GSM1974059: JS209; Homo sapiens; OTHER
DNA was isolated using a Qiamp DNA extraction kit(Qiagen) according to manufacturer's protocol. The isolated DNA was sheared for 12 minutes on a bioruptor with 30sec on 30 sec off.  Sheared DNA was end repaired, a-tailed, and ligated to dual indexed long Illumina adapters.  Libraries were mixed equimolar to 500ng and mixed with 5µg of cot1 and IDT blocking oligos and dried down.  Lockdown probes against HIV in the forward and reverse direction were added in seperate reactions to 3pmol.  Libraries were hybridized for 4 hours at 65˚ then bound to M-270 streptavin beads and washed.  HIV-Lockdown DNA was eluted and samples were split and treated with or without 5U UDG and 10U EndoIV for 2 hours at 37˚.  Samples were then PCRed with short Illumina primers for 22 cycles with Maxima Taq and purified with ampure beads.