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 UMGC offers two assays for spatial analysis:
- Visium HD at single cell-scale resolution
- 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.
Explore the UMN Spatialomics Initiative website to learn more about the Visium platform and to compare technical details to other spatial platforms.
Service Details
- 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.
Questions
Contact Dr. Fernanda Rodriguez at [email protected] with questions on the 10X Visium platform or to schedule a consultation.
UMN Rates
| Service | Savings Tier | Speed Tier | Priority Tier |
|---|---|---|---|
| Visium. Library Prep. | $237.81 | $416.56 | $714.47 |
| Turnaround time. | 7 to 10 days | 5 to 7 days | 2 to 4 days |
External Rates
| Service | Savings Tier | Speed Tier | Priority Tier |
|---|---|---|---|
| Visium. Library Prep. | $294.08 | $492.67 | $823.89 |
| Turnaround time. | 7 to 10 days | 5 to 7 days | 2 to 4 days |
Notes
Tiers: Turnaround time (TAT) is in business days. The TAT is for the above-stated services and does not factor in the TAT for sequencing or other companion services. Availability for the Priority Tier is limited; contact [email protected] to see if this is a current option. More information about Pricing Tiers.