Integration sites from Jurkat cells infected with inducible HIV-1
Lewinski et al. (2005) infected Jurkat cells with a VSV-G pseudotyped, GFP-expressing pEV731 HIV construct (LTR-Tat-IRES-GFP) [13] at an MOI of 0.1. The cells were sorted into GFP  and GFP- two to four days after infection. GFP  cells were sorted again two weeks after infection and cells that were again GFP  were collected for integration site sequencing. GFP- cells were sorted for GFP negativity twice more then stimulated with TNFalpha. Cells that were GFP  after stimulation were collected for integration site sequencing. DNA was digested with MseI or a combination of NheI, SpeI and XbaI, ligated to adapters for nested PCR, amplified and sequenced by Sanger capillary electrophoresis. Qualities have been filled with a default 20 quality value.