Update: Visium for FFPE

Visium FFPE update

Recently, 10x Genomics has launched their Visium for FFPE kit. At Single Cell Discoveries, we have decided to include this in our Visium Pilot Program.

What is Visium?

Visium Spatial Gene Expression allows you to analyze the whole transcriptome of your tissue section. Previously, this was only available for fresh frozen tissue sections. Now, it has been made available for FFPE (Formalin-Fixed, Paraffin-Embedded) as well.

How does it work?

FFPE is a common method to preserve tissue, but processing often damages RNA, complicating transcriptomics research. So, a solution had to be found to perform Visium on these tissues.

Similar to Visium for fresh-frozen tissues, the tissue is placed onto a Visium gene expression slide, followed by imaging. Each gene expression slide contains 4 capture areas with 5,000 barcoded spots. Each spot contains millions of capture oligonucleotides. In fresh-frozen tissue, the tissue is permeabilized so the RNA can bind the spots. In the Visium for FFPE assay, an extra step is necessary to capture the gene expression information.

In Visium for FFPE, probe pairs target specific sequences of the RNA. The probe pairs target around 18,000 genes in both human and mouse samples.  Once they hybridize with their target gene and are ligated to one another, the tissue is permeabilized.

Then, the ligated probe pairs are captured on the Visium slide by binding to the barcoded spots. Followed by library preparation and sequencing. 

Please note that since genes are targeted in this protocol, it is not yet possible to perform Visium for FPPE on species other than human and mouse.

What is the Visium Pilot Program?

The Visium Pilot Program is a complete Visium Spatial Gene Expression service. With the Pilot Program, we to gain more experience in working with the technology and learn more about the dos and don’ts regarding the sample preparation.

For your Visium project, this means that:

  • We may process your tissue type of interest for the first time.
  • You get an attractive discount on Visium as long as we offer the Pilot Program.
  • The results (images, cluster plots) can be used for marketing purposes, but we will always check this with you first.

Learn more about our Visium service or sign up using the form below.

Pilot Program

Ready to proceed? Use the form below to sign up for our Pilot Program. We’ll get in touch as soon as possible.