Table 2.
Comparative analysis of microfluidic-based scRNA-seq methods
| inDrop [155] | Drop-seq [90] | 10× Genomics [156] | |
|---|---|---|---|
| Resemblances | |||
| Isolation method | Droplet | ||
| Number of cells | 1000–10,000 | ||
| Cell barcode | Yes | ||
| Unique molecular identifier (UMIs) | Yes | ||
| cDNA coverage | 3′ tag | ||
| Differences | |||
| Amplification method | In vitro transcription (IVT) | Template switching (PCR) | Template switching (PCR) |
| Cell barcode capacity | 147,456 (384 × 384) | 16,777,216 (412) | 734,000 |
| Detection cost of 1000 cells | 250 USD | 100 USD | 500 USD |
| Reaction in droplets | Cell lysis | Cell lysis | Cell lysis |
| Primer release by UV | mRNA capture on beads | Primer release by bead dissolving | |
| mRNA capture | Reverse transcription | ||
| Reverse transcription | Template switch | ||
| Reaction after demulsification | 2nd strand synthesis | RT and template switch | PCR |
| In vitro transcription | PCR | cDNA fragmentation and ligation | |
| RNA fragmentation | Tn5 tagmentation | ||
| PCR | |||