10x Genomics Standard Visium, CytAssist

The standard Visium technology provides topographic whole-transcriptome profiling of tissues using human or mouse probes. The profiles are transferred from the tissue to the 55-µm spot resolution Visium standard capture slides using the CytAssist device. This is a sequencing-based, formalin-fixed paraffin-embedded (FFPE), fresh frozen or fixed frozen tissue compatible platform.

The standard Visium for CytAssist uses the 10x Genomics 55-µm spot resolution Visium Spatial Gene Expression slides with the Visium CytAssist instrument. This instrument facilitates the transfer of transcriptomic probes or antibody oligonucleotides from the respective treated tissues on standard glass slides to the Visium slides. Here, FFPE, fresh frozen or fixed frozen tissues sectioned onto standard glass slides are stained for hematoxylin and eosin, or immunofluorescence, and hybridized with human or mouse whole-transcriptome oligonucleotide probes.

After probe hybridization, two standard glass slides and a two-capture-area Visium CytAssist Gene Expression Slide are placed in the CytAssist instrument so that the tissue sections on the standard slides can be aligned on top of the two Visium capture areas. The instrument captures a brightfield image to provide spatial orientation for data analysis, followed by release and transfer of the hybridized probes to the standard Visium slide.

The probes are extended, and the sample is eluted and transferred to a new tube for library construction. Libraries are sent for sequencing, and both image and sequencing data are used in the 10x Space Ranger and Loupe Browser software tools, or third-party tools, to visualize and analyze spatial data.