Table 1.
Single-cell sequencing methods a
| Approach b | WGA method c | Enzyme d | Cells/nuclei e | Applications f | Coverage breadth g | Commercial kits h | References |
|---|---|---|---|---|---|---|---|
| SCS DNA-seq | |||||||
| SNS | DOP-PCR | Thermosequenase | Nuclei | Copy number profiling | ~10% | WGA4 Sigma | [34] |
| MALBAC | DOP-PCR | Bst | Cells | Copy number profiling | >90% | Bst NEB | [31] |
| BGI MDA | MDA | Phi29 | Cells | Genome/exome | >90% | Repli-G Qiagen | [30] |
| NUC-SEQ | MDA | Phi29 | Nuclei | Genome/exome | >90% | Repli-G Qiagen | [37] |
| SCS RNA-seq | |||||||
| Tang method | PolyA priming | Reverse transcriptase | Cells | Transcriptome | 3' bias | NA | [21] |
| Quartz-seq | PolyA priming | Reverse transcriptase | Cells | Transcriptome | 3' bias | NA | [24] |
| CEL-seq | PolyA priming | Transcription in vitro | Cells | Transcriptome | 3' bias | NA | [20] |
| STRT-seq | Template-switching | Reverse transcriptase | Cells | Transcriptome | Full-length | NA | [23] |
| Smart-seq | Template-switching | RT MMLV | Cells | Transcriptome | Full-length | Clontech | [22] |
| PMA | MDA | Phi29 | Cells | Transcriptome | 3' bias | NA | [25] |
aTable summarizes the methods for single-cell DNA sequencing and single-cell RNA sequencing. bName of the method; camplification method; denzyme used for amplification; edescription of whether the method was designed for analysis of cells or nuclei; fdescription of the type of molecular information that is best measured using the method; greference to the total number of bases that can be covered with sequencing data using the approach; hindication of whether any commercially available kits have been developed to perform the method. Abbreviations: BGI Beijing Genome Institute, Bst Bacillus stearothermophilus DNA polymerase, DOP-PCR degenerative-oligonucleotide PCR, MALBAC multiple annealing and looping-based amplification cycles, MDA multiple-displacement amplification, NA not applicable, PCR polymerase chain reaction, PMA Phi29 DNA-polymerase-based mRNA transcriptome amplification, RT MMLV reverse transcriptase Moloney murine leukemia virus, SNS single-nucleus sequencing, WGA whole-genome amplification.