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Rice

Table 2 Summary of transcriptome sequencing data produced by Illumina sequencing

From: Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction

Sample

Raw reads

Clean reads

Q20(%)a

Total mapped

Multiple mapped

Uniquely mapped

Comparison groups

Total DEGsb

DEGs (↑) b

DEGs (↓) b

PXO99A_1d1

41,010,840

38,918,214

97.37

36,505,039 (93.8%)

1,810,186 (4.65%)

34,694,853 (89.15%)

PXO99A vs Δimp (1d)

   

PXO99A_1d2

43,382,564

40,471,568

98.04

38,005,434 (93.91%)

1,189,639 (2.94%)

36,815,795 (90.97%)

1521

512

1009

PXO99A_1d3

46,857,330

43,599,626

97.43

40,981,207 (93.99%)

1,400,984 (3.21%)

39,580,223 (90.78%)

   

PXO99A_3d1

41,322,886

38,515,876

98.02

36,206,414 (94.0%)

1,032,570 (2.68%)

35,173,844 (91.32%)

    

PXO99A_3d2

42,797,162

40,443,546

97.68

38,023,873 (94.02%)

1,327,664 (3.28%)

36,696,209 (90.73%)

    

PXO99A_3d3

41,168,536

39,233,110

97.63

36,695,566 (93.53%)

1,663,516 (4.24%)

35,032,050 (89.29%)

PXO99A vs Δimp (3d)

   

imp_1d1

43,654,506

42,143,374

98.27

39,671,695 (94.14%)

1,815,819 (4.31%)

37,855,876 (89.83%)

227

51

176

imp_1d2

42,779,594

42,036,494

98.2

39,606,885 (94.22%)

1,597,159 (3.8%)

38,009,726 (90.42%)

   

imp_1d3

44,399,584

43,569,548

98.24

40,818,028 (93.68%)

2,022,181 (4.64%)

38,795,847 (89.04%)

    

imp_3d1

46,118,502

45,285,946

98.22

42,528,243 (93.91%)

1,860,138 (4.11%)

40,668,105 (89.8%)

    

imp_3d2

45,012,320

40,910,822

98.06

38,467,718 (94.03%)

1,574,795 (3.85%)

36,892,923 (90.18%)

PXO99A vs ΔxanA (1d)

   

imp_3d3

46,332,702

43,541,914

98.21

40,911,915 (93.96%)

1,550,638 (3.56%)

39,361,277 (90.4%)

131

39

92

xanA_1d1

44,739,304

41,884,126

97.65

39,206,960 (93.61%)

1,336,065 (3.19%)

37,870,895 (90.42%)

   

xanA_1d2

43,063,064

40,742,626

97.65

38,212,980 (93.79%)

1,217,254 (2.99%)

36,995,726 (90.8%)

    

xanA_1d3

41,941,700

41,167,914

98.21

38,935,614 (94.58%)

1,732,387 (4.21%)

37,203,227 (90.37%)

    

xanA_3d1

45,891,720

45,053,084

98.25

42,570,896 (94.49%)

2,120,406 (4.71%)

40,450,490 (89.78%)

PXO99A vs ΔxanA (3d)

   

xanA_3d2

44,893,464

44,085,224

98.27

41,603,500 (94.37%)

2,577,904 (5.85%)

39,025,596 (88.52%)

106

75

31

xanA_3d3

43,236,992

42,496,768

98.26

39,661,084 (93.33%)

1,542,173 (3.63%)

38,118,911 (89.7%)

   
  1. aQ20(%): The proportion of nucleotides with quality value larger than 20 in reads
  2. bDEGs: Differentially expressed genes. ↑: Upregulated. ↓: Downregulated
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