Table 1.
Primers, crRNAs and reporters used in this study.
| Oligo name | Oligo Sequence(5′-3′) | Usage |
|---|---|---|
| STD-N-F1 | CCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAAT | Fig. 1a |
| STD-N-F2 | CAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAAT | Fig. 1a |
| STD-N-F3 | TCAACTCCAGGCAGCAGTAGGGGAACTTCTCC | Fig. 1a |
| STD-N-R1 | GTTGGCCTTTACCAGACATTTTGCTCTCAAGCTGG | Fig. 1a |
| STD-N-R2 | TGGCCTTTACCAGACATTTTGCTCTCAAGCTG | Fig. 1a |
| STD-N-R3 | TTACCAGACATTTTGCTCTCAAGCTGGTTCAA | Fig. 1a |
| N–F0 | G*G*AACTTCTCCTGCTAGAATGGCTGGCAAT*G*G | Fig. 1e and g; Fig. S1a; throughout the paper when N gene was examined unless otherwise stated |
| N-R0 | G*G*CCTTTACCAGACATTTTGCTCTCAAGCT*G*G | Fig. 1e and g; Fig. S1a; throughout the paper when N gene was examined unless otherwise stated |
| N–F01 | G*GAACTTCTCCTGCTAGAATGGCTGGCAATG*G | Fig. 2c |
| N-R01 | G*GCCTTTACCAGACATTTTGCTCTCAAGCTG*G | Fig. 2c |
| N–F02 | G*G*A*ACTTCTCCTGCTAGAATGGCTGGCAA*T*G*G | Fig. 2c |
| N-R02 | G*G*C*CTTTACCAGACATTTTGCTCTCAAGC*T*G*G | Fig. 2c |
| N–F03 | G*G*A*A*CTTCTCCTGCTAGAATGGCTGGCA*A*T*G*G | Fig. 2c |
| N-R03 | G*G*C*C*TTTACCAGACATTTTGCTCTCAAG*C*T*G*G | Fig. 2c |
| N–F1 | C*C*AGGCAGCAGTAGGGGAACTTCTCCTGCTAGA*A*T | Fig. S1b-S1d |
| N–F2 | C*A*GGCAGCAGTAGGGGAACTTCTCCTGCTAGA*A*T | Fig. S1b-S1d |
| N–F3 | T*C*AACTCCAGGCAGCAGTAGGGGAACTTCT*C*C | Fig. S1b-S1d |
| N–F4 | A*G*AAATTCAACTCCAGGCAGCAGTAGGGGAA*C*T | Fig. S1b-S1d |
| N–F5 | G*C*AGTAGGGGAACTTCTCCTGCTAGAATGG*C*T | Fig. 1f; Fig. S1c-S1e |
| N–F6 | G*T*TCAAGAAATTCAACTCCAGGCAGCAGTA*G*G | Fig. 1f; Fig. S1e |
| N-R1 | G*T*TGGCCTTTACCAGACATTTTGCTCTCAAGCT*G*G | Fig. 1f; Fig. S1b-S1e |
| N1–F | A*G*AGGCGGCAGTCAAGCCTCTTCTCGTTCCTC*A*T | Fig. 1h and i |
| N1-R | C*A*GGAGAAGTTCCCCTACTGCTGCCTGGAG*T*T | Fig. 1h and i |
| ORF1ab-F11 | T*T*GCCTGGCACGATATTACGCACAACTAATG*G*T | Fig. S2a, S2b |
| ORF1ab-F18 | A*T*GGTGACTTTTTGCATTTCTTACCTAGAGT*T*T | Fig. 2d–f, 2h; Fig. S2a, S2c |
| ORF1ab-R2 | A*A*GTCAGTGTACTCTATAAGTTTTGATGGTGT*G*T | Fig. 2d–f, 2h; Fig. S2a-S2c |
| HPV16–F1 | G*T*TACAACGAGCACAGGGCCACAATAAT*G*G | Fig. S4a, S4b |
| HPV16–F2 | C*C*CAAATATTCAATAAACCTTATTGGTTACA*A*C | Fig. S4b |
| HPV16–F3 | A*A*TATTCAATAAACCTTATTGGTTACAACGAGC*A*C | Fig. S4b |
| HPV16–F4 | G*G*TTACAACGAGCACAGGGCCACAATAATGG*C*A | Fig. S4b, S4e; throughout the paper when HPV16 was examined unless otherwise stated |
| HPV16-R1 | C*C*CATGTCGTAGGTACTCCTTAAAGTTAGTATT*T*T | Fig. S4a |
| HPV16-R2 | A*C*TCCTTAAAGTTAGTATTTTTATATGTAG*T*T | Fig. S4a |
