Spatial Transcriptomics

The Emory NPRC Genomics Core is the proud owner of a 10x Genomics Visium CytAssist, the best-in-class slide instrument for advanced spatial profiling. This device allows us to meet all your spatial single cell sequencing needs with simplicity and accuracy.

The Visium CytAssist allows spatial profiling experiments to integrate seamlessly with standard histology workflows for tissue sectioning, placement, staining, and imaging. The Visium CytAssist creates the bridge between histology and genomics by facilitating the transfer of transcriptomic probes from standard glass slides to Visium slides.

We provide service for the Visium HD assay, which offers single cell-scale spatial resolution. Visium HD is a whole transcriptome probe-based gene expression assay and only available for human, rhesus, and mouse tissue samples. The Visium HD Spatial Gene Expression slides contain two 6.5 x 6.5 mm Capture Areas with a continuous lawn of oligonucleotides arrayed in millions of 2 x 2 µm barcoded squares without gaps. The data is output at 2 µm as well as multiple bin sizes, such as 8 x 8 µm.

The Visium HD workflow consistis of two main components - histology (tissue sectioning, tissue placement, staining, imaging, destaining, and decrosslinking) and genomics (probe hybridization, library preparation, and sequencing).

In partnership with the EPC Histology and Molecular Pathology Laboratories and the Winship Cancer Tissue and Pathology Shared Resource (CTPSR), we can support the full Visium HD workflow for formalin-fixed, paraffin-embedded (FFPE) tissues and hematoxylin and eosin (H&E) staining. The Genomics Core performs all the steps after imaging and coverslip removal, which includes Destaining, Decrosslinking, Probe Hybridization, CytAssist-enabled Probe release & Capture, Probe-based library Construction, and Sequencing.

Visium HD is also compatible with fresh frozen or fixed frozen tissue sections and immunofluorescence (IF) staining. The Genomics Core supports the workflow downstream of imaging or coverslip removal for any of these formats.

Sample prep and imaging; Probe hybridization and ligation; CytAssit probe capture; Probe extension; Library Construction; Sequencing; Data Processing and Visualization

Image credit: 10x Genomics