Table 1.

MGS-PCR primers and indices

A. Exponential PCR primers
Linker	GACCCGGGAGATCTGAATTC
Biotin-Lenti	5′Biosg/AGCTTGCCTTGAGTGCTTCA
Biotin-Foamy	5′Biosg/ACCGACTTGATTCGAGAACC
Biotin-Gamma	5′Biosg/CAGTTCGCTTCTCGCTTCTG

B. i5 and i7 Illumina primer library indices
i5 index	Sequence	i5 index	Sequence	i7 index	Sequence	i7 index	Sequence
D501	TATAGCCT	D505	AGGCGAAG	D701	ATTACTCG	D709	CGGCTATG
D502	ATAGAGGC	D506	TAATCTTA	D702	TCCGGAGA	D710	TCCGCGAA
D503	CCTATCCT	D507	CAGGACGT	D703	CGCTCATT	D711	TCTCGCGC
D504	GGCTCTGA	D508	GTACTGAC	D704	GAGATTCC	D712	AGCGATAG

C. Nested Illumina MiSeq PCR primers
Foamy2 Nested 504 (F.Stem/i504/F.Adapter/Primer)	AATGATACGGCGACCACCGAGATCTACAC/GGCTCTGA/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/GCTAAGGGAGACATCTAGTG
Foamy2 Nested 507 (F.Stem/i507/F.Adapter/Primer)	AATGATACGGCGACCACCGAGATCTACAC/CAGGACGT/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/GCTAAGGGAGACATCTAGTG
Lenti2 Nested 505 (F.Stem/i505/F.Adapter/Primer)	AATGATACGGCGACCACCGAGATCTACAC/AGGCGAAG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/AGTAGTGTGTGCCCGTCTGT
Lenti2 Nested 508 (F.Stem/i508/F.Adapter/Primer)	AATGATACGGCGACCACCGAGATCTACAC/GTACTGAC/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/AGTAGTGTGTGCCCGTCTGT
GammaLTR1 Nested506 (F.Stem/i506/F.Adapter/Primer)	AATGATACGGCGACCACCGAGATCTACAC/TAATCTTA/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/GTGGTCTCGCTGTTCCTTGG
Gamma LTR6 Nested 502 (F.Stem/i502/F.Adapter/Primer)	AATGATACGGCGACCACCGAGATCTACAC/ATAGAGGC/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/TCTGCTCCCCGAGCTCAATA
GammaLTR1501 (F.Stem/i501/F.Adapter/Primer)	AATGATACGGCGACCACCGAGATCTACAC/TATAGCCT/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/GTGGTCTCGCTGTTCCTTGG
Linker Primer2 701 (R.Stem/i701/R.Adapter/Primer)	CAAGCAGAAGACGGCATACGAGAT/ATTACTCG/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC/GATCTGAATTCAGTGGCACAG
Linker Primer2 702 (R.Stem/i702/R.Adapter/Primer)	CAAGCAGAAGACGGCATACGAGAT/TCCGGAGA/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC/GATCTGAATTCAGTGGCACAG
Linker Primer2 703 (R.Stem/i703/R.Adapter/Primer)	CAAGCAGAAGACGGCATACGAGAT/CGCTCATT/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC/GATCTGAATTCAGTGGCACAG
Linker Primer2 704 (R.Stem/i704/R.Adapter/Primer)	CAAGCAGAAGACGGCATACGAGAT/GAGATTCC/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC/GATCTGAATTCAGTGGCACAG
Linker Primer2 705 (R.Stem/i705/R.Adapter/Primer)	CAAGCAGAAGACGGCATACGAGAT/ATTCAGAA/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC/GATCTGAATTCAGTGGCACAG
Linker Primer2 706 (R.Stem/i706/R.Adapter/Primer)	CAAGCAGAAGACGGCATACGAGAT/GAATTCGT/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC/GATCTGAATTCAGTGGCACAG

Linker- and biotin-tagged LTR-specific primers are reported for lentiviral, gammaretroviral, and foamy viral vectors. Nested Illumina MiSeq–adapted primers are reported for lentiviral, gammaretroviral, and foamy virus vectors. The i5 and i7 indices library is also given with the corresponding sequences.