Table 1.
Comparison of scRNA-seq methodologies.
| Vendor | Method | # of Cells Loaded1 | Wet Lab Duration hrs | First Break hrs |
Bioinformatics Pipeline | Runtime | Cost per Cell2 | CITE-seq | WTA7 or Targeted | # of Genes | Sequencing Depth Required3 per cell |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 10X Genomics | 3’ v3 | 16,000 | 22 | 4 | Cell Ranger | 1 Week | $0.684 | Yes | WTA | 1,600 | 50,000 |
| 5’ | 17,400 | 24 | 4 | Cell Ranger | 1 Week | $0.305 | Yes | WTA | 1,200 | 50,000 | |
| BD Biosciences | Rhapsody | 20,000 | 16 | 6 | Seven Bridges Genomics | 1 Day | $0.364 | Yes | Targeted | 500 | 20,000 |
| Rhapsody (WTA)7 | 10,000 | 16 | 6 | Seven Bridges Genomics | 1 Day | $0.754 | Yes | WTA | 800 | 50,000 | |
| Takara/Illumina | SMART-seq | 96 | 22 | 7 | Open source | 1 Week | $80 | No | WTA | 8,0006 | 2 million |
1
Based on manufacturer’s maximum loading capacity (input).
2
Cost excludes tax, shipping, labor, and sequencing.
3
Based on manufacturer’s maximum recommendations for transcriptome only.
4
Based on 50-plex oligonucleotide antibodies used.
5
Based on 20-plex oligonucleotide antibodies used.
6
Referencing62
7
Whole transcriptome analysis