Table 2.
SRT methods
| SRT Technique | Sample type | Preservation technique | Resolution | References |
|---|---|---|---|---|
| ISS (padlock probe & RCA) |
cells and tissue | FF or FFPE | single cell (transcript level) | Ke et al., 201340 |
| FISH | cells and tissue | FF | single cell (transcript level) | Lubeck et al., 201441 |
| Tomo-seq | tissue slice | FF | multiple cells | Junker et al., 201442 |
| TIVA | intact live cells | none | single cell | Lovatt et al., 201443 |
| FISSEQ | cells and tissue | FF or FFPE | single cell | (Lee et al., 2015)44 |
| MERFISH/MER SCOPE | cells and tissue | FF or FFPE | single cell (transcript level/100 nm) | Moffitt et al., 201645 |
| LCM-seq | tissue | FF or FFPE | multiple cells | Nichterwitz et al., 201646 |
| 10X Genomics Visium | cells and tissue | FF or FFPE | multiple cells (55 μm) | Ståhl et al., 201647 |
| Geo-seq | cells and tissue | FF or FFPE | multiple cells | Chen et al., 201748 |
| STARmap | tissue | FF | single cell | Wang et al., 201849 |
| HDST | tissue | FF | near single cell (2 μm) | Vickovic et al., 201950 |
| DBiT-Seq | cells and tissue | FF or FFPE | near single cell (10 μm) | Liu et al., 202051 |
| NanoString GeoMx | tissue | FF or FFPE | multiple cells | Zollinger et al., 202052 |
| SlideSeq2 | tissue | FF | near single cell (10 μm) | Stickels et al., 202153 |
| BGI scStereo-seq | tissue | FF | single cell (transcript level/500 nm) | Xia et al., 202154 |
| Resolve Biosciences Molecular Cartography | tissue | FF | single cell (transcript level/200 nm) | Groiss et al., 202155 |
| NanoString CosMx | tissue | FF or FFPE | single cell (transcript level/50 nm) | He et al., 202156 |
An evolving list of SRT methods. Acronyms used: ISS, in situ sequencing; LCM-seq, laser capture microdissection; TIVA, transcriptome in vivo analysis; HDST, high definition spatial transcriptomics; FF, flash frozen; FFPE, formalin-fixed paraffin-embedded. Note that this list is not extensive, and there are several more SRT approaches available. Preference was given to newly developed or unique methods.