DCs display a transcriptional profile that is indicative of in vivo activation. (A-B) RNA was extracted from ex vivo purified mDCs and pDCs from uninfected and primary HIV-infected subjects at Fiebig stages V-VI and converted to cDNA. QPCR was conducted using primers for TLR7 (A) and IRF 7 (B). Expression levels were normalized using GAPDH. The mean relative gene expression levels in mDCs and pDCs from uninfected subjects (N = 5, □) and subjects with primary HIV infection (N = 5 subjects at Fiebig stages V-VI, ■) are shown. (C-F) RNA was extracted from ex vivo purified mDCs and pDCs and hybridized on Illumina Human HT-12 Expression Beadchips, which assays approximately 25 000 annotated genes with > 48 000 probes derived from the RefSeq (Build 36.2, Rel 22) and the UniGene (Build 99) databases. Comparisons of expression results were done in the Partek software using ANOVA. (C) PCA of complete gene expression profiles measured on each individual array. PCA was performed on log₂ transformed and quantile normalized expression data. Each colored sphere (primary HIV-infected) and triangle (uninfected) indicates complete expression profiles of individual samples with similarity between data sets displayed as proximity in 3-dimensional space (red = mDC, blue = pDC). The lines connect samples from the same subject. (D) Venn diagram indicating overlap of probe sets with differential expression in mDCs and pDCs from primary HIV-infected subjects compared with uninfected subjects as calculated using ANOVA. (E-F) Heat map of probe sets associated with immune activation in mDCs (E) and pDCs (F). Each column represents different subjects: uninfected (N = 4, light gray) and primary HIV-infected (N = 5, dark gray). Genes that are down-regulated by up to 2-fold are blue, and genes that are up-regulated by up to 2-fold are red.