Fig. 1: TNF (tumor necrosis factor)-induced RelA nuclear translocation and expression of NFκB target gene clusters.

Time-course nuclear NFκB abundance (a) and fold change (b) from fixed-cell immunofluorescence of MCF-7 cells treated with 1 ng mL⁻¹ TNF in Ctrl (Control) and siIκBα (IκBα knockdown). Line graphs represent the means of two biological replicates. Number of cells used to calculate the mean for each time point ranged from 1336 to 2374 cells (Supplementary Table 1). Gray lines indicate the time points where RNA-seq data was measured, and arrows indicate the time points where single-cell ATAC-seq data was measured. Statistical significance was observed for interpolated (same method used in mathematical modeling) time-course nuclear NFκB abundance (p value: 1.039e−4) and fold change (p value < 2.2e−16) between Ctrl and siIκBα from before stimulation and 75 min (the first peak time point of early response genes) after stimulation by one-tailed Wilcoxon rank-sum test. c Venn diagram of the TNF-induced DEGs in Ctrl and siIκBα. d Mean of fold change in the expression of five TNF-induced clusters (ERG, IRG, DRG, downregulated, and others) of DEGs in Ctrl. For these 5 clusters, statistical tests were performed for fold change in expression between Ctrl and siIκBα (*p value < 0.01 by one-tailed Wilcoxon rank sum test). e Two subclusters for each TNF-induced cluster (ERG, IRG, and DRG) in Ctrl (outlier PCSK5 excluded in line graph). For these 6 subclusters, statistical tests were performed for fold change in expression between Ctrl and siIκBα (*p value < 0.01 by one-tailed Wilcoxon rank-sum test). f κB motifs that were enriched at promoter regions (±50 bps TSS) of ERG subclusters 1 and 2, IRG subcluster 2, and DRG subcluster 2.