Table 1.
Current ST technologies.
| ST method | Category | Sample type | Resolution | Approach* | Advantages (+)/drawbacks (–) | Ref. |
|---|---|---|---|---|---|---|
| LCM-seq | LCM | Fresh-frozen | Cellular | WT, >16,000 genes in total | (+) Robust; full-length mRNA capture (-) Low throughput |
(59) |
| TIVA | LCM | Live cells | Cellular | WT, >16,000 genes per cell | (+) Full-length mRNA capture from single live cells (-) Low throughput and limited analysis of clinical samples |
(35) |
| tomo-seq | LCM | Fresh-frozen | Anatomical features | WT, ~23,000 gene in total | (+) Robust and high sensitivity; construction of 3D profiles (-) Limited applicability to clinical samples |
(60) |
| Geo-seq | LCM | Fresh-frozen | Multicellular | WT, >8000 genes/20 cells | (+) Full-length mRNA capture; construction of 3D profiles (-) Low throughput |
(34) |
| NICHE-seq | LCM | Live cells | Cellular/multicellular | WT, thousands of UMIs per cell | (+) High throughput (-) Limited to genetically engineered model organisms, so that not applicable for clinical samples currently. |
(36) |
| PIC | LCM | Fresh-frozen/FFPE | Subcellular | WT, ~8000 genes/cell | (+) Relatively lower cost; Subcellular resolution (-) Limited field of view; Require manual choice of regions |
(61) |
| immuno-LCM-RNAseq | LCM | Snap-frozen/RNAlater preserved | Multicellular | WT, >15,000 genes in total | (+) Compatible with low-quality samples; full-length RNA capture. (-) Low throughput |
(62) |
| par-seqFISH | ISH | Cell cultures | Cellular | Targeted, 105 genes | (+) Applicable to bacteria. (–) Cannot be applied to human samples |
(27) |
| smFISH | ISH | FFPE/Fresh-frozen | Subcellular | Targeted, several genes | (+) High sensitivity (–) Low throughput |
(63) |
| seqFISH | ISH | Fresh-frozen | Subcellular | Targeted, 249 genes | (+) Subcellular resolution (-) Need costly equipment; Limited field of view |
(29, 64) |
| MERFISH | ISH | Fresh-frozen | Subcellular | Targeted, 135 genes | (+) Highly multiplex; combined with IF for protein detection (-) Need costly equipment; Limited field of view |
(25, 65) |
| smHCR | ISH | Fresh-frozen | Subcellular | Targeted, 40 probes | (+) mRNAs detection in thick (0.5mm) slices. (-) Low throughput; Limited field of view |
(66) |
| RollFISH | ISH | FFPE | Subcellular | Targeted, several genes | (+) Applicable to FFPE samples (-) Low throughput |
(67) |
| osmFISH | ISH | Snap-frozen | Subcellular | Targeted, 33 genes | (+) Large range of detectable gene expression levels (-) Relatively low throughput |
(68) |
| RNAscope | ISH | FFPE | Subcellular | Targeted, 4 genes | (+) High sensitivity. Applicable to FFPE samples (-) Low throughput |
(69) |
| seqFISH+ | ISH | Fresh-frozen | Subcellular | Targeted, 10,000 genes | (+) Ultrahigh multiplex; Subcellular resolution (-) Limited field of view |
(23) |
| SABER | ISH | Frozen | Subcellular | Targeted, 18,000 probes | (+) High sensitivity. Relatively low cost. (-) Limited field of view |
(70) |
| Split-FISH | ISH | Fresh-frozen | Subcellular | Targeted, 317 genes | (+) High specificity. (-) Low throughput |
(28) |
| DNA microscopy | ISH | Cell cultures | Cellular | Targeted, 106 UMIs | (+) Relatively low cost. (-) Low throughput; Limited applicability to clinical samples |
(71) |
| GeoMX WTA | ISH | FFPE | Cellular | Targeted, 18,190 genes | (+) Ultrahigh multiplex (-) Limited field of view; Require manual choice of regions |
(72) |
| BOLORAMIS | ISH | Fresh-frozen | Subcellular | Targeted, 96 genes | (+) High sensitivity. (-) Low throughput |
(73) |
| ISS using barcode padlock probes | ISS | FFPE/Fresh-frozen | Subcellular | Targeted, 31 transcripts | (+) Subcellular resolution; ability to detect SNVs (-) Limited number of target genes; low throughput |
(30) |
