Primary CD4 + T cell reporter lines. (A) Histograms show GFP fluorescence (x axis) per normalized counts (y axis) for each integration site studied (iStrains, red) and control (blue) in both resting (upper panel) and CD3/CD28-activated (lower panel) conditions. (B) Graphs show relative LTR (left panel), eGFP (middle panel), and nLuciferase (right panel) expression assessed by qPCR under resting (blue) and CD3/CD28-activated (red) conditions. Bars represent the mean relative expression from two independent assays (biological replicates) ± SD. (C) LTR transcripts per cell (y axis), determined by qPCR, for each integration-positive clone and control, under resting (blue) and CD3/CD28-activated (red) conditions. CD4+ T cells infected with HIV-1YU2 served as positive control (black bar). Bars represent the mean of two independent assays (biological replicates) ± SD. (D) Relative expression determined by qPCR for host genes neighboring their respective reporter proviruses (iStrains, full bars) and control (striped bars) under resting (left panel, blue) and CD3/CD28-activated (right panel, red) conditions. Bars represent the mean relative expression of two independent assays (biological replicates) ± SD. (E) Correlation between the relative expression of LTR (y axis) for each primary T cell clone and their respective host gene (x axis), averaged across multiple clones to the same reporter integration site, under resting (left panel, blue) and activated (right panel, red) conditions. Pearson’s correlation coefficients, r, and two-tailed P values were computed for each condition.