Table 6 Clustering analysis of RNA aptamers against CCR7 to identify related sequence and structure groups.

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

Group

CCR7 aptamer

30-nt random sequence

Reads of each group (in top 50 unique sequences)

Frequencies of each group (in top 1000 unique sequences)

 

Initial library

Round 3

Round 5

Round 6

Round 7

Initial library

Round 3

Round 5

Round 6

Round 7

1

C-1A

TTTCGTCCTGAGTTCGTGTCCTCGTCTGTG

100

2,642

194,765

474,729

619,702

3.16%

45.58%

85.97%

84.05%

80.37%

↑

2

C-2A

AATTCGTCAAAGTCGTTTATTTCGTCTGTG

0

0

169

895

2,496

0.00%

0.00%

0.07%

0.16%

0.32%

↑

C-2B

AATTCGTCCATTTGTCGCTCATCGTCTGTG

0

0

0

0

746

0.00%

0.00%

0.00%

0.00%

0.10%

↑

C-2C

TTTCGTCCAATTTACGCTTCGTCGTCTGGC

0

0

0

552

1,208

0.00%

0.00%

0.00%

0.10%

0.16%

↑

3

C-5A

ATTTCGTCAACGCGTTTGTCTCGTCTGGTG

0

0

0

575

1,099

0.00%

0.00%

0.00%

0.10%

0.14%

↑

C-5B

ATTCCTCAAATTCATCGATCTCGTCTGGTG

0

0

0

563

1,105

0.00%

0.00%

0.00%

0.10%

0.14%

↑

4

C-6

TCCATCGTCTCTTATCGTCTCTTGTCGCGC

0

24

626

1,767

2,312

0.00%

0.41%

0.28%

0.31%

0.30%

↘→

Others

 

Orphan sequences

189

84

0

0

0

5.96%

1.45%

0.00%

0.00%

0.00%

↓

  

Total Reads of all the groups

289

2,750

195,560

479,081

628,668

      
  1. After alignment of the top 50 sequences, several groups of RNA aptamers were identified. The representative RNA aptamers, the reads of each group, and their frequencies in the top 1000 unique sequences were listed. Only the 30-nt random sequences of the aptamer core regions (5′-3′) are indicated.
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