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Table 2 The performance of two RNA-seq kits allowing low total RNA input of FFPE samples

From: A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded 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