title: Amplicon seq of HIV-1 LTR
design: DNA was quantified using QUBIT 3 Fluorometer and a dSDNA HS Dye. After the addition of an A nucleotide to the 3 ends, the adenylated fragments were ligated with loop adapters and cleaved with uracil-specific excision reagent (USER) enzyme. The DNA was further purified using AMPure beads and then enriched by PCR with 6 cycles using NEBNext Ultra II Q5 master mix (Cat. No. E7645L, New England Biolabs, Inc., Massachusetts, USA), Illumina universal primer, and sample-specific octamer primers. The amplified products were cleaned by using AMPure beads and the final DNA library was eluted in 15 l of 0.1X TE buffer. The volume of 1 L of the library was used to quantify by QUBIT 3 Fluorometer using dS DNA HS reagent. The fragment analysis was performed on Agilent 4150 Tape Station, by loading 1 l of the library to Agilent D1000 Screen Tape. The library was sequenced using the Illumina MiSeq system and MiSeq Reagent kit v3 (Cat. No. MS-102-3003, Illumina, San Diego, CA, U.S.A.) following the manufacturers instructions.