Table 1 Comparison of four RNA library preparation kits for FFPE and FF samples
Kits | KAPA | TaKaRa | Vazyme | QIAGEN | ||||
|---|---|---|---|---|---|---|---|---|
Sample | FFPE | FF | FFPE | FF | FFPE | FF | FFPE | FF |
Recommended input | 25 ng-1 μg | 5–50 ng | 0.25–10 ng | 100 ng-1 μg | 100 ng-5 μg | |||
Input total RNA (ng) | 100 | 100 | 10 | 10 | 100 | 100 | 100 | 100 |
PCR cycles | 15 | 15 | 16 | 13 | 15 | 15 | 15 | 15 |
Library (ng) | 178.4 | 1048.0 | 792.0 | 944.0 | 317.5 | 945.0 | 196.8 | 408.0 |
Total raw data (G) | 35.7 | 33.6 | 21.7 | 18.1 | 35.4 | 42.2 | 36.8 | 31.2 |
Downsampled data (G) | 18.0 | 18.0 | 18.0 | 18.0 | 18.0 | 18.0 | 18.0 | 18.0 |
Clean bases (G) | 16.4 | 16.2 | 14.0 | 14.0 | 15.8 | 15.6 | 16.8 | 16.9 |
rRNA (%) | 1.46 | 1.29 | 13.47 | 12.77 | 1.20 | 0.82 | 0.72 | 0.54 |
Q30 (%) | 90.84 | 90.49 | 93.98 | 93.91 | 90.42 | 90.15 | 92.69 | 92.60 |
GC (%) | 53.25 | 55.87 | 53.02 | 53.90 | 49.22 | 52.05 | 49.58 | 50.82 |
Total mapping rate (%) | 96.32 | 96.41 | 91.63 | 93.90 | 95.38 | 94.84 | 97.36 | 97.46 |
Unique mapping rate (%) | 80.90 | 79.10 | 79.33 | 80.61 | 84.56 | 81.66 | 85.54 | 84.49 |
Multiple mapping rate (%) | 15.42 | 17.31 | 12.30 | 13.29 | 10.82 | 13.18 | 11.82 | 12.97 |
Exon (%) | 53.39 | 75.06 | 64.78 | 70.25 | 44.87 | 67.21 | 48.50 | 70.46 |
Intron (%) | 44.52 | 23.12 | 33.55 | 26.87 | 52.95 | 30.81 | 49.47 | 27.92 |
Intergenic (%) | 2.09 | 1.82 | 1.68 | 2.88 | 2.18 | 1.98 | 2.03 | 1.62 |
Transcript (FPKM > = 0.3) | 23,749 | 22,099 | 22,046 | 32,221 | 24,420 | 22,718 | 23,788 | 22,397 |
Transcript (FPKM > = 1) | 18,667 | 16,255 | 16,782 | 18,079 | 19,501 | 17,247 | 18,892 | 16,712 |