Treated Typical Progressor HIV-1 infected PBMC
DNA preparation  0.2-2 million CD4+ cells from HIV-1 infected patients were lysed in Proteinase K buffer (100mM Tris [pH8], 0.2% SDS, 200mM NaCl, 5mM EDTA) and 5-10uL of 20mg/mL Proteinase K. Genomic DNA was extracted by phenol chloroform and fragmented by sonication (Covartis) to yield a 300-1000bp distribution of DNA fragments. DNA was blunted by End-It DNA Repair Kit (Epicenter), purified, then adenosine-tailed by Klenow fragment 3 → 5’ exo- (NEB) and purified. Fragments were ligated to 200pmol of annealed linkers (Table S2). Virus sequences were eliminated by digestion with BglII (NEB) and fragments were purified.     Integration site amplification   Semi-nested ligation-mediated PCR was performed on linker-ligated DNA. All PCRs were performed using the Phusion Polymerase system (Thermo). DNA was divided into 700ng aliquots and subjected to single-primer PCR with biotinylated LTR1 [1x(98C-1min) 12x(98C-15s, 62C-30s, 72C-30s) 1x(72C-5min)] (Table S2). Each reaction was spiked with pLinker and subjected to additional cycles of PCR [1x(98C-1min) 25x(98C-15s, 62C-30s, 72C-30s) 1x(72C-5min)]. Products of 300-1000bp were isolated by agarose gel electrophoresis and magnetic streptavidin bead purification. Semi-nested PCR was performed on the magnetic beads first with a single primer LTR2 [1x(98C-1min) 12x(98C-15s, 62C-30s, 72C-30s) 1x(72C-5min)] followed by spiking in pLinker and additional cycles [1x(98C-1min) 25x(98C-15s, 62C-30s, 72C-30s) 1x(72C-5min)] (Table S2). Products of 300-1000bp were isolated by agarose gel electrophoresis.     Paired-end library preparation  Linkers were digested by AscI such that a 6-nucleotide barcode (CGCGCC) was left on the DNA fragments, indicating linker-dependent amplification. Fragments were blunted by End-It DNA Repair Kit (Epicenter), purified with AmPure beads (Agencourt) and ligated to NextFlex paired-end adapters. Adaptor-ligated fragments were enriched by 35 cycles of PCR with NextFlex primers (X and X, Table X) [1x(98C-1min) 35x(98C-15s, 66C-30s, 72C-30s) 1x(72C-5min)] and fragments between 300-1000bp were isolated by gel electrophoresis. Three libraries were mixed in equimolar ratios and sequenced by either 150bp paired-end sequencing on Illumina MiSeq or 150bp or 100bp paired-end sequencing on an Illumina 2500.