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Fig. 6 | Genome Biology

Fig. 6

From: Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance

Fig. 6

Differential chromatin accessibility across cell types and informativeness of context-specificity. a Purified human innate and adaptive cell types/models analysed for chromatin accessibility by ATAC-seq profiling. b Bar plot showing the median number of recurrent ATAC peaks on the y-axis and sample size on the x-axis for each cell type. One outlier (black dot) was excluded from the clustering analysis in c. c Phylogenetic tree showing the relatedness of chromatin accessibility amongst cell types based on hierarchical clustering using Average method and Jaccard similarity measure. d Clustered binary matrix showing the 164,381 ATAC consensus peaks across 21 datasets derived from 5 cell types. Dark and white indicate presence and absence of recurring ATAC regions in each dataset respectively. e Bar plots showing correlation of log2 fold change of ATAC peaks upon HD vs. UT (left) and LDHD vs HD (right), between iPSMs and MDMs. Pearson’s r are shown on the y-axis. ***p < 0.001. f Example of a locus with clustered pro-inflammatory genes that have nearby tissue- (MDMs in purple, iPSMs in red, CD14 monocytes in orange, CD4 T cells in green, CD8 T cells in blue and CD19 B cells in grey) and context-specific (UT/HD/LDHD for MDMs and iPSMs) ATAC regions. The normalized signals across the replicates of each cell type are shown on the y axis. See also Figs. S5 and S6

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