10X Genomics Visium
The Visium platform from 10x Genomics combines histology and spatially resolved whole transcriptome gene expression profiling to localize and quantify gene expression in the tissue context. The UMN Genomics Center (UMGC) offers two assays for spatial analysis: 1) Visium HD at single cell-scale resolution and 2) Spatial Gene Expression (Visium Standard) at 55 uM resolution. Visium is compatible with a variety of tissues and species, depending on the specific assay you choose to employ. Visium Spatial Gene Expression for fresh frozen tissue leverages a poly(A)-based capture chemistry and is therefore species agnostic. Visium CytAssist (HD and Spatial Gene Expression) is a probe-based assay that enables analysis of fresh frozen, fixed frozen, and FFPE tissue sections from human or mouse samples.
Key Features:
- High spatial resolution: The Visium HD assay achieves single-cell spatial resolution through Visium HD slides. The features on the Visium HD slide are 2 x 2 μm barcoded squares with no gaps between squares.
- Sample preparation methods: Start the workflow from H&E or IF-stained fresh frozen, fixed frozen, or FFPE tissue blocks and freshly sectioned onto glass slides, or from pre-sectioned tissue slides. This FFPE compatibility provides access to archived samples.
- Optimized conditions for numerous tissues: The direct placement Visium assay for fresh frozen tissue has been optimized for healthy and diseased fresh frozen tissues in diverse organisms, including human, mouse, rat, and zebrafish. Up-to-date list of fresh frozen tissues optimized for the Visium assay.
- Two library prep options: Training to run the Visium assay is available through the UMGC CoLab, or the UMGC Spatial Services will manage the probe transfer and prepare gene expression libraries.
- Sequence compatibility: The UMGC sequences Visium libraries on the Illumina NovaSeq X Plus or the low-cost Element AVITI instruments. The choice of sequencing platform depends on the project size: smaller projects are more cost-effective on the Aviti platform, while larger projects are better suited for the NovaSeq X Plus.
- Data analysis solutions: 10x Genomics provides two software tools to process and visualize Visium data, Space Ranger and Loupe Browser. The UMGC will provide output files from Space Ranger that can be used in Loupe Browser or third-party tools to visualize and apply spatial analysis methods to the data.
Additional Information:
Visium Standard vs HD
| Visium Features | Standard | Standard | HD |
|---|---|---|---|
| Species | Agnostic | Mouse, Human | Mouse, Human |
| Sample preservation method | Fresh frozen | FFPE, fixed, fresh frozen | FFPE, fixed, fresh frozen |
| Chemistry | PolyA capture | Probe-based (CytAssist) | Probe-based (CytAssist) |
| Distribution of capture oligos | 55 micron spots | 55 micron spots | 2 micron tiles |
| Number of distinct capture elements | ~5,000 | ~5,000 | ~10 million |
Capture size (mm) | 6.5 x 6.5 | 11 x 11 or 6.5 x 6.5 | 6.5 x 6.5 |
Library Prep Options
Reseachers have self-service and full-service options for Visum library prep:
- Full-service: UMGC Spatial Services will manage the probe transfer and prepare gene expression libraries.
- Self-service: Training to run the Visium assay is available through the UMGC CoLab.
The UMGC CoLab provides a co-working space with shared access to the UMGC’s lab and instruments, and training in genomic methods. Training and bench space access are provided at no cost to UMN researchers.
For researchers wanting training on the Visium or Curio workflows, researchers will follow the library preparation protocol under the guidance of a UMGC scientist. Before a CoLab training date is set, researchers will meet with Bionet and the UMGC to discuss sample preparation, sectioning, and mounting on slides. Researchers have the option to provide samples already cut on slides or request the service through Bionet.
FAQs
What tissue stains are compatible with Visium?
Visium is compatible with hematoxylin and eosin (H&E) staining for morphological information and with immunofluorescence (IF) staining for protein co-detection.
What Visium datasets are available?
Access free, publicly available data from a number of different sample types generated with Visium spatial solutions. View datasets on the 10X website.
Where can more information be found?