Table 5 Bioinformatics analysis of high throughput sequencing data from selection rounds.

From: High throughput sequencing analysis of RNA libraries reveals the influences of initial library and PCR methods on SELEX efficiency

 

Initial library

HeLa-CCR7 cell-SELEX

HeLa-CD2 cell-SELEX

Round 3

Round 5

Round 6

Round 7

Round 3

Round 5

Round 6

Round 7

Total Reads

40,174,712

57,383,383

49,925,077

57,778,216

51,453,049

15,346,437

16,615,193

18,644,363

21,236,560

Usable reads

37,951,292

54,654,814

45,474,572

51,503,799

44,593,424

13,682,508

14,585,023

16,629,267

19,596,020

% Usable

94.47%

95.25%

91.09%

89.14%

86.67%

89.16%

87.78%

89.19%

92.27%

Total reads of top 1000 unique sequences

3,169

5,797

226,559

564,840

771,042

326,175

6,766,517

9,237,787

16,182,954

Frequencies of top 1000 in all the usable reads

0.008%

0.011%

0.498%

1.097%

1.729%

2.384%

46.394%

55.551%

82.583%

Molecular enrichment (fold) (top 1000)

1.00

1.83

71.49

178.24

243.31

102.93

2135.22

2915.05

5106.64

  1. The total reads and useful reads were defined. The most frequent 1,000 unique sequences and their percent in all the usable reads were identified. The molecular enrichment at each round was calculated by the formula: total reads of top 1000 unique sequences at round X/unselected round (initial library).
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