Experimental outline for integration site mapping in newly infected cells. A: Schematic representation of Red-Green-HIV-1 (RGH) used in this study. The virus contains a Gag fused eGFP marker under the control of the LTR promoter as well as a constitutively expressed mCherry marker under the control of the CMVIE promoter inserted into the nef position. B: Schematic representation for isolation of productively and non-productively infected (RGH) Jurkat cells used for integration site mapping. Total RGH infected Jurkat cells were sorted based on eGFP and mCherry expression to greater than 90% purity four days post-infection. Genomic DNA from approximately 5 x 105 cells of each sorted cell-population was isolated and used to map HIV-1 integration sites by 454 deep sequencing.