Supplementary Table 1. Oligonucleotides Used in This Study s1

Supplementary Table 1. Oligonucleotides used in this study.

Oligonucleotide Sequence (5’- 3’)a Targetb NotI-WdV001 GCGGCCGCATGGCAGGAAGAAGCGGAG 5551 - 5570 WdV002 CATCAAGTTTCTCTATCAAAGCAACCCACCTC 5603 - 5626 WdV003 CAAAGCAACCCACCTCCCAACCCCGAG 7972 - 7992 NotI-WdV004 GGAGTCAGGAACTAAAGAATAGCGGCCGC 8225 - 8246 NotI-WdV005 GCGGCCGCATGGAGCCAGTAGATCCTAGAC 5412 - 5434 WdV006 CATCAAGTTTCTCTATCAAAGCAACCCACCTC 5603 - 5626 WdV007 CTATCAAAGCAACCCACCTCCCAACCCCGAGG 7972 - 7993 NotI-WdV008 GGAGTCAGGAACTAAAGAATAGCGGCCGC 8225 - 8246 NotI-WdV011 ATAAGAATGCGGCCGCATGGGTGGCAAGTGGTCAA 8390 - 8416 AAAGTAG NotI-WdV012 ATAGTTTAGCGGCCGCTCAGCAGTTCTTGAAGTACT 8983 - 9010 CCGGATG WdV020 GGGGACAAGTTTGTACAAAAAAGCAGGCTTCACCA attB1-hrGFP TGGTGAGCAAGCAGATCCTG WdV021 GCAGCCTGCACGAGTGGGTGTAATACCCAGCTTTC attB2-hrGFP TTGTACAAAGTGGTCCCC WdV022 CCCAAGCTTGCGTAGAACCTGCGGCCGCTAATCTC polylinker GTGCGAG WdV023 GCAAGGCCTAGGCGATGATAGTTATGAGAGCTCGC ACGAGATTAGCGGCC polylinker WdV024 CGCCTAGGCCTTGCTTCGCTCGAGCATCTGATTCGC polylinker CGGTGATCCG WdV025 AGCTACAAGCATGCACGATACAGTTAATTAAAACG polylinker GATCACCGGCGAATC SphI-WdV034 ACATGCATGCTGGGGATGCGGTGGGCTCTATGGAT EF1α promoter GTCGCGTGAGGCTCCGGTGCCCG WdV035 CAAAGTTTTTTTCTTCCATTTCAGGTGTCGTGATTC EF1α promoter ACCATGGAG WdV036 GGTGTCGTGATTCACCATGGAGGGCTGCGGCAAGG hrGFP GCAACATCCTG BamHI-WdV037 CGGGATCCCGAGGCCGGTGATGGTCTTCTTCATCAC hrGFP GGGGCCGTCG BamHI-WdV038 CGGGATCCGCCCTTGTACTCCACGCGGTACACGAA hrGFP CATCTC WdV039 TGCCCTTGCCGCAGCCCTCCATGGTGAATTTACTTG hrGFP C WdV040 CCCTCCATGGTGAATTTACTTGCTTTAAAAAACCTC SV40 pA CCAC EcoRI-WdV041 GGAATTCACATGCATGCTGGGGATGCGGTGGGCTCT SV40 pA ATGGTGCAGACATGATAAGATACATTGATGAGTTT GGAC HindIII-WdV047 CCCAAGCTTGGGCGTGAGGCTCCGGTGC EF1α promoter WdV049 AGGTGTCGTGATATTCCTTCGGGCCTGTCG 7997 - 7978 NotI-WdV050 GCTCTAGTCTAGGATCTGCGGCCGCTAAACTATT 5422 - 5405 AvrII-WdV051 GTCCTAGGAGATCCTAGACTAGAGCCCTG 5874 - 5895 WdV52 CAGGCCCGAAGGAATACTGTGCCTTCTAGTT 8000 - 8016 NotI-WdV053 CCGCGGCCGCGAAGGAATACTGTGCCTTCTAGTTG BGH-polyA CCAGC PacI- WdV054 CCTTAATTAACCATAGAGCCCACCGCATC BGH-polyA WdV055 TCAAATATTGGTGTCACGACACCTGAAATG EF1α