Table 1.
A comparison of important features of key spatial transcriptomic techniques currently in wide use.
| Technology | Technique | Aim of study | Efficiency of transcript detection | Transcriptome-wide or targeted profiling | Single cell | Tissue area |
|---|---|---|---|---|---|---|
| Image-based | smFISH e.g. RNAScope |
Hypothesis testing | High | Targeted | Yes | Limited |
| ISS e.g. Xenium 10x Genomics |
Hypothesis testing | Low | Targeted | Yes | Limited | |
| Sequencing- based |
Barcoding e.g. Visium 10x Genomics |
Hypothesis generating | Low | Transcriptome-wide | No | Large |
| ROI e.g. GeoMx DSP NanoString |
Hypothesis generating | Low | Transcriptome-wide | Yes | Limited by ROI |
smFISH, single molecule fluorescence in situ hybridisation; ISS, in situ sequencing; ROI, region of interest; DSP, digital spatial profiler.