Table 1 Summary of average mRNA/gene detection sensitivities and capture rates for each single-cell RNA-seq method
From: Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
Method | Avg Multiplet Rate | Avg Cell Capture Efficiency | Avg Library Pool Efficiency | Median nUMIs (EL4) | Median nGenes (EL4) | GD50 EL4 (FPKM) | Avg nDE genes | Avg nDE genes (> 1.5 FC in bulk) | Recall (mean ± sd) | Precision (mean ± sd) |
|---|---|---|---|---|---|---|---|---|---|---|
10x 3’ v2 | 0.46% | 29.50% | 57.90% | 21,570 | 3,882 | 20.2 | 3,314 | 2,711 | 0.462 ± 0.005 | 0.818± 0.003 |
10x 3’ v3 | 1.75% | 61.90%* | 75.90% | 28,006* | 4,776* | 13.6* | 4,005 | 3,388 | 0.577 ± 0.007 | 0.846 ± 0.004 |
10x 5’ v1 | 0.49% | 50.70% | 76.50% | 25,988 | 4,470 | 16.8 | 4,797* | 3,491* | 0.595 ± 0.006* | 0.728 ± 0.008 |
ddSEQ | 0.45%* | 1.01% | 18.10% | 10,466 | 3,644 | 25 | 2,740 | 2,397 | 0.501 ± 0.002 | 0.875 ± 0.003 |
Drop-seq | 0.55% | 0.36% | 17.80% | 8,791 | 3,255 | 26.7 | 2,824 | 2,504 | 0.453 ± 0.004 | 0.887 ± 0.003* |
ICELL8 3' DE | 2.18% | 8.63% | 93.00%* | 16,909 | 2,849 | 37.9 | 1,815 | 1,528 | 0.260 ± 0.004 | 0.842 ± 0.008 |
ICELL8 3' DE-UMI | 0.98% | 7.20% | 92.90% | 2,792 | 1,288 | 112.1 | 985 | 861 | 0.147 ± 0.005 | 0.873 ± 0.00 |