Productive and non-productive RGH infections occur at similar viral integration sites across the genome. A: Viral integration sites were mapped by 454 pyrosequencing in RGH infected Jurkat cells sorted for eGFP and mCherry expression. Data is shown for 1,195 eGFP- mCherry- integrations, 2,900 eGFP- mCherry+ integrations, and 4,271 eGFP+ mCherry+ integrations. Integrations and gene density across 1 Mb windows are plotted for chromosome one (left panel) and the entire genome (right panel). The outer track (black histogram) depicts gene density as annotated in the UCSC hg18 reference genome, while the inner tracks (colored line plots) indicate relative numbers of viral integrations. B: Integration density is plotted against gene density (genes per chromosome) for each sample. A linear regression line of the plotted points is shown. Samples were tested for significance by Spearman correlation. Rho coefficients and p values are listed. C: The proportion of total integrations in each chromosome is shown for each sorted cell population. Error bars represent standard deviations of triplicate experiments * p < 0.05 (Student’s T test).