Extended Data Fig. 4: CTCF depletion in iMacs attenuates the acute inflammatory response to endotoxins.

a, Genome-wide aggregation of normalized Hi-C signal anchored at cohesin loops during transdifferentiation with DMSO or auxin. b, Distance distribution between enhancers and TSS of genes responsive (n = 378) or unresponsive (n = 380) to LPS (P, two-sided Wilcoxon rank-sum test). c, CTCF enrichment at promoters and enhancers d, of genes responsive (n = 378) or unresponsive (n = 378) to LPS (P, two-sided Wilcoxon rank-sum test). e, Differential gene expression between LPS-induced iMac treated with auxin or DMSO (n = 2 biologically independent samples, P-adj two-tailed likelihood ratio test followed by FDR correction). f, Gene ontology analysis of the significantly (p < 0.01) upregulated (n = 746) and downregulated (n = 694) genes in LPS-induced iMacs treated with auxin compared to DMSO (q-value, FDR-corrected Fisher exact test). g, Overlap of upregulated (top) and downregulated (bottom) genes (AUX vs DMSO) between non-induced iMacs (NI) and iMacs treated with LPS (LPS). h, LPS-upregulated genes in iMacs exposed to DMSO compared to auxin (n = 2,470 genes, P two-sided Wilcoxon rank-sum test). i, RNA expression in non-induced (NI) iMacs of genes upregulated after LPS stimulation of DMSO treated iMacs (n = 2,470). j, RNA expression of key transcription factors and receptors of the LPS signalling pathway (n = 2 biologically independent samples). k, CTCF binding at promoters of genes deregulated in LPS-induced iMacs treated with auxin as compared to DMSO. l, Micrographs show uptake of fluorescent beads (shown in red) by iMacs treated with DMSO or auxin (Scale bar represents 10 µm). The experiment was repeated 3 times with similar results. m, Quantification of phagocytosis assay. Upper panel shows percentage of cells with bead uptake; lower panel shows mean fluorescent intensity (MFI). Bars represent mean values of n = 3 biologically independent samples and error bars denote standard deviation. All box plots depict the first and third quartiles as the lower and upper bounds of the box, with a thicker band inside the box showing the median value and whiskers representing 1.5x the interquartile range.