PRJNA213846
HIV integration in latent and active human CD4-positive t-cells
Naive CD4+ T cells were purified by negative selection from peripheral blood mononuclear cells. The cells were activated with anti-CD3 and anti-CD28 (+TGF-beta, anti-IL-12, and anti-IL-4) to generate “non-polarized” cells (the in vitro equivalent of central memory T cells). Five days after isolation, cells were infected with an NL4-3-based virus with GFP in place of Nef and the LAI envelope (X4) provided in trans at a concentration of 500 ng of p24 as measured by ELISA per million cells. Based on previous experience with this model, this amount of p24 should produce an MOI of approximately 0.15. Cells were cultured in the presence of IL-2. Two days post-infection, cells were sorted for GFP+; this active population expresses GFP even when treated with flavopiridol, although for this study they were not treated. The inducible population was the set of GFP negative cells from the initial sort that, 9 days post-infection, were activated with anti-CD3 and anti-CD28 and sorted for GFP production. Genomic DNA from the inducible and expressed populations was digested with MseI, ligated to an adapter, and amplified by ligation-mediated PCR essentially as in Wu et al. [42] and Mitchell et al. [43] except that the nested PCR primers included sequence for the Ion Torrent P1 adapter and adapter A sequence with a 5 base barcode sequence specific to the inducible or expressed conditions. Amplicons were sequenced using an Ion Torrent Personal Genome Machine (PGM) according to manufacturer’s instructions using an Ion 316 chip and the Ion PGM 200 Sequencing kit (Life Technologies). The sequence reads were sorted into samples by barcode. All reads were required to match the expected 5'' sequence with a Levenshtein edit distance less than 3 from the expected barcode, 5'' primer and HIV long terminal repeat (LTR). The 5'' primer and HIV sequence, along with the 3'' primer if present, were trimmed from the read. Sequences with less than 24 bases remaining or containing any eight base window with an average quality less than 15 were discarded. Duplicate reads and reads forming an exact substring of a longer read were removed.