10x Genomics
Visium Spatial Gene Expression

Space Ranger1.3, printed on 11/22/2024

What is Visum for FF?

The Visium Spatial Gene Expression workflow measures RNA levels in intact, fresh frozen (FF) tissue sections, by capturing mRNA using spatially barcoded oligonucleotides attached to the Visium slide. The workflow begins by first determining the optimal permeabilization time for the tissue. The tissue is stained, and imaged followed by cell permeabilization to release mRNA which binds to the poly(dT) region of spatially barcoded oligonucleotides present on the slide surface. Libraries are generated from the barcoded cDNA of a captured transcript and are sequenced.

Visium Spatial Gene Expression relies on Space Ranger analysis software which uses STAR aligner to perform splicing-aware alignment of transcript reads to the genome. Space Ranger uses the transcript annotation GTF file to identify exonic reads, which when compatible with a single gene annotation, are considered for UMI counting.

Resources and additional information are available below:

• Visium Glossary
• Running spaceranger count
• Understanding Outputs
• Manual Fiducial Alignment in Loupe Browser