Extended Data Fig. 5: Chromatin remodeling following type I interferon (IFN-I) exposure.

(a) Patterns of gene expression as determined by RNA-seq for representative ATAC–seq-identified genes. Genes upregulated and downregulated in CD133⁺CD24⁺CD44^+high (CD44H) cells induced by IFN-I are in red and blue, respectively. (b) Western-blot (WB) analysis of the levels of KDM1B in the indicated parental (PAR) cell lines and the same cell lines engineered to overexpress or down-express KDM1B (Kdm1b^OVER and Kdm1b^KD). Actin beta (b-ACTIN) is used as loading control. The table reports data quantification from one experiment. (c) Evaluation of the impact on KDM1B on chromatin remodeling by ATAC–seq. Representative loci for the illustrated genes in Kdm1b^OVER and Kdm1b^KD MCA205 cells are reported. (d) Evaluation of gene regulatory mechanisms downstream of KDM1B by ChIP–seq on immunogenic cell death (ICD)-induced CD44H cells isolated from MCA205 cells and Gene Ontology (GO) terms enrichment analysis. Genes are categorized as illustrated. (d) One-sided hypergeometric test followed by Benjamini–Hochberg correction for multiple comparisons.