Question: What is Visium Spatial Gene Expression for FFPE, and how does it work?
Answer: The Visium platform is now being expanded to interrogate tissue biology of formalin fixed, paraffin embedded (FFPE) samples.
- Tissue fixation is the first and one of the most important steps in all studies that require tissue preservation. To preserve the tissue structure and integrity of macromolecules like proteins and nucleic acids, resected tissue is usually immediately immersed in a chemical fixative. Tissues fixed with formalin can be embedded in paraffin wax for long-term storage. Samples are often stored for years or even decades.
- Due to crosslinking and degradation caused by formalin fixation and storage, a direct poly(A) capture approach of mRNA molecules is unlikely to yield high-quality data from FFPE samples.
- Visium Spatial Gene Expression for FFPE utilizes Transcriptome Probe Panels to detect mRNA molecules. The Probe Panels consist of probe pairs generated against the protein-coding transcriptome for both human and, very soon, mouse tissues.
- In the assay, these probes contiguously hybridize to the target mRNA and are ligated together. The ligation product is captured, and spatially barcoded on-slide and is used to count transcripts.
Products: Spatial Gene Expression for FFPE