previous arrow
next arrow

Spatial Transcriptomics


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
10x Image Data Tissue Slide Visium FFPE 1


STOmics Image 4K

Stereo-seqTM (SpaTial Enhanced Resolution Omics-Sequencing): Whole transcriptomics for discovery applications (range of 1000-2000 genes/cell) 

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)


xenium data image 1