Products Area of Interest Resources Support Company Careers 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. Request Pricing See How It Works Resources: Product Catalog Download Fresh Frozen Product Sheet Download FFPE Product Sheet Download App Note Access more sample types Compatible with both FFPE and fresh frozen tissue samples. 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. Diverse sample compatibility Demonstrated on a diverse set of organs across species (human, mouse, rat, and more). Protein co-detection Combine whole transcriptome spatial analysis with immunofluorescence protein detection. 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 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. Download Product Sheet Detect the whole transcriptome across entire FFPE tissue sections with high sensitivity and specificity Examine biobanked FFPE tissue samples to discover new biomarkers Immunofluorescence Protein co-detection Enable discovery of novel cell types and their spatial organization by combining immunofluorescence and whole transcriptome spatial gene expression. Download Product Sheet View Product Page Explore transcriptome and protein relationships with simultaneous spatial detection Discover new tissue biomarkers with cell-type specificity 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. View Product Page 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 Videos Watch to learn how customers are using Visium Spatial Gene Expression. View all Publications Resources Learn more about Visium Spatial Gene Expression 10x Genomics, April 2021 See how oncology translational researchers are using Visium Spatial Gene Expression Elizabeth Jaffee, Elana Fertig, and Luciane Kagohara, Johns Hopkins University Getting Started with 10x Visium Spatial for FFPE Jacob Stern and Francesca Meschi, PhD, June 2021 View all Our end-to-end solution Visium Spatial Gene Expression 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 Space Ranger Our analysis pipelines Loupe Browser Our visualization software World-class technical and customer support Our expert support team can be contacted by phone or email. Workflow 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 Tissue Preparation Guide Optimized Fresh Frozen Tissues Fresh Frozen How-To Videos FFPE Tissues Tested FFPE How-To Videos 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 Imaging Guidelines Visium Fresh Frozen User Guide Visium FFPE User Guide 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 Visium Fresh Frozen User Guide Visium FFPE User Guide (Coming Soon) 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 Sequencing Requirements 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 Space Ranger Analysis Pipelines Loupe Visualization Software Downloadable Datasets Frequently Asked Questions What does Visium Spatial Gene Expression enable you to do? What types of samples are compatible? Is this a proven technology? How do I analyze my Visium Spatial Gene Expression data? Does the Visium assay require tissue optimization? Related Products View All 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 Chromium X Series Chromium Controller Chromium Connect Chromium X Series Chromium Controller Get Started Request Pricing ABOUT Products Platform Company Careers Contact Employment Verification LEGAL NOTICES Privacy Policy Terms of Use Email Preferences Other Legal Notices HEADQUARTERS +1 925 401 7300 +1 800 709 1208 info@10xgenomics.com RESOURCES Publications Support Videos SOCIAL SIGN UP FOR PRODUCT AND EVENT UPDATES Subscribe © 2021 10x Genomics. All Rights Reserved. English中文日本語