Table S1.
List of adapter, primers, and probes
| Target | Oligonucleotide | Sequence (5′- 3′) |
| Small noncoding RNA | ||
| EBER1 | Stem-loop RT | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGAAAACATGCG |
| Forward | AGGACCTACGCTGCCCTAGA | |
| Stem-loop Reverse | ATTCAGTTGAGAAAACATGCGG | |
| EBER2 | Stem-loop RT | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGAAAAATAGCG |
| Forward | AGGACAGCCGTTGCCCTAGTGGTTTC | |
| Stem-loop Reverse | ATTCAGTTGAGAAAAATAGCGG | |
| vtRNA1-1 | Stem-loop RT | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGAAAAGGACTG |
| Forward | GGCTGGCTTTAGCTCAGCGG | |
| Stem-loop Reverse | ATTCAGTTGAGAAAAGGACTGG | |
| RNY1 | Stem-loop RT | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGAAAAGACTAG |
| Forward | GCTGGTCCGAAGGTAGTGAG | |
| Stem-loop Reverse | ATTCAGTTGAGAAAAGACTAGT | |
| 5′-adapter-EBER1 | RA5 adapter | GUUCAGAGUUCUACAGUCCGACGAUC (Illumina #15013205) |
| Forward (adapter) | GTTCAGAGTTCTACAGTCCGA | |
| Reverse (EBER1) | AAAACATGCGGACCACC | |
| miRNA | ||
| EBV BART1-5p | Stem-loop RT | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGACAGCACG |
| Forward | ACACTCCAGCTGGGTCTTAGTGGAAGTGAC | |
| Probe | TTCAGTTGAGACAGCACG | |
| Reverse | CTCAACTGGTGTCGTGGAGTCGGCA | |
| EBV BART8-3p | Stem-loop RT | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTACGACC |
| Forward | ACACTCCAGCTGGGGTCACAATCTATGGGG | |
| Probe | TTCAGTTGAG CTACGACC | |
| Reverse | CTCAACTGGTGTCGTGGAGTCGGCA | |
| EBV BART17-5p | Stem-loop RT | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGCTTGTATG |
| Forward | ACACTCCAGCTGGGTAAGAGGACGCAGGCA | |
| Probe | TTCAGTTGAGCTTGTATG | |
| Reverse | CTCAACTGGTGTCGTGGAGTCGGCA | |
| EBV BHRF1-2* | Stem-loop RT | CTCAACTGGTGTCGTGGAGTCGGCAATTCAGTTGAGGCTATCTG |
| Forward | ACACTCCAGCTGGGAAATTCTGTTGCAGCA | |
| Probe | TTCAGTTGAGGCTATCTG | |
| Reverse | CTCAACTGGTGTCGTGGAGTCGGCA | |
| hsa-miR21-5p | TaqMan MicroRNA Assay ID 000397 | |
| hsa-miR451 | TaqMan MicroRNA Assay ID 001105 | |
| mRNA | ||
| IFN-β | Forward | CCTGAAGGCCAAGGAGTACA |
| Reverse | AAGCAATTGTCCAGTCCCAG | |
| IFITM1 | Forward | ATGTCGTCTGGTCCCTGTTC |
| Reverse | GTCATCAGGATGCCCAGAAT | |
| IFITM3 | Forward | ATGTCGTCTGGTCCCTGTTC |
| Reverse | GGGATGACGATGAGCAGAAT | |
| OAS2 | Forward | GGTGAACACCATCTGTGACG |
| Reverse | ACCATCGGAGTTGCCTCTTA | |
| MX1 | Forward | GATTTTGGGGCTTTCCAGTC |
| Reverse | GATGATCAAAGGGATGTGGC | |
| TLR3 | Forward | TCACTTGCTCATTCTCCCTT |
| Reverse | GACCTCTCCATTCCTGGC | |
| TLR7 | Forward | TGCTCTGCTCTCTTCAACCA |
| Reverse | AACCATCTAGCCCCAAGGAG | |
| TLR9 | Forward | ACACAGCTGCGCAAGCTTAAC |
| Reverse | TCGAGTGAGCGGAAGAAGATG | |
| PKR | Forward | GGGACCTTGGAACAATGGAT |
| Reverse | CCTTGTTCGCTTTCCATCAT | |
| RIG-I | Forward | ATATCCGGAAGACCCTGGAC |
| Reverse | GAGAAAAAGTGTGGCAGCCT | |
| IFIT1 | Forward | TACCTGGACAAGGTGGAGAA |
| Reverse | GTGAGGACATGTTGGCTAGA | |
| IFIT3 | Forward | CTTACGGCAAGCTGAAGAGT |
| Reverse | AATTGCCAGTCCAGAGGAGA | |
| IFIT5 | Forward | GGCCATTCTGTTGGAGTTAG |
| Reverse | GCTTCTTCAAGCTGGTCCAT | |
| MVP | Forward | ATCTGAGGCGTTTGTTGCAG |
| Reverse | GGATGCGGATGATGAACTCT | |
| La/SSB | Forward | TAATGAAAAGATGGCTGCCC |
| Reverse | AAGGTACCCAGCCTTCATCC | |
| TIM1 | Forward | CCAGTAGCCACTTCACCATCTTCAC |
| Reverse | CGGTGTCATTCCCATCTGTTGTG | |
| TIM4 | Forward | ACAGGACAGATGGATGGAATACCC |
| Reverse | AGCCTTGTGTGTTTCTGCG | |
| GAPDH | Forward | GAGTCAACGGATTTGGTCGTAT |
| Reverse | ATGGGTGGAATCATATTGGAAC | |
| EBV DNA | ||
| EBNA1 QK | Forward | GCCGGTGTGTTCGTATATGG |
| Reverse | CAAAACCTCAGCAAATATATGAG | |
| Probe 1 | TCTCCCCTTTGGAATGGCCCTG-fluorescein | |
| Probe 2 | LCRed640-ACCGGCCCACAACCTG | |
| Cloning | ||
| EBER1 | Forward | TGCAAGATCTTAATACGACTCACTATAGGAGGACCTACGCTGCCATAGA |
| Short Forward* | TGCAAGATCTTAATACGACTCACTATAGGAGGACC | |
| Reverse | ACGTTCTAGAAAACATGCGGACCACCAGC |
The T7 promoter sequence is underlined.
*
Added after 20 rounds of amplification to increase PCR efficiency and yield.