promoter Oligonucleotide Sequence (5’- 3’) Target WdV056 AGGTGTCGTGACACCAATATTTGAGGGCTTC 8187 - 8167 NotI-WdV057 GAGGTCTTCGTCGCTGTCTCCGCTGCGGCCGCTAAA 5562 - 5538 CTAT AvrII-WdV058 AGCCTAGGAGCGGAGACAGCGACGAAGAC 5562 - 5583 WdV059 GAAGCCCTCAAATATTGGTGCTGTGCCTTC 8187 - 8207 WdV60 CTAGAAGGCACAGCACCAATATTTGAG BGH-polyA WdV061 GATGGTGCTACTCACGACACCTGAAATGGAAG EF1α promoter WdV062 CAGGTGTCGTGAGTAGCACCATCCAAAGG 8801 - 8784 NotI-WdV063 ATAGTTTAGCGGCCGCACAAGTAGCAATACAGCAG 8542 - 8518 CTACC AvrII-WdV064 AGCCTAGGACAAGTAGCAATACAGCAGCTAC 8518 - 8541 WdV065 AGAAGGCACAGGTAGCACCATCCAAAGGTC 8799 - 8818 WdV066 GATGGTGCTACCTGTGCCTTCTAGTTGCCAGC BGH-polyA PKF2 TCGTGCGAGCTCTCATAACTATC BGH-polyA NotI-PKR2 GATAGTTATGAGAGCTCGCAC pEF1α promoter HindIII-PKF4 CAGAAGCTTCTTCCATTTCAGGTGTCGTG pEF1α promoter BamHI-PKR4 ATAGGATCCTCGAGCCATAGAGCCCACCGC BGH-polyA AT SalI-PKF5 CACGTCGACTGCAGATATCTAGCATTTCATCACGTG -179 - –161 G HindIII-PKR5 CGGAATGCC AAGCTT TATTGAGGCTTAAGCAG 59 - 81 SalI-PKF6 GACGTCGACTGCAGATATCCTTTCGTCTTCAAGAAT 7tetO TCC HindIII-PKR6 TCGAAGCTTAGGTCAAAACAGCGTGGATGGC 7tetO PKF8 GGCCGCAATTGATAGGTATCTAGACCTAGGCCGCG polylinker GATCCGATATCACGTGCCGC XbaI-PKR9 AGCTCTAGACACGACACCTGAAATGGAAG polylinker PKR13 GGCACGTGATATCGGATCCGCGGCCTAGGTCTAGA polylinker TACCTATCAATTGC MunI-PKF13 GATCAATTGCCGCCAGAACACAGGTAAG EF1α intron SacI-T7p-PKF16 CAGGAGCTCCAAAAAAAAGCCCGCTCATTAGGCGGG 8416 - 8438 CGCGTAATACGACTCACTATAGGGTGGTTGGATG GCCTACTGTAA asT7p-XbaI- GATTCTAGACAAAAAAAAGCCCGCTCATTAGGCGGG 8674 - 8695 PKR16 CGCGTAATACGACTCACTATAGGGTGAATTAGCC CTTCCAGTCC NcoI-PKF21 CATGGGTGCCTGGCTAGAAGCACATTCAAGAGATG 8552 - 8571 TGCTTCTAGCCAGGCACTTG BamHI-PKR21 GATCCAAGTGCCTGGCTAGAAGCAGATCTCTTGAAT 8552 - 8571 GTGCTTCTAGCCAGGCACC Nef-B/X ATCCCGGGATCCACCTCAGGTACCTTTAAGAC 8552 - 8603 AntiU3-att TGGAAGGGCTAATTCACTCC 8650 - 8631 IFN-βF GATTCATCTAGCACTGGCTGG Human IFN-β IFN-βR CTTCAGGTAATGCAGAATCC gene

a HIV sequences are underlined and restriction sites are in italics. T7 promoter sequences are

in bold, T7 terminator are in bold and italics. b Numbers refer to the nucleotide position on the

genomic HIV-1 RNA transcript, with +1 being the capped G residue.