Supplementary Figure 2: Genetic loss or pharmacologic inhibition of TBK1/IKKε exerts only minor effects on TNF-induced gene-activation.

(a,b) MEFs TNF^-/- (a) and control or TNF KO; TBK1/IKKε DKO L929 (b) cells were pre-treated with or without the inhibitor MRT as indicated followed by TNF-stimulation (200 ng/mL) for the indicated times and subjected to lysis, followed by western blot analysis. (c) A549 WT cells were pre-treated with either vehicle (DMSO) or the respective inhibitors MRT or TPCA-1 followed by TNF-stimulation (200 ng/mL) for either 0 hr, 1 hr or 4hrs. Three independent experiments for each stimulation time and type of treatment were performed. Cells were then lysed, their total RNA extracted and RNA-Seq analysis performed. The heatmap illustrates the major change of expression across the dataset. The genes selected to be shown were the 100 most highly correlated with PC2 (see Fig 2b). For clarity of comparison the 'rlog' expression data of each row was zeroed at time-point zero hour and then scaled by the standard deviation. The RNA-Seq raw dataset is available in the SRA repository and can be accessed by using the following BioProject accession: PRJNA422567 or SRA accession: SRP126844 (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP126844). (a,b) One experiment representative of two independent experiments is shown. Unprocessed original scans of blots are shown in Supplementary Figure 7.