Fig. 3

Analysis of innate immune transcriptome in latent JLat9.2 cells. a Gene set enrichment analysis (GSEA) of differentially expressed gene function modules between untreated (mock) Jurkat and JLat9.2 cells. Genes were ranked using a t statistic. b Differential expression (DE) analysis of IFN-induced genes in Jurkat or JLat9.2 cells after mock treatment (media, 4 h) or stimulation with 100 IU/ml IFNβ for 4 h, 8 h, or 12 h. One experiment was performed with three biological replicates per treatment condition. Heat map shows significant ISGs in IFNβ-treated Jurkat cells relative to mock-treated Jurkat cells (left) or IFNβ-treated JLat9.2 cells relative to mock-treated JLat9.2 cells (right). FC > 1.5, p < 0.05. Significantly enriched pathways (Ingenuity) were grouped into 6 modules depicted by colored blocks on the left, and annotated on the right with select highly significant pathways. All identified genes and pathways are listed in Additional file 2: Table S1. c Differential of differential expression (DDE) analysis comparing expression of IFN-induced genes in JLat9.2 cells relative to Jurkat cells treated as described above for panel b. For expression analyses in panels b and c, FC > 1.5, p < 0.05