The Mayo Clinic Spatial Biology Facility's service lines include:

  • Conventional nCounter analysis to determine RNA abundance.
  • GeoMx Digital Spatial Profiling platform to determine protein and RNA abundance.

The facility has three GeoMx instruments, three nCounter digital analyzers and four sample preparation systems. It is now beta-testing the CosMx Spatial Molecular Imaging platform.

The facility's team is open to talking about future collaborations that need single-cell spatial analysis of protein and RNA. Team members see themselves as collaborators rather than providers of core services. The facility is committed to working closely with collaborators on early-stage design of spatial biology analyses.

Stained triple-negative breast cancer sample

A triple-negative breast cancer sample is stained with immunofluorescent antibodies. Cytokeratin, which visualizes tumor cells, is shown in green. CD45, which visualizes white blood cells that protect the body from infection, is shown in yellow. CD68, which visualizes macrophages — cells that detect and destroy bacteria and harmful organisms — is shown in red. Nuclei were stained blue with SYTO 13. The samples were incubated with antibodies or crossbreeding probes, each affected by a UV-labile cross-linker to a unique synthetic oligodeoxyribonucleotide. The oligonucleotides are bar codes for the target-specific proteins or transcripts.

Micron region of interest

The 600-micron region of interest marked with a white circle includes green tumor cells that are cytokeratin positive and red stromal cells that are cytokeratin negative.


Computer-generated "masks" guide UV laser illumination of these niches: tumor, shown as green (cytokeratin positive), and stroma, shown as red (cytokeratin negative). These niches were illuminated sequentially to release target-bound oligonucleotides. Then these oligonucleotides were quantified by nCounter or next-generation sequence analysis.