Fig. 6.

Single cell RNA sequencing identification of HIV-regulated genes in primary CD4 + T cells CD4 + T cells from two healthy human donors (#1 & 2) were mock-infected (media) or were HIV-infected (NanoLuc HIV, MOI 2.0) for 24 h, then suppressed with ART (10 μm raltegravir and 1 μm efavirenz) for 7 days and analyzed by scRNA-seq (see protocol schematic in Fig. 5b). a, b UMAPs show clustering of vRNA + cells and vRNA- cells, or viral RNA expression level per cell in all combined samples (CD4 + T cells from two human donors, mock- or HIV-infected, ± IFNβ). c HIV RNA counts in vRNAhi, vRNAlo, and vRNA- cell subsets for each donor. d, e HIV regulated genes identified through differential expression analysis of vRNAhi and vRNAlo cells relative to mock-infected cells (FC > 1.2, p < 0.05). 80 significant genes were identified across both donors (see Additional file 3: Table S2). Dot plot shows scaled average expression of these genes, and bar graph shows the top ten significantly enriched modules of HIV-regulated genes