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. Author manuscript; available in PMC: 2018 Aug 28.
Published in final edited form as: Nature. 2018 Feb 28;555(7695):251–255. doi: 10.1038/nature25786

Figure 2. AEPs possess a distinct transcriptome and chromatin architecture enriched for cell cycle and progenitor cell pathways.

Figure 2

(A) RNA-seq and ATAC-seq was performed on AEPs and AT2s. PCA plot of the top 500 most variable genes showing that AEPs segregate into a distinct population from AT2. By ATAC-seq, more than 40% of the genome was differentially accessible in AEPs (16.2%) or AT2 cells (24.1%). (B) ATAC-seq heatmap showing genome wide regions of differential open chromatin peaks in AT2s versus AEPs. (C) AEP-enriched ATAC-seq peaks compared to RNA-seq expression shows that a majority of genes associated with AEP open chromatin are not differentially expressed but primed for rapid activation. (D) A subset of these primed genes are associated with cell cycle activation. Full details on the experimental design and statistical methods for these analyses are available in the Methods.