Table 2.
Detailed comparison of current and potential methods and technologies of sc/snRNA-seq for FFPE samples.
| Approach | Technology | Input | Samples | Throughput | Target | SN or SC? | Genes Measured |
Reads/Sample | UMI | Full-Length | Refs |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Based on dA-tailing | Pick-Seq | FFPE | Human tonsil, breast cancer | Low | Poly-A RNA | 5~10 cells | 2700, 4640 |
/ | No | No | [29] |
| FRISCR | Fixed | hESCs | Low | Poly-A RNA | SC | 12,000 | / | No | Yes | [30] | |
| Smart-3SEQ | FFPE | DCIS | Low | Poly-A RNA | No | ~3000 | / | No | No | [31] | |
| Smart-total-seq | Cell lines | Fibroblasts, HEK293T, and MCF7 |
Low | Total RNA | SC | / | / | No | Yes | [32] | |
| scifi-RNA-seq | Fixed | Clone E6-1 | High | Poly-A RNA | SN | / | / | 2000~6000 | No | [33] | |
| inCITE-seq | Fixed | Hela | High | Poly-A RNA | SN | 1158 | / | 2655 | No | [34] | |
| FD-seq | Fixed | A549 cells | High | Poly-A RNA | SC | ~3000 | 58.6 K | ~8000 | No | [35] | |
| VASA-seq | Frozen | HEK293T and mESCs | High | Total RNA | SC | ~10,000 | 750 K | / | Yes | [36] | |
| snFFPE-Seq | FFPE | Brain | High | Poly-A RNA | SN | 276 | 154 | / | No | [10] | |
| Based on targeted probe | TempO-Seq | Cell lines | Reference RNA | Low | Target mRNA | No | 2244 | 1.9 M | No | No | [37,38] |
| TAC-seq | FF | Endometrial biopsies | Low | Target mRNA | No | / | / | Yes | No | [39] | |
| Fixed-RNA | FFPE | Breast | High | Target mRNA | SN | 1850 | / | / | No | [9,11] | |
| Based on random primer | SPLiT-seq | Fixed | 293T, 3T3, and Hela-S3 | High | Total RNA | SN | ~5000 | >500 K | 12,000~15,000 | No | [40] |
| scFAST-seq | FF | K562, A549, and HCC827 | High | Total RNA | SC | ~1000 | / | ~2000 | Yes | [41] | |
| snRandom-seq | FFPE | 293T, 3T3, and some organs | High | Total RNA | SN | ~4000 | 25~29 K | ~10,000 | Yes | [12] |
Total RNA: RNA other than rRNA; Fixed: fixation with formaldehyde or paraformaldehyde; FF: fresh frozen; FFPE: formalin-fixed paraffin-embedded; SC: single cell; SN: single nuclei; hESCs: human embryonic stem cells; DCIS: ductal carcinoma in situ; HEK293T: human embryonic kidney 293; MCF7: breast cancer cells; Clone E6-1: human Jurkat cells; A549: human lung adenocarcinoma cells A549; mESCs: mouse embryonic stem cells; K562: chronic myeloid leukemia cancer cells; HCC827: human non-small-cell lung cancer cells.