Figure 6. HCMV latency in monocytes is associated with reduced immune-response gene signatures.

RNA-seq was performed on HCMV- infected CD14+ Monocytes that were sorted according to cell-surface levels of CD74 at 3dpi. (A) Normalized viral gene expression in CD74^high and CD74^low cells. P value, calculated using likelihood ratio test on logistic regression of viral reads, is indicated. (B) Summary of gene set enrichment analysis (GSEA) of differential expressed genes identified in RNA-seq analysis of CD74^high and CD74^low cells using annotated GO biological processes and Reactome pathways. (C) Representative pathways from GSEA of genes ranked by their differential expression between CD74^high and CD74^low cells. (D) tSNE plot of scRNA-seq of latent monocytes colored by expression level of the pathways shown in C. (E) Monocyte priming gene set from Velten et al. (2017) analyzed on GSEA. Genes are ranked by their differential expression between CD74^high and CD74^low monocytes. (F) tSNE plot of scRNA-seq of latent monocytes colored by the expression level of the monocyte priming gene set from Velten et al. (2017).

Figure 6—figure supplement 1. Viral gene expression profile of infected CD14+ monocytes correlates between CD74^high and CD74^low cells and to late lytic profile.

Scatterplot showing read number of all viral genes in CD74^high compared with CD74^low cells at 3dpi (A) Scatterplot showing read number of all viral genes in CD74^high+CD74^low cells at 3dpi compared to lytically infected monocyte-derived macrophages at 4dpi (B).

Figure 6—figure supplement 2. Comparison of changes detected in bulk RNA-seq and scRNA-seq data.

Relationship between the fold changes in RNA-seq of CD74^high vs. CD74^low infected monocytes and correlation with viral transcript levels in infected monocyte scRNA-seq. Only genes that were differentially expressed in the bulk RNA-seq with p values<0.01 are shown.