Table 1 Up- and downregulated bovine genes in response of viral infection.

From: Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing

Gene

logFC

logCPM

F

p value

FDR

A Mock

A 1 h

A 2 h

A 4 h

A 6 h

A 8 h

A 12 h

B Mock

LASP1

 − 1.603

7.534

25.183

3.22E−06

2.68E−03

23.42

14.10

30.48

35.71

28.13

27.23

69.40

50.27

HDAC7

 − 1.543

6.646

22.935

2.74E−06

2.54E−03

24.54

6.75

13.89

12.13

12.54

6.98

29.46

23.32

CARM1

 − 1.502

6.245

15.415

1.11E−04

4.65E−02

11.73

5.62

17.47

13.48

10.97

9.30

5.55

18.85

SLC44A2

 − 1.292

6.672

16.843

5.35E−05

2.63E−02

28.01

9.64

14.85

15.38

21.75

18.07

8.26

28.72

HSPG2

 − 1.181

8.739

17.042

1.26E−04

4.85E−02

73.59

46.38

68.00

76.82

82.47

58.73

31.34

127.45

IL11

 − 1.145

7.292

16.439

6.87E−05

3.19E−02

31.56

15.26

72.50

21.98

4.79

4.76

26.81

44.88

PRKAR2B

5.413

4.788

15.010

1.34E−04

4.85E−02

0.00

4.89

2.33

1.89

6.15

2.52

0.33

0.00

DDIT3

2.729

6.686

41.826

1.08E−09

8.94E−06

3.54

21.28

11.61

5.37

6.40

22.23

17.68

5.39

IRF9

2.648

5.658

14.900

1.41E−04

4.85E−02

1.18

5.97

9.10

3.56

4.65

26.30

9.19

1.80

TSC22D1

2.582

7.034

38.345

2.14E−09

8.94E−06

2.39

20.10

32.15

7.04

20.21

11.41

16.77

6.30

GADD45A

2.057

6.715

28.559

1.91E−07

3.18E−04

3.56

23.38

8.06

7.02

14.02

18.19

22.52

7.18

CXCL5

1.727

7.452

29.238

1.39E−07

2.90E−04

14.00

34.66

42.34

18.98

12.54

7.05

5.52

6.26

LOC100174924

1.650

7.675

24.507

2.44E−06

2.54E−03

16.32

32.22

23.16

18.94

28.14

62.75

107.37

10.76

SRSF5

1.630

7.249

24.298

1.43E−06

1.70E−03

11.67

31.88

40.02

18.95

18.68

15.69

40.50

11.67

IFRD1

1.611

7.468

16.111

8.08E−05

3.55E−02

8.15

14.02

13.39

18.81

31.23

78.46

172.07

1.76

MT2A

1.538

7.832

25.980

9.59E−07

1.33E−03

11.73

43.15

38.09

47.80

25.03

20.72

9.98

26.96

GADD45B

1.534

7.406

22.150

4.04E−06

3.06E−03

9.38

24.93

21.11

12.17

35.79

33.81

39.22

9.86

LOC100847143

1.505

8.114

17.505

1.37E−04

4.85E−02

24.49

42.70

23.01

22.45

39.01

71.76

65.48

19.74

LOC100847759

1.427

9.291

30.238

9.06E−08

2.52E−04

49.00

87.55

72.80

80.38

82.58

141.86

216.50

37.69

ATF3

1.421

6.627

14.844

1.45E−04

4.85E−02

11.62

27.55

13.47

3.61

7.96

20.24

34.46

8.07

TMEM190

1.352

7.169

17.749

3.44E−05

1.92E−02

15.16

26.56

12.80

13.89

20.28

22.34

7.87

11.66

HMGN3

1.300

7.304

17.452

3.96E−05

2.06E−02

12.86

30.23

26.94

18.97

15.69

22.59

8.98

19.77

SQSTM1

1.266

7.963

20.451

9.10E−06

5.42E−03

21.03

46.80

59.72

46.16

25.00

27.07

9.70

17.94

ID2

1.265

8.106

21.046

6.81E−06

4.37E−03

27.98

52.08

41.91

22.30

51.43

45.32

57.00

25.13

HNRNPDL

1.148

9.144

