Table 2.
The performance of two RNA-seq kits allowing low total RNA input of FFPE samples
| Kits | TaKaRa kit | KAPA kit | ||
|---|---|---|---|---|
| Sample-Input | GM12878- FFPE-50 ng | GM12878- FFPE-10 ng | GM12878- FFPE-100 ng | GM12878- FFPE-50 ng |
| PCR cycles | 13 | 16 | 15 | 15 |
| Library (ng) | 944.0 | 792.0 | 128.4 | 22.4 |
| Total raw data (G) | 20.1 | 21.7 | 35.7 | 24.5 |
| Downsampled data (G) | 20.0 | 20.0 | 20.0 | 20.0 |
| Clean bases (G) | 16.1 | 15.6 | 18.2 | 18.5 |
| rRNA (%) | 10.49 | 13.46 | 1.46 | 0.89 |
| Q30 (%) | 93.92 | 93.98 | 90.84 | 92.58 |
| GC (%) | 51.03 | 53.02 | 53.25 | 47.97 |
| Total mapping rate (%) | 92.10 | 91.62 | 96.36 | 97.57 |
| Unique mapping rate (%) | 80.47 | 79.15 | 80.73 | 87.95 |
| Multiple mapping rate (%) | 11.63 | 12.47 | 15.63 | 9.62 |
| Exon (%) | 61.01 | 64.74 | 53.36 | 46.15 |
| Intron (%) | 37.23 | 33.55 | 44.50 | 51.78 |
| Intergenic (%) | 1.76 | 1.71 | 2.14 | 2.07 |
| Transcript (FPKM 0.3~1) | 5496 | 5312 | 5240 | 3769 |
| Transcript (FPKM 1~5) | 9168 | 8680 | 9013 | 8229 |
| Transcript (FPKM 5~10) | 3612 | 3551 | 4337 | 4428 |
| Transcript (FPKM10~50) | 4139 | 3832 | 4664 | 5368 |
| Transcript (FPKM> = 50) | 730 | 733 | 621 | 631 |