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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

Extended Data Figure 10. Combination ATAC-seq and RNA-seq emphasizes the Wnt- and FGF-responsive nature of AEPs and identifies several novel AEP-enriched direct Wnt target genes.

Extended Data Figure 10

(A) Schematic representation of the design of the human RNA-seq experiments. (B) GO Term analysis of the top 300 hAEP enriched genes shows enrichment of several categories associated with lung progenitor cell function, similar to what was observed in mAEP. (C) Evaluation of the chromatin accessibility in the mouse genome near common AEP enriched genes demonstrates a significant overrepresentation of Tcf binding sites, particularly in 5kb immediate upstream putative regulatory regions. Full details of enrichment analysis are found in the Methods. (D) Schematic depiction of areas of AEP-enriched open chromatin near selected AEP-enriched genes. Peak height represents coverage of the indicated genomic region in the ATAC library, while the number indicates the fold enrichment in the indicated peak. (E) ChIP QPCR on AEP vs AT2 chromatin demonstrates Ctnnb1 antibody binding at the differentially accessible genomic regions near Etv4, Sftpa, Lamp3, and Gpr116 in AEP cells, indicating that these genes are direct Wnt targets. Data is shown as mean with individual data points showing summary data from 2 independent ChIP experiments with multiple technical replicates. (F–J) Fgfr2 activation in mAEPs drives increased proliferation and formation of larger organoids. Quantification in (E). Correlate to Figure 4. (K) RNAscope showing enriched expression of Fgfr2 (red) in lineage labeled AEPs. (L–Q) Similar to Fgf7, Fgf10 treatment drives increased colony forming efficiency in both mAEP (L–P) and hAEP (Q). Data shown in F–J,L–Q represent a minimum of N=12 wells across 2 individual experiments. Statistics are representative of all biological replicates. Data was analyzed with ANOVA followed by preplanned pairwise comparisons and adjustment for multiple comparison testing and shown centered on mean with bars indicating standard deviation with *=p<0.05, **=p<0.01, ***=p<0.001, ****=p<0.0001.