MOESM5 of Innate immune defects in HIV permissive cell lines

Additional file 5: Figure S3. Principal component analysis of RNA-Seq libraries including activated CD4+ T cells. The figure shows the first two principal axes of the whole transcriptome Principal Component Analysis (PCA) analysis of the 13 samples shown in Supplemental Figure 1 plus 4 samples corresponding to Activated CD4+ T cells at 8h (red) and 24h (orange) after TCR activation. The percentage of variance explained by each axis is indicated. PCA was performed on the variance-stabilized transformation of read counts as described in Methods. As in Supplemental Figure 1, the first principal axis (PC1) of the PCA separated samples according to their permissiveness to HIV infection. Thus, activated CD4+ T cells mapped in an intermediate position along PC1, between primary resting CD4+ T cells and permissive cell lines.