery—Envision the spatial organization of newly discovered cell types, states, and biomarkers with protein detection and whole transcriptome analysis

Proven results

Proven results

Videos

Watch how customers are using Spatial Gene Expression.

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Publications

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Maynard KR, et al. Nature (2021).

Maynard KR, et al. Nature (2021).

Mapping the developing human immune system across organs

Mapping the developing human immune system across organs

Suo C, et al. Science (2022).

Suo C, et al. Science (2022).

Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer

Single-cell and spatial analysis reveal interaction of FAP+ fibroblasts and SPP1+ macrophages in colorectal cancer

Qi J, et al. Nature Communications (2022).

Qi J, et al. Nature Communications (2022).

Our end-to-end solution

Visium Spatial Gene Expression Slides

Visium Spatial Gene Expression 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 at [email protected]

Workflow

  1. 1Step 1

    Prepare your sample

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

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  2. 2Step 2

    Stain and image the tissue

    Utilize standard fixation and immunofluorescence (IF) staining to visualize tissue sections and protein markers using a fluorescent microscope.

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  3. 3Step 3

    Permeabilize tissue and construct library

    For fresh frozen tissue, the tissue is permeabilized 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 generate a sequencing-ready library. For FFPE tissues, tissue is permeabilized to release ligated probe pairs from the cells, which bind to the spatially barcoded oligonucleotides present on the spots. Spatial barcodes are added via an extension reaction. The barcoded molecules are then pooled for downstream processing to generate a sequencing-ready library.

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  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.

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  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

The Visium Spatial Gene Expression workflow is compatible with most fluorescence imaging systems, so the number of protein targets you can detect is dependent on your antibody selection and imaging configuration. We support up to four IF markers and recommend that DAPI be used for one of the channels. Please review our imaging guidelines (FFPE | Fresh frozen) for additional information.

Yes, there are several key differences between standard IF and the IF protocol used with Visium. Please refer to the IF Demonstrated Protocol (FFPE | Fresh frozen) for additional details.

Impact on Visium performance may vary from tissue to tissue due to the high sensitivity of the Visium assay. However, the spatial organization of gene expression and cell cluster detection is comparable between H&E and IF.

Visium is compatible with fresh frozen and FFPE tissues containing mRNA. We have separate kits that utilize different chemistries for fresh frozen and FFPE tissues. A list of tissues successfully tested in-house with the Visium assay can be found below.

Successfully tested tissues: FFPE tissues | Fresh frozen tissues

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 Genomics Support site at no cost.

Single Cell Gene Expression

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