*Please note: Visium for FFPE is now available for human and mouse samples. More information coming soon.*
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 (link 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 firstname.lastname@example.org to schedule a meeting to discuss your proposed experiment and timeline!
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.