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Table 1 Overview over smRNA and mRNA sequencing and assembly statistics

From: Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals

Library name

4°C

16°C

34°C

36°C

20 g

60 g

DC

DS

Noon

Experimental treatment

[4°C 4hs]

[16°C 4hs]

[34°C 12hs]

[36°C 4hs]

[20 g/L NaCl 4hs]

[60 g/L NaCl 4hs]

[midnight]

[24hs dark]

[reference]

smRNA

         

Total base pairs

476,999,446

327,143,288

185,735,770

254,824,059

427,785,834

220,539,256

258,016,695

133,416,325

361,512,933

No. of reads (after trimming)

17,193,220

12,593,192

8,433,048

10,658,877

15,378,342

8,725,667

10,662,995

6,131,326

13,591,577

Mean read length

28

26

22

24

28

25

24

22

27

No. of reads (after smRNA filtering)

16,404,546

12,102,929

8,234,625

10,180,915

14,747,100

8,399,643

10,259,502

6,025,546

13,017,083

No. of unique reads

2,288,514

2,198,132

1,633,046

2,338,445

2,352,632

1,705,659

1,964,913

1,405,173

1,881,585

No. of miRNAs (miRDeep2)

118

96

131

114

136

104

129

115

138

Mean readcount of miRNAs

149

418

300

199

257

170

253

171

446

No. of miRNAs w/ miRNA* (miRDeep2)

55

83

84

66

61

70

77

75

81

No. of miRNAs (after manual inspection)

21

21

21

21

21

21

21

21

21

mRNA

         

No. of read pairs (2 x 100 bp)

26,119,370

34,506,164

41,918,850

30,712,175

39,211,121

34,918,126

28,787,997

36,782,164

29,985,278

No. read pairs mapped

16,777,195

23,084,001

27,761,160

19,905,837

24,920,330

23,277,719

19,357,409

24,141,222

20,023,519

No. of 58,649 genes expressed (FPKM > 0)

55,881

56,353

57,389

55,518

55,287

56,526

56,292

56,041

56,778

No. of 58,649 genes expressed (FPKM > 5)

40,078

39,125

39,246

37,256

37,435

39,198

38,041

38,422

40,206

Median FPKM

12.58

12.29

11.87

11.42

11.13

12.38

11.41

11.66

12.49

BLASTX annotation [%]

44.81

44.51

43.80

45.10

45.39

44.44

44.59

44.81

44.18

Pfam [%]

34.50

34.23

33.63

34.71

34.87

34.13

34.27

34.43

33.98

GO annotation [%]

34.90

34.67

34.08

35.14

35.32

34.59

34.71

34.89

34.39

DEGs all (vs. noon)

119

37

351

2,465

138

48

67

60

-

DEGs up (vs. noon)

47

12

105

293

21

14

22

28

-

DEGs down (vs. noon)

72

25

246

2,172

117

34

45

32

-

log2 difference (minimum/maximum)

−8.30/+6.61

−7.27/+5.27

−6.84/+7.34

−8.43/+8.17

−10.43/+5.46

−7.02/+6.24

−7.32/+5.19

−7.06/+7.64

-

log2 difference (mean)

2.93

3.15

2.29

2.79

2.73

3.27

2.99

3.01

-

  1. DEG = Differentially Expressed Gene.
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BMC Genomics

ISSN: 1471-2164

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