Fig. 2

PAF1 KO cells exhibit a distinct immune gene expression profile. A PCA shows distinct gene expression profile of PAF1 KO relative to ncgRNA. The counts for immune genes (GO:0002376) were corrected with a variance-stabilizing transformation via DESeq2, and the variability of biological replicates and immune activation were removed as batch effects with ComBat. PCA was performed on the resulting counts, with the top 2 principal components being plotted. Cell lines are represented by shape (circle: ncgRNA, triangle: PAF1 KO) and stimuli are dictated by color. B Volcano plots show differential gene expression of immune genes in PAF1 KO relative to ncgRNA across stimuli. Contrasts were performed within the DESeq2 pipeline. The resulting log2 foldchanges and –log10 p-values are plotted for immune genes, with the top-10 positive and negative log2 foldchanges being highlighted/labeled. Cutoffs are set at log2 foldchange > 1.5 or < − 1.5, and p-value < 0.05