Visium Spatial Gene Expression

Map the whole transcriptome within the tissue context

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

Spatial Gene Expression

Resources:

  • Access more sample types

    Access more sample types

    Compatible with both FFPE and fresh frozen tissue samples.

  • 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.

  • Diverse sample compatibility

    Diverse sample compatibility

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

  • Protein co-detection

    Protein co-detection

    Combine whole transcriptome spatial analysis with immunofluorescence protein detection.

  • Streamlined data analysis

    Streamlined data analysis

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

Explore what you can do

  • Gain a complete view of disease complexity

  • Discover new biomarkers

  • Map the spatial organization of cell atlases

  • Identify spatiotemporal gene expression patterns

More than a tissue slide

FFPE compatibility

FFPE

FFPE compatibility

Combine the benefits of histological techniques with the massive throughput and discovery power of RNA sequencing to detect the whole transcriptome in FFPE samples.

  • Detect the whole transcriptome across entire FFPE tissue sections with high sensitivity and specificity
  • Examine biobanked FFPE tissue samples to discover new biomarkers
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
Whole transcriptome or targeted assays

Flexible transcriptomic analysis

Whole transcriptome or targeted assays

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

  • Powerful discovery—Envision the spatial organization of newly discovered cell types, states, and biomarkers with whole transcriptome analysis of fresh frozen or FFPE tissues
  • Targeted gene expression—Focus on all of the relevant genes and pathways with the convenience of pre-designed targeted panels for fresh frozen tissues

Proven results

Proven results

Videos

Watch to learn how customers are using Visium Spatial Gene Expression.

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 Neuroscience 2021.

Maynard KR, et al. Nature Neuroscience 2021.

Spatiotemporal analysis of human intestinal development at single-cell resolution

Spatiotemporal analysis of human intestinal development at single-cell resolution

Fawkner-Corbett D, et al. Cell 2021.

Fawkner-Corbett D, et al. Cell 2021.

TGFβ-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts

TGFβ-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts

Grauel AL, et al. Nature Communications 2020.

Grauel AL, et al. Nature Communications 2020.

Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma

Multimodal analysis of composition and spatial architecture in human squamous cell carcinoma

Ji AL, et al. Cell 2020.

Ji AL, et al. Cell 2020.

Resources

Find the latest app notes and other Spatial Gene Expression documentation

Inside Visium spatial capture technology

Inside Visium spatial capture technology

Brochure, 10x Genomics

Brochure, 10x Genomics

Grant writing resource for Visium Spatial Gene Expression

Grant writing resource for Visium Spatial Gene Expression

Grant Application Resource, 10x Genomics

Grant Application Resource, 10x Genomics

Prostate cancer app note

Prostate cancer app note

App Note, 10x Genomics

App Note, 10x Genomics

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.

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.

    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

    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.

    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, which combines histological spatial information with whole transcriptome gene expression profiles (fresh frozen or FFPE) or targeted gene expression profiles (fresh frozen only).

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: Fresh Frozen | FFPE tissues

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 (including Sanger, SciLife, Broad, USC, and Garvan) have been able to generate spatial gene expression profiles for a number of different sample types. Internally, over 30 different fresh frozen tissues and a variety of different FFPE tissues have been tested successfully.

Publication page

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.

Support page

The Visium Spatial Gene Expression assay for FFPE tissues does not require tissue optimization. However, the Visium Spatial Gene Expression assay for fresh frozen tissues does require tissue optimization due to differences in the chemistry and molecular biology between the Visium assays for the two sample preparation types.

Related Products

Products

Spatial Gene Expression

View details

Single Cell Gene Expression

View details

Single Cell Immune Profiling

View details

Single Cell ATAC

View details

Capabilities

  • 3' whole transcriptome gene expression
  • Targeted gene expression
  • Compatible with FFPE and fresh frozen tissue sections
  • 3' whole transcriptome gene expression
  • Targeted gene expression
  • Sample multiplexing
  • Paired full-length TCR / BCR sequencing
  • 5’ whole transcriptome gene expression
  • Targeted gene expression
  • Epigenomic landscape by open chromatin profiling

Extensions

  • Spatial Gene Expression with Immunofluorescence
  • Immunofluorescence protein co-detection
  • Sample multiplexing
  • Cell Surface Protein
  • CRISPR Screening
  • Cell Surface Protein
  • Antigen Specificity

Instruments

  • Chromium X Series
  • Chromium Controller
  • Chromium Connect
Single Cell Gene Expression

Get Started