10X Visium CytAssist Spatial Transcriptomics services are available for standard and HD (single cell resolution) slides!
In collaboration with the TRIP lab, the GEC offers services for the Visium CytAssist Spatial Transcriptomic Gene Expression for FFPE Human and Mouse Transcriptome assays.
Check out the Halberg lab 
Visium slides are available in two formats; Standard 6.5×6.5mm and 11 x 11mm & HD 6.5×6.5mm.
The 10X Visium CytAssist technology allows labs to section, stain, and image their FFPE tissues of interest on conventional glass slides. The CytAssist system will take tissue slides, after a probe hybridization step, and transfer to a Visium slide containing an array of uniquely barcoded spots approximately 55uM apart for standard and approximately 2uM apart for HD (5,ooo spots for 6.5×6.5 mm slides and ~14,000 spots for 11x11mm slides) for downstream Visium library preparation and sequencing. Imaging is done a second time during this transfer. The initial stained images and CytAssist images along with sequencing data are all used to visualize expression across tissue. See how it works here.
The GEC collaborates with the TRIP lab for tissue sectioning, and slide prep. Libraries are prepared in the GEC and sequenced with the DNA Sequencing group on the NovaSeq X Plus. Bioinformatic services from SpaceRanger through downstream analysis are available by the UWBC Bioinformatics Resource Center. SpaceRanger data may be 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).
Brief Overview of the CytAssist System
Visium Spatial Gene Expression Submission Guidelines
- First time users, we strongly recommend setting up a meeting with the GEC and TRIP lab to discuss the specifics of the experiment. Returning clients are also encouraged to meet to ensure the specifics of the experiment are clear to all parties involved.
- All experiments must be coordinated and scheduled with GEC and TRIP prior to sample submission. All service requests must be entered into the on-line UWBC Requester Portal. If you do not have an account, please email gecinfo@biotech.wisc.edu. Following approval of service request, GEC staff will confirm project submission date.
- A Reference Guide for supported tissue types is available from 10X Genomics.
- We strongly recommend doing a pilot for projects with tissue types not supported by 10X.
- To assess the quality of FFPE tissue, it is recommended RNA be extracted from a representative section of the block and assessed by DV200. A DV200 >30% is recommended.
- Clients are responsible for coordinating tissue block submissions with the TRIP lab. TRIP will section and prepare slides for H&E staining and discuss Region of Interest (ROI) with the pathologist and research group. Clients may also use their own histologist.
- ROI should fit either on a 6.5 x 6.5mm area or 11 x 11mm area. GEC will place an order for the appropriate kit once the size of template is known.
- Once the ROI is confirmed, the TRIP Lab will communicate timeline with the GEC for staining, imaging, and handoff to GEC for CytAssist processing. The client is responsible for the pickup of slide(s) from TRIP and transport to GEC.
- Currently only mouse and human sample kits are available.
- Sequencing recommendation is based upon the ROI of each slide area. 10X currently recommends 25,000 read pairs per tissue spot covered on the capture area (ROI) for standard slides. However, from our experience, we strongly recommend 40,000-50,000 read pairs per tissue spot covered for the best data analysis.
To request a quote please contact gecinfo@biotech.wisc.edu
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.