Experimental design and data. (A) Flow-chart of the experimental setup and analysis methodology. The epithelial-mesenchymal transition (EMT) was induced using TNF and TGFβ in spheroid cultures. Cells were collected before and after treatment (4 days), and whole-genome gene expression and chromatin profiles of 18 histone modifications and variants were obtained. From the paired data sets we measured differential gene expression and calculated differential epigenetic profiles (DEP). The DEPs were calculated individually for gene and enhancer loci and subsequently clustered. Analyses of the resulting epigenetic gene and enhancer clusters included functional enrichment profiling, network partitioning / ranking, and transcription factor (TF) binding. The results were shown to be consistent with a chromatin-mediated feedback model that involves specific TFs binding activated enhancers that upregulate expression in EMT-related gene clusters. (B) Table of histone modifications assayed. Histone modifications shown to be correlated and enriched at enhancer loci are indicated.