Spatial transcriptomics is the study of gene expression patterns within the context of tissue architecture and can provide a more complete understanding of cell-cell interactions. It is a powerful tool for anyone interested in understanding the complexity of biological systems and tissue organisation at high resolution.
The SAGC has 3 platforms for spatial transcriptomics: Visium (10X Genomics), Stereo-seqTM (BGI STOmics) and Xenium (10X Genomics)
Visium: Whole transcriptome mapping within morphological context of complex tissue samples
- Each slide contains 5000 spatially barcoded spots giving you high-resolution (1-10 cells) per spot from standard tissue sectioning and staining
- Compatible with both formalin-fixed, paraffin-embedded (FFPE) and fresh frozen tissue samples
- Whole transcriptome analysis – no need to select targets or specific region of interest
- Demonstrated on a diverse set of tissues across species
Leverages in situ mRNA capture and cDNA sequencing with barcoded spatial coordinates to create a spatial transcriptomic profile of the tissue section for analysis.
- Subcellular spatial localization of mRNA
- Chip design ~320 M spatially barcoded spots/cm2
- Spot size = 200 nm diameter
- Range of field size to accommodate larger tissue samples (up to 13 cm x 13 cm)
Xenium In Situ: Targeted gene expression and protein quantification at subcellular resolution
Xenium is an end-to-end platform that enables high-throughput subcellular mapping of RNA targets.
- Menu of off-the-shelf gene panels + order 100 custom add-on genes
- Compatible with fresh frozen and FFPE tissues
- Microscopy based read-out (no NGS), allows H&E post-run
- Single molecule RNA and Protein targets (subcellular resolution)