Table 1.
Comparison of commercially available spatial transcriptional profiling platforms
| 10x Genomics Visium | Nanostring GeoMx DSP | |
|---|---|---|
| Tissue compatibility | Best compatibility with fresh-frozen | Fresh-frozen and FFPE |
| RNA quality | RNA Integrity Number (RIN) ≥ 7 required | No requirement |
| Tissue preparation | Mounting on specialized Gene Expression Slide | Mounting on standard microscope slide |
| Tissue size | Maximum of 6.5 mm x 6.5 mm per capture area | Maximum of 14.6 mm x 36.2 mm |
| Geographic bounds of detection | Feature-based detection within full capture area | User-defined regions of interest (ROIs) |
| Cellular resolution | Approx. 10 cells/feature | Approx. 20-200 cells/ROI |
| Direct RNA detection | No – cDNA amplification required | Yes |
| Concurrent protein detection | Yes – up to 3 multiplexed antibodies | Yes – up to 3 multiplexed antibodies |
| Concurrent H&E staining | Yes | No |
| Amount of data generated | Whole coding transcriptome | Panel-based detection |
| Type of RNA captured | Poly-adenylated RNA only | Any RNA to which a probe can be designed |
| Instruments required | Fluorescent and brightfield imaging system; Illumina NGS platform | NanoString GeoMx Digital Spatial Profiler; NanoString nCounter or Illumina NGS platform |
| Sequencing depth required | Min. of 50k read pairs per spot covered by tissue | No NGS required if using nCounter instrument |