Table 1:
Overview of spatial transcriptomic techniques discussed
| Method | Number of Targets | Advantages | Limitations |
|---|---|---|---|
| Single Molecule Fluorescent in situ Hybridization (smFISH) [28] | See derivatives of technique (MERFISH and seqFISH) | Absolute quantification (100% sensitivity); High signal:noise; High sensitivity to image RNA in low abundance | Target must be selected, biasing the results |
| Multiplexed Error Robust FISH (MERFISH) [33–35, 37] | ~10,000 | Detects and corrects errors; Same as smFISH | Requires transcripts longer than 3kb; Special equipment |
| Sequential FISH (seqFISH) [31, 32] | 10,000+ | Single cell resolution; Reduces the number of necessary multiplexing cycles; Same as smFISH | Decreased detection sensitivity with each cycle; Time consuming protocol |
| In-situ sequencing (ISS) [44] | 100+ | Heighten target binding specificity; Can detect Small Nuclear Polymorphisms (SNPs) | Padlock probes are costly; Time consuming protocol |
| Proximity Ligation in situ Hybridization (PLISH) [38] | Unlimited targeted detection 4 transcripts/cycle | High signal to noise; Cost effective; Detects low abundant RNAs | Laborious protocol; Time consuming protocol |
| Spatially-resolved Transcript Amplicon Readout Mapping (STARmap) [45] | 1,000 transcripts/6 imaging cycles | 1,000 genes in only six imaging cycles | Padlock probes are costly |
| Spatial Transcriptomics [50] | Entire transcriptome/non-targeted | Similar protocol as RNA-seq; High transcript count | Lower sensitivity for low abundant transcripts; Not single cell resolution (~100um); Special slide needed; Sequencing data analysis |
| Slide-Seq [52] | Entire transcriptome/non-targeted | Single cell resolution (10um) | Lower sensitivity for low abundant transcripts; Sequencing data analysis |
| Fluorescent in situ RNA Sequencing (FISSEQ) [47] | Entire transcriptome/non-targeted | Unbiased sequencing; Maintains sample integrity | Low target detection; Very time consuming protocol |