Fig. 4
Treatment with LPS ± IFNγ (6 h) evidences differential transcriptomic changes between C/EBPβfl/fl and LysMCre-C/EBPβfl/fl microglia. a Hierarchical clustering of total RNASeq RPKM normalized values separate samples neatly by treatment. Remarkably, C/EBPβfl/fl and LysMCre C/EBPβfl/fl groups are mixed in the control condition, but separate into subgroups once any treatment is applied to microglia (Euclidean distance). b Linear model fitting of filtered genes (RPKM sum of genes through samples >2) detects 10,888 genes as differentially expressed (DEGs) (lfc > 1, adjusted p value <0.01 Benjamini–Hochberg correction). Contrasts between groups are shown on the Venn diagram. More specifically, 1068 genes are detected as DEGs for the C/EBPβfl/fl vs LysMCre-C/EBPβfl/fl contrast. c Heatmap of C/EBPβfl/fl and LysMCre-C/EBPβfl/fl DEGs (n = 1068) with applied hierarchical clustering (average linkage, Euclidean distance). Values are represented as SD from the normalized average for each gene. Sample clustering evidences three main groups; with cluster 1 (pink) corresponding to the control condition which contain subclusters separating C/EBPβfl/fl and LysMCre-C/EBPβfl/fl. Remarkably, clusters 2 (magenta) and 3 (purple) correspond to C/EBPβfl/fl and LysMCre-C/EBPβfl/fl conditions and contain subclusters organized by treatment. On the other hand, gene cluster classification (A–M) evidences the combination of patterns of expression among samples. In this figure, WT and KO refer to C/EBPβfl/fl and LysMCre-C/EBPβfl/fl, respectively