Spatial Transcriptomics Solutions

Spatial transcriptomics is a technology that describes expression profiling of cells with spatial context. Which allows scientists to see differences in expression across organs, tissues and diseases by looking at transcripts at multiple spatial sites within a tissue. By combining conventional single-cell sequencing technologies with in situ technologies and other omics approaches, spatial transcriptomics enables the study of cellular heterogeneity with spatial resolution. It provides a more specific research agenda for disease research and contributes to disease biology and targeted therapeutic development.

There are two common methods: pre-freezing and embedding or simultaneous freezing and embedding. Pre-freezing process is a quick, cold immersion in isopentane with a pre-cooled forceps, till the tissue is completely frozen, and then embedding in OCT compound. The simultaneous approach consists of depositing new tissue in a petri dish, adding room temperature OCT embedding medium, so that an OCT coat surrounds the tissue, and placing it in an OCT embedding mould and freezing on dry ice or in isopentane.

Direct freezing in liquid nitrogen is not recommended, as the boiling process might cause cavitation around the tissue, leading to asynchronous cooling in different regions, potentially altering the internal structure or even causing tissue fragmentation.

Visium spatial transcriptomics services utilize fresh tissue samples and poly(A)-based capture chemistry, making it species-independent. Most fresh tissues, such as tumor, brain, heart, liver, etc., are suitable. Tissues must be immediately frozen following extraction to preserve cellular and gene expression integrity - ideally within 30 minutes of collection. Visium CytAssist, in contrast, uses probe detection, mainly for fresh frozen, fixed frozen, and formalin-fixed paraffin-embedded (FFPE) tissue sections of human and mouse specimens.

The Visium Spatial slides are equipped with a high-density array of oligonucleotide probes, each carrying a unique spatial barcode. After permeabilization, mRNA is released and binds to the probes, with the resulting transcript information acquired during sequencing carrying spatial barcode data. Software analysis then precisely matches gene expression data with the spatial location on the tissue section.

Dewaxing removes paraffin to re-expose the tissue, while antigen retrieval restores antigen epitopes masked during the fixation process, thereby enhancing mRNA accessibility. This facilitates the efficient binding of spatial barcode probes and accurate gene expression capture.

For a biological perspective, integrate spatial transcriptomics data with other data types like single-cell RNA sequencing, whole-genome sequencing, tissue histology, and immunofluorescence staining to give you the full biological picture. Dedicated software and bioinformatics tools can also be used to visualize and interpret spatial transcriptomics data.