21.068

6.74E−06

4.37E−03

53.68

104.19

86.67

83.79

84.15

103.59

94.65

55.65

Gene

B 1 h

B 2 h

B 4 h

B 6 h

B 8 h

B 12 h

C Mock

C 1 h

C 2 h

C 4 h

C 6 h

C 8 h

C 12 h

LASP1

5.40

8.80

17.40

39.01

30.62

52.60

57.81

22.77

28.37

21.45

36.46

29.21

47.09

HDAC7

8.89

17.13

15.90

14.64

9.51

20.66

35.24

10.70

16.28

22.92

14.01

7.30

2.12

CARM1

5.64

2.83

5.87

14.62

7.90

13.22

19.75

5.28

17.87

5.91

10.03

17.36

18.87

SLC44A2

8.27

19.38

5.93

17.09

15.39

5.22

19.87

12.35

17.71

17.77

13.38

14.60

2.00

HSPG2

45.97

19.97

84.90

60.99

70.68

62.40

172.12

63.24

90.40

54.97

65.03

50.20

33.23

IL11

11.17

31.19

5.93

7.32

7.56

26.49

46.58

27.25

42.11

12.00

7.30

5.47

38.12

PRKAR2B

4.04

2.96

6.99

6.06

5.53

0.20

0.00

2.32

2.84

2.01

0.96

2.73

3.18

DDIT3

46.93

9.66

10.15

9.79

13.49

18.18

4.28

15.81

7.55

17.84

16.40

8.20

10.63

IRF9

8.14

8.90

5.74

1.28

4.22

10.36

0.06

6.93

10.55

4.71

4.53

9.12

7.08

TSC22D1

28.51

60.43

11.56

14.66

6.06

3.26

2.92

21.68

39.73

15.61

14.53

16.45

10.39

GADD45A

24.35

15.73

11.53

12.21

17.32

16.27

7.05

23.76

8.51

12.53

11.17

20.08

39.67

CXCL5

31.57

48.42

28.83

11.02

13.17

17.90

18.26

50.14

52.29

37.98

18.02

7.29

12.20

LOC100174924

60.14

27.63

21.67

31.73

30.82

50.16

12.76

24.04

10.33

32.82

44.95

31.03

40.26

SRSF5

37.17

35.74

31.62

12.24

6.07

5.89

8.56

26.16

32.53

24.50

17.39

14.61

3.84

IFRD1

22.30

21.67

8.80

37.80

40.34

68.65

9.78

16.35

13.31

22.93

39.27

31.93

66.35

MT2A

49.29

17.76

40.35

30.50

34.50

26.18

11.42

52.93

46.65

38.68

41.58

49.31

31.11

GADD45B

48.75

31.34

15.94

25.64

26.89

31.58

16.86

21.59

21.97

31.19

29.70

27.38

27.94

LOC100847143

91.92

44.82

50.39

39.05

40.32

75.89

18.43

33.05

21.91

63.83

54.47

31.02

50.62

LOC100847759

163.93

70.04

95.09

81.71

114.80

175.93

45.20

82.76

56.50

158.07

116.74

94.02

165.44

ATF3

16.38

16.42

5.82

23.09

13.56

16.17

4.38

19.63

9.44

8.73

10.57

15.51

22.65

TMEM190

39.10

34.36

20.24

17.10

11.70

2.89

12.76

29.48

25.40

37.21

22.46

13.69

1.95

HMGN3

31.92

28.30

24.55

17.11

15.51

3.19

7.22

36.11

28.26

38.44

27.02

22.82

10.21

SQSTM1

48.73

43.13

37.53

31.70

13.71

13.29

26.79

52.51

84.56

57.73

29.15

30.13

18.94

ID2

61.03

41.71

15.98

63.38

63.04

70.70

12.86

40.92

39.27

35.01

46.50

52.03

55.76

HNRNPDL

136.17

140.92

138.16

89.02

86.11

44.96

42.44

81.53

85.76

123.50

120.66

71.19

45.41

  1. We detected significant upregulation in 19 and 6 downregulation in 6 host genes in all of the three biological replicates.
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