Fig. S2.

Gene-expression changes caused by Etv5 deficiency. (A) Heat map of the top 50 most differentially expressed genes in Etv5^+/+ Sftpc^CreERT2/+ Rosa^tdTomato/+ tdTomato⁺ cells compared with Etv5^fl/- Sftpc^CreERT2/+Rosa^tdTomato/+ tdTomato⁺ cells at 7 d after the last dose of tamoxifen. (B) Gene set enrichment analysis identifying Gene Ontology Biological Process gene sets that show significant enrichment when comparing differential expression based on RNA-seq fromEtv5^+/+ Sftpc^CreERT2/+ Rosa^tdTomato/+ and Etv5^fl/- Sftpc^CreERT2/+Rosa^tdTomato/+ tdTomato⁺ cells. (C) Cell-cycle genes identified by Gene Ontology analysis that are significantly down-regulated in Etv5^fl/− Sftpc^CreERT2/+Rosa^tdTomato/+ tdTomato⁺ cells compared with Etv5^+/+ Sftpc^CreERT2/+ Rosa^tdTomato/+ cells. (D) Volcano plots indicating the difference in gene expression between tdTomato⁺ cells and whole-lung tissue (Left) and between ΔEtv5 and Etv5^+/+ tdTomato⁺ cells (Right). There were 2,819 genes more highly expressed in tdTomato⁺ cells than in whole-lung tissue (Benjamini–Hochberg adjusted P < 0.05, fold-change >2), and 321 genes were expressed at lower levels in ΔEtv5 tdTomato⁺ cells than in wild-type cells (Benjamini–Hochberg adjusted P < 0.05, fold-change is less than −2). The Venn diagram shows the overlap of these two gene sets. (E) Single-cell qRT-PCR of AT1 and AT2 marker genes. Each point represents one gene and shows the t statistic comparing Etv5^+/+ tdTomato⁺ and ΔEtv5 tdTomato⁺ cells isolated from tamoxifen-treated Sftpc^CreERT2/+Kras^LSL/+ mice as in Fig. 3A. Genes that are significantly changed (Benjamini–Hochberg adjusted P < 0.05) are shown in orange. (F) Single-cell qRT-PCR of AT1 and AT2 marker genes. Each point represents one gene and shows the t statistic comparing Etv5^+/+ lineage⁻ CD24⁻ Epcam⁺ and ΔEtv5 lineage⁻ CD24⁻ Epcam⁺ cells isolated from tamoxifen-treated Rosa^CreERT2/+ mice. Genes that are significantly changed (Benjamini–Hochberg adjusted P < 0.05) are shown in orange. (G) Heatmap showing the row scaled signal for Etv5 and H3k4me3 on 1,000 randomly selected ETV5 sites on a 5 kb+/5 kb− window. The H3k4me3 window is centered on the Etv5 binding site. (H) The graph indicates the degree of enrichment of ChIP-seq–identified peaks adjacent to the AT1 and AT2 marker genes compared with background calculated by Macs2.