Table 2 Comparative analysis of microfluidic-based scRNA-seq methods
From: Microfluidics applications for high-throughput single cell sequencing
|  | 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 | Â | Reverse transcription | |
Reverse transcription | Â | 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 | Â | |
PCR | Â | Â | |