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Table 3 Comparison on the performance of the TaKaRa kit and the KAPA kit with different quality total RNA from 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

Samples

Sample13

Sample14

Sample15

Sample16

Sample17

Sample18

Sample19

Sample20

Sample21

Sample22

Sample23

Sample24

Sample25

Sample26

Sample27

R-Sample22

R-Sample23

R-Sample24

R-Sample25

R-Sample27

DV200(%)

75

77

76

61

51

52

52

46

42

2

1

11

17

26

27

2

1

11

17

27

Kits

T

K

T

K

T

K

T

K

T

K

T

K

T

K

T

K

T

K

T

T

T

T

T

T

T

T

T

T

T

PCR cycles

13

15

13

15

13

15

13

15

13

15

13

15

13

15

13

15

13

15

13

13

13

13

13

13

13

13

13

13

13

Library (ng)

115.6

48.8

448.0

31.2

242.0

17.2

91.2

9.3

472.0

24.4

280.0

38.6

62.4

5.6

200.0

13.9

155.2

4.4

48.8

83.2

216.0

98.0

161.2

344.0

8.3

14.1

58.4

20.0

123.2

Total raw data (G)

18.1

43.7

19.2

37.3

21.8

28.3

11.6

5.0

13.6

16.8

13.8

28.6

12.2

12.1

8.3

12.0

12.5

10.6

10.7

10.9

10.3

11.2

8.6

11.2

11.0

8.9

12.0

Downsampled data (G)

18.0

18.0

18.0

18.0

18.0

18.0

10.0

5.0

10.0

10.0

10.0

10.0

10.0

10.0

8.3

10.0

10.0

10.0

10.0

10.0

10.0

10.0

8.6

11.2

11.0

8.9

12.0

Clean bases (G)

15.4

15.9

15.2

16.3

14.7

16.1

6.7

4.6

7.1

9.4

7.2

9.3

7.1

6.0

6.6

5.0

3.6

5.2

7.0

6.1

6.6

6.1

2.3

5.2

8.0

4.8

6.2

rRNA (%)

5.24

5.27

4.78

2.07

10.08

5.31

20.29

1.62

14.32

0.84

14.92

1.33

12.01

28.24

14.96

39.42

47.13

35.78

15.00

38.30

24.70

41.03

47.59

34.50

11.37

31.46

39.02

Q30 (%)

94.13

91.86

94.58

92.11

93.98

92.19

91.53

92.62

92.28

93.40

92.36

93.42

89.81

92.12

93.00

91.51

77.57

83.75

90.66

87.62

91.66

92.74

73.78

82.37

89.04

84.89

90.43

GC (%)

45.27

49.86

47.05

49.16

48.40

49.70

50.79

46.64

51.58

46.71

51.02

45.99

48.20

48.91

46.07

52.38

51.23

56.66

48.76

54.56

52.66

55.30

49.17

58.32

46.99

51.75

55.23

Total mapping rate (%)

83.47

93.94

89.11

94.09

82.30

95.16

82.13

97.65

92.06

98.34

90.81

97.86

83.77

85.57

97.66

74.45

64.92

78.71

90.58

75.13

78.59

79.15

58.24

78.68

90.65

75.04

82.26

Uniquely mapping rate (%)

71.29

84.63

78.79

84.82

67.87

84.20

69.59

90.75

81.53

90.98

80.20

91.10

74.44

76.58

91.60

63.62

48.73

60.68

77.32

58.19

65.33

62.98

43.58

60.25

82.44

61.53

69.46

Multiple mapping rate (%)

12.18

9.31

10.32

9.27

14.43

10.96

12.54

6.90

10.53

7.36

10.61

6.76

9.33

8.99

6.06

10.83

16.19

18.03

13.26

16.94

13.26

16.17

14.66

18.43

8.21

13.51

12.80

Exon (%)

59.52

66.59

60.61

57.39

67.71

71.48

57.56

49.35

58.56

47.48

55.42

46.88

38.56

41.19

33.20

42.10

32.98

43.84

31.52

47.36

36.54

57.09

25.40

44.02

29.46

43.89

56.80

Intron (%)

38.31

31.86

37.68

40.92

30.50

27.40

40.80

48.93

39.86

50.68

43.08

51.40

58.92

57.05

64.95

55.48

59.33

51.77

64.92

48.06

60.59

40.88

61.77

51.68

67.10

51.15

41.47

Intergenic (%)

2.17

1.55

1.71

1.68

1.79

1.12

1.63

1.72

1.58

1.85

1.50

1.72

2.53

1.76

1.85

2.43

7.69

4.39

3.56

4.59

2.88

2.03

12.83

4.30

3.43

4.96

1.74

Transcript (FPKM 0.3~1)

5662

4724

6142

3729

5844

3118

5689

3003

6545

4496

6394

5441

5447

5212

2426

4885

2858

4560

5389

4819

5135

5755

2134

3840

4407

3636

4956

Transcript (FPKM 1~5)

9132

8294

10,045

8337

8398

6828

10,700

8659

11,841

10,819

11,566

10,839

10,888

10,865

8175

11,333

9972

10,364

11,455

10,959

11,847

9961

7588

8939

10,665

9193

9535

Transcript (FPKM 5~10)

3444

3644

3882

4359

3156

3437

3446

3627

4277

4991

3934

4192

4849

5003

4838

5554

4687

4814

5797

4918

5690

4198

4316

4544

5926

4806

4335

Transcript (FPKM10~50)

3938

4311

4146

5053

3568

4052

2539

3226

3735

4300

3132

3375

5195

4762

5441

4723

3796

4759

5538

3849

4562

4359

4175

4982

5886

4446

4572

Transcript (FPKM> = 50)

747

741

712

662

763

706

570

433

566

467

595

481

633

601

516

555

474

525

586

593

585

658

620

599

603

597

640