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