| FISSEQ | ISS | FFPE/Fresh-frozen | Subcellular | WT, 8102 genes in total | (+) Subcellular resolution; Applicable to FFPE samples (-) Low sensitivity; limited field of view; low experimental throughput |
(33) |
| BaristaSeq | ISS | Cell cultures | Subcellular | Targeted, several probes | (+) Relatively high amplification efficiency (-) Limited field of view; low experimental throughput |
(31) |
| STARmap | ISS | FFPE/Fresh-frozen | Subcellular | Targeted, 1020 genes | (+) High sensitivity. Applicable to FFPE samples (-) Limited field of view; low experimental throughput |
(32) |
| INSTA-Seq | ISS | FFPE/Fresh-frozen | Subcellular | Targeted, >820 genes | (+) High resolution; cDNA length up to 4750 nt (-) Limited field of view, low experimental throughput |
(74) |
| BARseq | ISS | Fresh-frozen | Cellular | Targeted, 1.5 million barcodes | (+) High sensitivity and specificity (-) Limited field of view |
(75) |
| HybISS | ISS | Fresh-frozen | Subcellular | Targeted, 119 genes | (+) Robust. High specificity. (-) Limited number of target genes |
(76) |
| pciSeq | ISS | Fresh-frozen | Cellular | Targeted, 99 genes | (+) low misdetection rates. Relatively large field of view. (-) Limited number of target genes |
(77) |
| sci-Space | ISS | Fresh-frozen | 200 μm | WT, 1231 genes per cell | (+) larges field of view. (-) Low resolution. |
(78) |
| ExSeq | ISS | FFPE/Fresh-frozen | Subcellular | WT/targeted, 3039/297 genes | (+) Support targeted and WT sequencing; multi-scale resolution; allow for AS detection. (-) Relatively low sensitivity |
(79) |
| 10x Genomics Visium | ISB | FFPE/Fresh-frozen | 55 μm | WT, >20000 genes in total | (+) Robust; matched tools for downstream data analysis (-) multicellular resolution |
(17, 39) |
| Slide-seq | ISB | Fresh-frozen | 10 μm | WT, a median of 59 UMIs per cell | (+) Cellular resolution (-) Limited field of view; low sensitivity |
(40) |
| HDST | ISB | Fresh-frozen | 2 μm | WT, 63.5 UMIs per cell | (+) Ultrahigh resolution; high throughput (-) Limited field of view; low sensitivity |
(42) |
| Slide-seqV2 | ISB | Frozen | 10 μm | WT, a median of 550 UMIs per cell | (+) Higher sensitivity than Slide-seq and HDST (-) Limited field of view |
(41) |
| PIXEL-seq | ISB | Frozen | 1 μm | WT, >1100 UMIs per cell | (+) Ultrahigh resolution; high sensitivity (-) Limited field of view; not accessible currently |
(48) |
| Seq-Scope | ISB | Fresh-frozen | 0.5-0.8 μm | WT, ~4700 UMIs per cell | (+) Ultrahigh resolution; ultrahigh sensitivity (-) Limited field of view |
(46) |
| XYZeq | ISB | Fresh-frozen | Cellular | WT, a median of 1596 UMIs (629 genes) per cell | (+) Centimeter-scale field of view. (-) Relatively low sensitivity; Customized array |
(80) |
| Stereo-seq | ISB | FFPE/Fresh-frozen | 0.22 μm | WT, 1910 UMIs (792 genes) per cell | (+) Ultrahigh resolution; ultrahigh sensitivity; multi-scale field of views (from 0.5 to 174.24 cm2) (-) Customized array |
(43) |
| ZipSeq | ISB | Live cells | Cellular | WT, 3550 genes per cell | (+) Single-cell resolution; high sensitivity (-) Costly reagents; Limited applicability to clinical samples |
(45) |
| Nanostring DSP | ISB | FFPE/Fresh-frozen | Cellular | Targeted, 1412 genes or 44 proteins + 96 genes per cell | (+) FFPE compatible; multiomics spatial sequencing (-) Require manual choice of regions; Limited field of view; |
(44) |
| APEX-seq | ISB | Live cells | Subcellular | WT, >25,000 transcripts in total | (+) Ultrahigh resolution; allow for AS detection. (-) Cannot be applied to human clinical samples; low throughput |
(47) |
*The number of genes/transcripts/probes/UMIs that can be detected. LCM, laser capture microdissection. ISH, in situ hybridization. ISS, in situ sequencing. ISB, in situ barcoding. WT, whole transcriptome. FFPE, formalin fixed paraffin-embedded. UMI, unique molecular identifier. IF, immunofluorescence. AS, alternative splicing.