TABLE 2.
Primers and probes used in this study and full-length sequences of circRNA J616285.1:30092|29489
| Primer set name | Primer name | Sequence (5′ to 3′) |
|---|---|---|
| Divergent primer | ||
| circHIPK3 | circHIPK3-F circHIPK3-R |
TTCAACATATCTACAATCTCGGT
ACCATTCACATAGGTCCGT |
| 126350 | 108139 | P1-F P1-R |
AGAAACGCCGGTCGGTAAAA
TCTTGGAAGCCGATGCAACA |
| 125634 | 108139 | P2-F P2-R |
CTGACGTGCATGATTTGCCG
TCTTGGAAGCCGATGCAACA |
| 121883 | 108133 | P3-F P3-R |
CAGTCTTGCGGTTCCGTCTC
AAGCCGATGCAACAACGGTA |
| 56901 | 54433 | P4-F P4-R |
GCAATGACTGCGTACCGTTT
GGCTCTTTGCTCGAAGGTGA |
| 108485 | 108137 | P5-F P5-R |
ATAGCGCGTAGACGGACATC
TTGGAAGCCGATGCAACAAC |
| 153076 | 152061 | P6-F P6-R |
CCGACATCGTGGACAAATGC
GTACGCCGATAACGACGACT |
| 30026 | 29573 | P7-F P7-R |
CCTCAGCAGACGAGAGGATG
TTCGTGGGTCGCTTCGTGAA |
| 227402 | 225559 | P8-F P8-R |
CAGTTGCGAACGTCACCGGA GGTTCGCTAATCGCACGGAA |
| 138288|134886 | P9F | GCGAGAGGAAGTCGATCTGG |
| P9R | TGTTGACGTCGTCCAGTGAG | |
| 108488|108179 | P10F | GAGGAGACGACTGTCGGTAG |
| P10R | AAGGTGCGGGAGACTAGGTC | |
| 227109|75825 | P11F | AATGCGGTCCACCATCTTCA |
| P11R | GTAACTTCAGTGGGCCCGTC | |
| 227109|45042 | P12F | CGTGACTTGCTGGATCTCGT |
| P12R | GTAACTTCAGTGGGCCCGTC | |
| Convergent primers | ||
| GAPDH | GAPDH-F GAPDH-R |
GCACCGTCAAGGCTGAGAAC
TGGTGAAGACGCCAGTGGA |
| IE1/2 | IE1/2-F IE1/2-R |
CCAAGAGAAAGATGGACCCTG
AACATAGTCTGCAGGAACGTC |
| UL105 | 105F | GTGCCGGTATCTCAACGGAT |
| 105R | CGCGTACAGACTGGTGTGAT | |
| UL111A | UL111AF | GTCTCTTCCTCTCTGGTCCTG |
| UL111AR | CTTTCTCGAGTGCAGATAC | |
| Probes for ampFISH | ||
| DP-positive | GTTACAGACGACTCCCACAGTCCCGAGGGGATATAAATCACCGGACT | |
| AP-positive | GAGGGCTATGTTTTTTGCTATGTACGGGACTGTGGGAGTCGTCTGTAACTACTTCATGTTACAGACGACTCCCAC | |
| DP-negative | GTTACAGACGACTCCCACAGTCC CGTACATAGCAAAAAACATA GGACT | |
| AP-negative | CTCGACGGTGATTTATATCCCCTCGGGACTGTGGGAGTCGTCTGTAACTACTTCATGTTACAGACGACTCCCAC | |
| DP-linear 29489 | GTTACAGACGACTCCCACAGTCC-CGAGGACACCGCCGTCTACT-GGACT | |
| AP-linear-29489 | GAGGGCTATGTTTTTTGCTATGTACG -GGACTGTGGGAGTCGTCTGTAACTACTTCATGTTACAGACGACTCCCAC | |
| circHIPK3-ve DP | GTTACAGACGACTCCCACAGTCC GTATGGCCTCACAAGTCTTGGTCTGGACT | |
| circHIPK3-ve AP | ATATCTACAATCTCGGTACTACAG GGACTGTGGGAGTCGTCTGTAACTACTTCATGTTACAGACGACTCCCAC | |
| circHIPK3+ve DP | GTTACAGACGACTCCCACAGTCC CTGTAGTACCGAGATTGTAGATAT GGACT | |
| circHIPK3+ve AP | TAGACCAAGACTTGTGAGGCCATAC GGACTGTGGGAGTCGTCTGTAACTACTTCATGTTACAGACGACTCCCAC | |
| Full-length sequences of circRNA J616285.1:30092|29489 | ||
| circRNAnumber 5 | CCTCGCGTACATAGCAAAAAACATAGCCCTCGTCCGAGATGAGGCACACAGCGGTCTTCTTCTGCTGATCCGGCGACAACACGCCCTCGTTCACGAAGCGACCCACGAAGGCCAGGCGCGTCTGGCAACACAGGTAGTGACTCCAAGCCTTCACGTCCTCCGGTTTGAAGTCCTCGTCCGTCTCGATCTCCTGCAGCACTAGGTTCCAGCCCGGCGGCCAGACCACGGGCAACACCTGGCCTGCGTTGATGCGCACGTAAGCTTCCAGACAGCCCAGGCCGAACTCGGCCGTGAGCGCCAGGCTAGCCAGATCGCTCATGTGACGCGCCGAGTCAGTGGGCGAGCCCGGGGGCCCGTCGCACACCACGCTCCGTCTTCTTGTCCTCACCGCGGCCAGCGTGGCGAGGACACTTTCCGCGCCCGAGGCTGTATCTTCGGTTTGCCCGCCGGAGCCGGCCCTCACTATATAACGTCCCGCCCGGGTCTCCTCCATGTATGCAGGTAAGCAACTGAGCCGAACGCACCTCAGCAGACGAGAGGATGTCGTCGCGGCGTCGCAGCTCGTCACGTCGCTCTGGCGAACCCTCGACGGTGATTTATATCC | |