Table 10 Clustering analysis of RNA aptamers in ddPCR-driven SELEX to identify related sequence and structure groups.
Group | CCR7 aptamer | 30-nt random sequence | Reads of each group (top 50 unique sequences) | Frequencies of each group (in top 1000 unique sequences) | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Initial library | Round 1 | Round 3 | Round 5 | Round 6 | Round 7 | Initial library | Round 1 | Round 3 | Round 5 | Round 6 | Round 7 | |||||
ddPCR-driven SELEX | 1 | C-1A | TTTCGTCCTGAGTTCGTGTCCTCGTCTGTG | 155 | 113 | 191 | 1363 | 2,668 | 5,801 | 4.79% | 3.36% | 5.75% | 18.81% | 17.41% | 16.29% | ↑ |
2 | DD9-2 | TTACTATTCAACTCGGCTCTTCGTTCTGTG | 0 | 0 | 0 | 131 | 103 | 207 | 0.00% | 0.00% | 0.00% | 1.81% | 0.67% | 0.58% | ↑↘ | |
3 | DD9-3 | TCCTGGTGTTGTTGGTTGTCTGCGCTGCCC | 0 | 0 | 0 | 0 | 45 | 147 | 0.00% | 0.00% | 0.00% | 0.00% | 0.29% | 0.41% | ↑ | |
DD9-7 | TCCCATCGTTGAAGTTGATCTGGCCCGCCA | 0 | 0 | 0 | 0 | 0 | 110 | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 0.31% | ↑ | ||
DD9-8 | TCCCGAAGCATGTCGGTTGTCTGTGCGCGC | 0 | 0 | 0 | 0 | 0 | 115 | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 0.32% | ↑ | ||
4 | DD9-5 | TCCCGGTGTGTAAGTTGTCTGCTGCCTGGC | 0 | 0 | 0 | 0 | 40 | 105 | 0.00% | 0.00% | 0.00% | 0.00% | 0.26% | 0.29% | ↑ | |
5 | DD9-9 | TGCCGCACATTAGTCTCTGGTTGCCCACGC | 0 | 0 | 0 | 0 | 0 | 60 | 0.00% | 0.00% | 0.00% | 0.00% | 0.00% | 0.17% | ↑ | |
6 | DD9-14 | TCCGCGAGTTCATTGAGTTGTTGCGCCCCA | 0 | 0 | 0 | 0 | 25 | 62 | 0.00% | 0.00% | 0.00% | 0.00% | 0.16% | 0.17% | ↑ | |
7 | C-6 | TCCATCGTCTCTTATCGTCTCTTGTCGCGC | 0 | 0 | 0 | 17 | 41 | 0 | 0.00% | 0.00% | 0.00% | 0.23% | 0.27% | 0.00% | ↘ | |
Others | Orphan sequences | 186 | 187 | 192 | 312 | 828 | 2078 | 5.75% | 5.56% | 5.78% | 4.30% | 5.40% | 5.84% | → | ||
Total Reads of all groups | 341 | 300 | 383 | 1823 | 3750 | 8685 | ||||||||||
