DNA Strand

The GRT Hub provides several services for spatial profiling. We currently have three options for spatial profiling: 10x Genomics Xenium, 10x Genomics CytAssist/Visium, and NanoString GeoMx.

Spatial profiling assays include Poly(A) mRNA capture, whole transcriptome probe profiling for humans or mice, and targeted RNA probe detection.

Sample Submission Guidelines

  • In general, samples should be prepared with preserving RNA integrity in mind. Samples with unknown RNA quality should be checked before running the assay.
  • For FFPE samples, the DV200 value should be determined for each sample.
  • For fresh-frozen samples, the RIN score should be determined for each sample.
  • The morphology of your tissues should also be checked to ensure everything is intact and not damaged during sample preparation.
  • Input into each platform varies. Please see below for the requirements for each platform.

10x Genomics Xenium

  • This platform is compatible with both FFPE and fresh-frozen samples. Samples are sectioned onto Xenium sample slides for further processing. The mountable/capture area is about 11x24mm.

10x Genomics CytAssist/Visium

  • This platform is compatible with both FFPE and fresh-frozen samples. Samples are sectioned onto regular histology-grade glass slides for further processing. The mountable area varies based on the slide selected. Consult 10x Genomics manual for dimension. For final data capture, there are two sizes to choose from, 11x11mm and 6.5x6.5mm.

10x Genomics Visium Direct Placement

  • This platform is compatible with fresh-frozen samples only. Samples are sectioned onto the Visium slide. Capture areas on these slides are 6.5x6.5mm.

NanoString GeoMx

  • This platform is compatible with both FFPE and fresh-frozen samples. Samples are sectioned onto regular histology-grade glass slides for further processing. The mountable area is about 14x36mm. Final data capture has to be decided during the ROI (region of interest) selection of the workflow.
  • Please email us and set up a meeting to discuss your project in more detail and we can provide more specific guidance for your experiment.