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University of Wisconsin–Madison

Gene Expression Center

The UW-Madison Biotechnology Center is currently open and following the university's COVID-19 Response regarding campus operations.

10X Genomics Visium Spatial Gene Expression

10x picture

The 10x Genomics Visium Spatial Gene Expression Assay combines histological tissue sectioning and RNA sequencing to map gene expression location patterns throughout a whole tissue section at a resolution of 1-10 cells. In this assay, a tissue section is placed on a slide above an array of 5,000 spots, each containing barcoded oligo(dT) capture oligonucleotides that imprint the spatial position of a captured mRNA molecule into the downstream cDNA sequencing read. The sequencing data from these spots are overlaid with imaging data from the tissue section to allow for users to visualize the location of gene expression within the tissues and identify clusters based on differential gene expression.

The Gene Expression Center offers the Visium Spatial Gene Expression Assay in collaboration with the UW-Madison TRIP lab, which provides the imaging service. Libraries are prepared in the GEC and sequenced on the NovaSeq in collaboration with the UWBC DNA Sequencing Facility followed by optional analysis by the UWBC Bioinformatics Resource Center.  The resulting data can then by analyzed and explored using the freely downloadable Loupe Browser software (click here for an overview of the Loupe Browser, including links to the software download, tutorials, and sample data).

For more information, please see this presentation put together by TRIP lab and GEC staff. 

Please e-mail to schedule a meeting to discuss your proposed experiment and timeline!

Visium Overview

Visium Spatial Gene Expression Submission Guidelines 

  • Coordinate with the TRIP lab for tissue handling and submission specifics.
    • General guidelines
      • Tissue freezing in liquid nitrogen-cooled isopentane prior to OCT embedding or simultaneous OCT embedding and freezing should be performed immediately after tissue is available.
      • Store the OCT embedded tissue block in a sealed container at -80C for long-term storage until ready for processing.
      • The recommended section thickness for most tissue types is 10 μm.  Some tissues require thicker sections; see list of optimized tissues.
    • For more information, see the 10x Genomics Tissue Preparation Guide.
    To request a quote please contact

    10x Genomics Single Cell Features

    • Workflow from single cell suspensions.
    • 8-channel microfluidic chip allowing up to 8 samples to be processed simultaneously.  Samples are barcoded individually for a multiplexed sequencing reaction.
    • 10x Chromium instrument capable of capturing 100 to 10,000 cells per sample; up to 80,000 cells per chip in ~7 minutes.
    • Recovers up to 65% of cells (typically closer to 50% depending on cell type)
    • Low doublet rate: ~0.8% per 1,000 cells; ~1.6% per 2,000 cells; ~2.3% per 3,000 cells; ~3.1% per 4,000 cells; ~3.9% per 5,000 cells; etc.
    • 50,000 reads per cell should be sequenced for saturating gene detection.  70,000 reads per cell is appropriate for expression analysis. 
    • Nuclei suspension can also be prepared and sequenced.
    All data and services provided by the University of Wisconsin Biotechnology Center Gene Expression Center are intended for research purposes only. Services are not intended nor certified for diagnostic or clinical use.