| HPV16-R3 | T*A*CTGCGTGTAGTATCAACAACAGTAACAA*A*T | Fig. S4a, S4b, S4e; throughout the paper when HPV16 was examined unless otherwise stated |
| HPV16-R4 | T*A*TTTGTACTGCGTGTAGTATCAACAACAG*T*A | Fig. S4a |
| HPV16-R5 | T*A*GTATCAACAACAGTAACAAATAGTTGGT*T*A | Fig. S4a |
| HPV18–F1 | G*C*ATAATCAATTATTTGTTACTGTGGTAGATACC*AC*T | Fig. S4c, S4d |
| HPV18–F2 | A*T*AACAATGGTGTTTGCTGGCATAATCAATTAT*T*T | Fig. S4d |
| HPV18–F3 | T*G*GTTACATAAGGCACAGGGTCATAACAAT*G*G | Fig. S4d |
| HPV18–F4 | A*A*TTATTTGTTACTGTGGTAGATACCACTCGC*A*G | Fig. S4d, S4f; throughout the paper when HPV18 was examined unless otherwise stated |
| HPV18–F5 | C*A*CAGGGTCATAACAATGGTGTTTGCTGGCAT*A*A | Fig. S4d |
| HPV18-R1 | A*A*ATTTGGTAGCATCATATTGCCCAGGTAC*A*G | Fig. S4c, S4d |
| HPV18-R2 | T*G*GTAGCATCATATTGCCCAGGTACAGGAGAC*T*G | Fig. S4c, S4d, S4f; throughout the paper when HPV18 was examined unless otherwise stated |
| HPV18-R3 | T*A*GCATCATATTGCCCAGGTACAGGAGACTG*T*G | Fig. S4c |
| HPV18-R4 | T*T*GGTAGCATCATATTGCCCAGGTACAGGAGAC*T*G | Fig. S4c |
| HPV18-R5 | T*T*GGTAGCATCATATTGCCCAGGTACAGGAG*A*C | Fig. S4c |
| qPCR primers and probes | Proprietary | Fig. 4b and d; Fig. S5-S8 |
| crRNA-N0 | UAAUUUCUACUAAGUGUAGAUcugcugcuugacagauugaacc | throughout the paper when N gene was examined unless otherwise stated |
| crRNA-N1 | UAAUUUCUACUAAGUGUAGAUuugaacuguugcgacuacgugau | Fig. 1h and i |
| crRNA-ORF1ab | UAAUUUCUACUAAGUGUAGAUgugcaguugguaacaucuguuac | Fig. 2d–f, 2h; Fig. S2 |
| crRNA-HPV16 | UAAUUUCUACUAAGUGUAGAUuugggguaaccaacuau | throughout the paper when HPV16 was examined |
| crRNA-HPV18 | UAAUUUCUACUAAGUGUAGAUacaauaugugcuucuacaca | throughout the paper when HPV18 was examined |
| n-reporter-0 | /56-FAM/TTATT/3Bio/ | Fig. 3a–c |
| FQ1 | /56-FAM/TTATT/3BHQ1/ | Fig. 1a, 1e-1i; Fig. 2a and c; Fig. S1; Fig. S2; Fig. S3; Fig. S4 |
| FQ3 | /56-FAM/TTCCTT/3BHQ1/ | Fig. S3 |
| FQ4 | /56-FAM/TTCCCTT/3BHQ1/ | Fig. S3 |
| FQ5 | /56-FAM/TTCCCCCTT/3BHQ1/ | Fig. S3 |
| FQ7 | /56-FAM/TTCCCCTT/3BHQ1/ | Fig. S3 |
| FQ8 | /56-FAM/AAAAAA/3BHQ1/ | Fig. 2b |
| FQ9 | /56-FAM/TTTTTT/3BHQ1/ | Fig. 2b |
| FQ10 | /56-FAM/GGGGGG/3BHQ1/ | Fig. 2b |
| FQ11 | /56-FAM/CCCCCC/3BHQ1/ | Fig. 2b; Fig. 4; Fig. S3; Fig. S5; Fig. S6; Fig. S7; Fig. S8 |
| reporter-1 | /56-FAM/T(dT-BHQ1)ATT | Fig. 3g |
| reporter-2 | /56-FAM/T*(dT-BHQ1)ATT | Fig. 3g |
| reporter-3 | /56-FAM/T(dT-BHQ1)CCCCTT | Fig. 3h |
| reporter-4 | /56-FAM/T*(dT-BHQ1)CCCCTT | Fig. 3h |
| n-reporter-1 | /56-Bio/T(dT-DIG)ATT/3FAM/ | Fig. 3e |
| n-reporter-2 | /56-Bio/T*(dT-DIG)ATT/3FAM/ | Fig. 3e and i, Fig. S3d, S3e |
| n-reporter-3 | /56-Bio/T*(dT-DIG)CCCCTT/3FAM/ | Fig. 3i; Fig. 5 |