Extended Data Fig. 8: ATAC-seq and RNA-seq of IFN-β response across time and cofactor inhibitions at endogenous ISGs.

A) Differential ATAC-seq accessibility of TF motif types after IFN-β stimulation (two biological replicates). B) Differential RNA-seq expression after IFN-β (two biological replicates). C) Average ATAC-seq accessibility relative to ISREs genome-wide, Tn5-bias corrected and RPM normalized for samples with (red) and without (pink) IFN-β (two biological replicates). D) Average ATAC-seq accessibility with (red) and without (pink) IFN-β relative to the TSSs of genes upregulated with stimulation (identified by RNA-seq) that contain at least three ISREs within the 500 bp window. Gray line is average ATAC-seq accessibility for non-ISG promoters that are matched to the pre-stimulation expression level (TPM) of plotted ISG promoters. Shaded error regions are 95% confidence intervals from bootstrapping (two biological replicates). E) Average ATAC-seq accessibility as in D with no inhibitor (gray), BAF inhibition for 12 h (purple), and p300 inhibition for 24 h (cyan). F) Average ATAC-seq accessibility as in D for conditions in E after IFN-β addition. G) Average ATAC-seq accessibility relative to ISREs genome-wide as in C for conditions in F. H) ATAC-seq tracks of normalized chromatin accessibility without (top) and with (bottom) IFN-β with BAF inhibition for 12 h (purple), p300 inhibition for 24 h (cyan), and no inhibitor (black) for IFI6, ISG15, and USP18. I) RNA expression of endogenous ISGs before (pink) and after (red) IFN-β (two biological replicates). J) ATAC-seq tracks of normalized chromatin accessibility over an IFN-β timecourse for IFI6, ISG15, and USP18. Black lines denote the region that was installed at the reporter.