Integration sites sequencing of HIV infection on ZNF417 ZNF587 dKO 293T cells

We infected ZNF417 ZNF587 dKO 293T or control 293T with NL4.3 virus for 48 hours. Then genomic DNA was purified from cell lysis with by phenol chloroform. DNA was sheared into 300 bp-500 bp random fragments using Covaris Adaptive Focused Acoustics (Covaris, Woburn, MA). Sheared DNA was ligated with a linker and PCR with primers targeting HIV LTR and linker. PCR products were performed second PCR with Illumina adaptor primers. Libraries were so constructed and sequenced on Novaseq 6000. ZNF417 and ZNF587 dKO 293T cells were infected with HIV virus for 48 hours and genomic DNA was harvested for integration sites deep sequencing.