Table 1

Primers for RT-PCR and probes for RNA FISH used in this work.

Name

Sequence 5' > 3'

PRIMERS FOR RT-PCR

HIV_UP5

GGCGAGCCCTCAGATCCTGC

HIV_START

GGGTCTCTCTGGTTAGACCAGATCTGAGCC

HIV_RT

AGTCGCCGCCCCTCGCCTCCTGC

HIV_SPLICED

GGATTAACTGCGAATCGTTCTAGC

HIV_NUC

CGTCTGTTGTGTGACTCTGGTAACT

HMBOX_E1s

GTCTCTTTCCTCACTTCTTTCT

HMBOX_E1a

TCACAGTTTCCAGAACTCCAC

HMBOX_E2s

GGAATGGAACAGTGAAGAAGCA

HMBOX_E3s

AATGGTAGATAACGCAGATCATC

HMBOX_E3a

ACCACTGGAAAGGAACTAAGCA

PROBES FOR RNA FISH

HIV_MS2

AxGTCGACCTGCAGACAxGGGTGATCCTCAxGTTTTCTAGGCAATxA

HMBOX_E1a

AxAGTTTCCAGAAxTCCACACCGGAGACCCCACxTCCAGGATTCAAACCxT

HMBOX_E1b

CxCAGCGTCCGCxCACTTCCTCCCCAAAACCCCxCCAAAAAAATTGTTxT

HMBOX_I2a

AxGGTTGGTATAAACACAxAAAGCATGGTGGTxGTCTGGAGCTGGGGTTxA

HMBOX_I2b

AxTGCAGTGAGCCATGAxCACACCACAGTACxACAGCCTGGGTGATGAAxA

HMBOX_I2c

AxATTGCTGTCCTAAxCAGACTGCACCTGTGGxGTGGCTCTGACTGGTxA

HMBOX_I2d

AxGGTATGGTGGCAAAxCGACTCCCCCAGxACAACCACCAGAATATCAGxA

HMBOX_E4a

AxACGCCGAAGTCGCxGAAGCAGATCTATCTGCxCTATGGTAAATCTGGxA

HMBOX_E4b

AxATAACTGTTGCTAGGxGACGGGGACATTCCCGAAxGCTGCGTCTGTxA

Modified aminoallyl thymidines in the probes are indicated with "x". The sequence of one binding site for MS2 is underlined in the HIV_MS2 probe.

De Marco et al. Retrovirology 2008 5:98   doi:10.1186/1742-4690-5-98