Fig. 3

Open chromatin status and transcriptional factors in the acquisition of inflammatory signature. A Hierarchical clustering analysis revealed chromatin accessibility among Matrigel organoids, collagen sphere, and dFEnS. B Overlap of COL-UP (1880 genes) and FEnS-UP (1769 genes) with genes showing adjacent COL-OPEN (1169 sites) and FEnS-OPEN (1367 sites) is visualized respectively. The p value of statistical significance is indicated. C ATAC sequencing tracks illustrate dynamic chromatin opening at Tead4, Wwtr1, and Tacstd2 in COL-ENRWN and dFEnS. The open chromatin region is highlighted with a red bar. D Top three enriched TF motifs in open chromatin of the collagen sphere and dFEnS identified by ATAC sequencing analysis are shown