| Vector and region amplified |
Primers and probes dedicated for the amplification of lentiviral or transgenic DNA sequences |
Primers and probes dedicated for the amplification of internal control DNAs (cellular genome or plasmid) |
Ref |
| HIV-1 (R-U5) | Forward primer (78–97)(1) AGCTTGCCTTGAGTGCTTCA Reverse primer (161–141) TGACTAAAAGGGTCTGAGGGA Probe (107–129) F-TGCCCGTCTGTTGTGTGACTCTG-T |
Normalization with the amplification of a human albumin DNA fragment (intron 12) Forward primer GCTGTCATCTCTTGTGGGCTGT Reverse primer GCTGTCATCTCTTGTGGGCTGT Probe V-CCTGTCATGCCCACACAAATCTCTC-T |
Scherr et al |
| HIV-1 (U5-Psi) | Forward primer (103–122) TGTGTGCCCGTCTGTTGTGT Reverse primer (245–226) GAGTCCTGCGTCGAGAGAGC Probe (179–198) F-CAGTGGCGCCCGAACAGGGA-T |
Quantification of genomic DNAs by prior ampli- fication of a human mitochondrial DNA fragment Forward primer ACCCACTCCCTCTTAGCCAATATT Reverse primer GTAGGGCTAGGCCCACCG Probe Te-CTAGTCTTTGCCGCCTGCGAAGCA-T |
Butler et al |
| HIV-1 (30 LTR-Alu) | Forward primer (9131–9153) AACTAGGGAACCCACTGCTTAAG Reverse primer (Alu) TGCTGGGATTACAGGCGTGAG Probe (9644–9251) F-ACACTACTTGAAGCACTCAA GGCAAGCTTT-T |
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| HIV-1 (U5-U3, 2LTR) |
Forward primer (9131–9153) Reverse primer (245–226) TCCACAGATCAAGGATATCTTGTC Probe (9644–9251) |
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| HIV-1 and EIAV (eGFP) |
Forward primer (438–461)(2) CAACAGCCACAACGTCTATATCAT Reverse primer (515–495) ATGTTGTGGCGGATCTTGAAG Probe (464–488) F-CCGACAAGCAGAAGAACGGCATCAA-T |
Absence of normalization (only quantification of viral RNA genomes) |
Ikeda et al |
| HIV-1 (PBS-Psi) | Forward primer (198–218) ACCTGAAAGCGAAAGGGAAAC Reverse primer (342–320) CACCCATCTCTCTCCTTCTAGCC Probe (225–248) F-AGCTCTCTCGACGCAGGACTCGGC-T |
Verification of plasmid DNA remnants in transduced target cells by the amplification of an ampicillin DNA fragment Forward primer (472–490) ACTCGCCTTGATCGTTGGG Reverse primer (563–543) GTTGCCATTGCTACAGGCATC Probe Te-CTAGTCTTTGCCGCCTGCGAAGCA-T |
Sastry et al |
| EIAV (CMV promoter) |
Forward primer CATATATGGAGTTCCGCGTTACAT Reverse primer GTATGTTCCCATAGTAACGCCAATAG Probe F-TGGCTGACCGCCCAACGACC-T |
Normalization with the amplification of a human b-actin DNA fragment Forward primer (584–601) AGCGCGGCTACAGCTTCA Reverse primer (660–641) GGCGACGTAGCACAGCTTCT Probe (632–612) V-TCACGCACGATTTCCCGCTCG-T |
Martin-Rendon et al |
| HIV-1 (WPRE) | Forward primer CCGTTGTCAGGCAACGTG Reverse primer AGCTGACAGGTGGTGGCAAT Probe V-TGCTGACGCAACCCCCACTGGT-T |
Normalization with the amplification of a human albumin DNA fragment Forward primer (1554–1578) TGAAACATACGTTCCCAAAGAGTTT Reverse primer (1634–1609) CTCTCCTTCTCAGAAAGTGTGCATAT Probe (1581–1607) F-TGCTGAAACATTCACCTTCCATGCAGA-T Normalization with the amplification of a human b-actin RNA fragment Forward primer (347–366) GCGAGAAGATGACCCAGATC Reverse primer (449–431) CCAGTGGTACGGCCAGAGG Probe (388–413) F-CCAGCCATGTACGTTGCTATCCAGGC-T |
Lizee et al |
| HIV-1 (U5-Psi) | Forward primer (103–122) Reverse primer (245–226) Probe (179–198) Cf Butler et al49 |
Absence of normalization | Van Maele et al |
| HIV-1 (30 LTR-Alu) | Forward primer (9635–9655) GTGCCCGTCTGTTGTGTGACT Reverse primer (Alu) Cf Butler et al49 Probe (9665–9697) F-TCCACACTGACTAAAAGGG TCTGAGGGATCTCT-T |
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| HIV-1 (U5-U3, 2LTR) |
Forward primer (9131–9153) Cf Butler et al49 Reverse primer (8639–8664) CTTGTCTTCTTTGGGAGTGAATTAGC Probe (9665–9697) |
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| HIV-1 (R-U5) | Forward primer (78–98) AGCTTGCCTTGAGTGCTTCAA Reverse primer (153–129) AGGGTCTGAGGGATCTCTAGTTACC |
Charrier et al | |
| HIV-1 (RFP) | Forward primer (157–174) GCCCTTCGCCTGGGACAT Reverse primer (221–200) GGTGCTTCACGTACACCTTGGA Probe (176–198) F-CTGTCCCCCCAGTTCCAGTACGG-T |
Normalization with the amplification of a human albumin DNA fragment forward and reverse primers cf Scherr et al4 |
Scherr et al |
| F: 6-FAM, T: TAMRA, V: VIC, Te: TET. For assays where no probe sequence is listed, the amplification signal is given by the incorporation of the SybRGreen I binder agent | |||
