Table 1.
Comparison of scRNA methods
| Method | Capture format | cDNA amplification | Transcript coverage | Molecule identifier | Strength | Weakness | References |
|---|---|---|---|---|---|---|---|
| Drop-seq | Droplets | PCR | 3′ end | UMI | For individual cells; simultaneous analysis without losing the original transcript; high throughput, lower costs and reduction of the mRNA amplification noise | Only 3′ end is enabled for specific the amplification | [38] |
| 10× Genomics Chromium | Droplets | PCR | 3′ end | UMI | Increased throughput, cost effective and time efficient | Only 3′ end is enabled for specific amplification, efficiency losses | [45] |
| InDrop | Droplets | IVT | 3′ end | UMI | Detects rare cell populations; high throughput, low noise profile | Low cell capture efficiency | [35] |
| CEL-seq 1 & 2 | Plate | IVT | 3′ end | UMI | For complex tissues containing multiple cell populations; improved accuracy and higher sensitivity; reduces mRNA amplification noise | Low cell capture efficiency | [36, 37] |
| Smart-seq 1 & 2 | Plate | PCR | Full length | UMI | Increases thermal stability of DNA base pairs | Lower detection efficiency, limited throughput and read coverage | [31, 32] |
| MATQ-seq | Plate | PCR | Full length | NA | For low-abundance genes and noncoding and non-polyadenylated RNA; highly sensitive with quantitative detection efficiency | Low throughput | [43] |
| Quartz-seq 1 & 2 | Plate | PCR | Full length | NA (Quartz-seq), UMI (Quartz-seq 2) | For different cell cycle phases and transcriptome heterogeneity detection; high quantity and efficiency in limited sequence reads | Requires skilled technician | [33, 34] |
| SCRB-seq | Plate | PCR | 3′ end | UMI | For heterogeneous population identification; high throughput, low cost, simple steps, fewer potential biases, reduced mRNA amplification noise | Requires skilled technician | [46] |
| FB5P-seq | Plate | PCR | 5′ end | UMI | For BCR and TCR repertoire identification; cost and time effective; integrative analysis of transcriptome | 3′ end scRNA-seq protocols are not suitable | [30] |
| STRT-seq | Plate | PCR | 5′ end | UMI | Improves efficiency and tracking of cell origin; no quantitative bias against long transcripts | Technical variation | [47] |
| TCR-seq | Plate | PCR | 3′ end | NA | For T-cell diversity identification | No standardized thresholds, disparities between different studies | [44] |
| MARS-seq 1 & 2 | Plate | IVT | 3′ end | UMI | For in vivo transcriptional states in thousands of single cells; minimizes amplification bias | Requires skilled technician | [48] |
IVT In vitro transcription, UMI Unique molecular identifiers