Spatial Collaborative Services

The Visium spatial transcriptomics platform enables whole tissue, spatially resolved, gene expression profiling in both fresh frozen and FFPE material. The system provides transcriptomic information within the context of tissue architecture, tumor microenvironments and cell groups.

The platform relies on custom Visium slides, with either two or four capture areas upon which tissue sections are affixed. Capture areas are either 6.5 x 6.5 mm with 5000 tiled capture spots or 11 x 11 mm with 14,00 capture spots. Each spot has an average capture radius of 50 uM and contains millions of oligonucleotides with a polyA capture sequence, a unique molecule identifier (UMI) and an indexed spatial barcode. After capture, Illumina-sequencing compatible libraries are generated from the probe products and used for high-throughput sequencing.

10X Visium v1 workflow (courtesy of 10x Genomics)

The VisiumHD spatial transcriptomics platform expands on the Visium v1 platform to enable whole tissue, spatially resolved gene expression in FFPE material. The system provides higher-resolution transcriptomic information with no dropout areas, allowing for near-single-cell assessment of tissue architecture, microenvironments and co-expression networks.

The assay relies on Visium HD slides containing two capture areas, each 6.5 x 6.5 mm.  Capture areas are arrayed with a continuous 2×2 uM lawn of barcoded oligonucleotides. The assay utilizes probe-based gene expression chemistry; probes are hybridized to H&E- or IF-stained FFPE material on a glass slide and imaged to capture spatial orientation. The 10x CytAssist instrument then is used to transfer the transcriptomic probes to the Visium HD slide and extended to add location-specific barcodes.  After capture, Illumina sequencing compatible libraries are generated from the probe products and used for high-throughput sequencing.

Source: 10x Genomics Grant application Resources for Visium Spatial Gene Expression

Xenium is a high-resolution, imaging-based spatial profiling system that can characterize up to 5,000 genes and multiplexed proteins in the same tissue section. This system combines spatial fidelity with subcellular resolution in FFPE and fresh frozen tissue, facilitating experiments desiring detailed cell type characterization or exploring cell-cell interactions and transcriptional pathways within their biological contexts. Tissues can be assayed using pre-designed, validated disease or tissue-focused gene panels, fully customized panels, or a mix of the two. 

Processing starts with tissue immobilized on a custom Xenium slide, which contains 10.5 x 22.5 mm of surface area to assay multiple tissue sections at a single time; up to two slides can be prepared per run. Probes are hybridized to RNA in the tissue, amplified, and sequenced via cyclic fluorescent images taken at a 200nm per-pixel resolution. Data is visualizable via desktop software from 10X or third parties to localize RNA and protein signals and perform secondary analysis.

Source: 10x Genomics Xenium In Situ Gene Expression Protocol Planner (CG000601 rev F)

The GeoMx DSP enables spatially resolved, region of interest targeted, profiling of both mRNA and proteins in both fresh frozen and FFPE tissue.

The assay is performed on standard negatively charged slides upon with the tissues of interest are mounted; antibodies or RNA probes coupled to photo-cleaveable barcode oligos are incubated with both the tissue and morphology markers.  After staining, regions of interest (ROI) can be chosen and optionally subsectioned based on morphology.   Oligos from the selected regions are then released by exposure to UV light, incorporated into an Illumina sequencer compatible library and used for high throughput sequencing.

Nanostring GeoMx DSP workflow (Courtesy of Nanostring)

Available Nanostring Region of Interest (ROI) segmentation options (courtesy of Nanostring)