Fig. 3: Loss of Prdm3/16 influences cell differentiation.
a–c Bulk RNA-Seq analysis of sorted EpCAM+ epithelial cells from E17.5 Control (n = 6) and Prdm3/16ShhCreΔ/Δ (Prdm3/16Δ/Δ) (n = 5) lungs. Wald test (default for DESeq2 r-package) was used for differential expression analysis utilizing standard cutoffs of |log2 fold change| > 0.58 and p-value < 0.05. a Volcano plot showing 1438 genes with decreased expression and 2124 genes with increased expression, highlighting genes that are associated with epithelial cell development and mis-regulated in AT1 and AT2 cells. b Heatmaps of normalized gene expression of AT1 and AT2 associated genes, showing an increase in genes associated with AT1 cells and a decrease in genes associated with AT2 cells, a reflection of cell type population size. Asterik (*) denotes statistical change in both bulk RNA-seq and single cell RNA-seq. c Functional enrichment of gene sets with either increased expression (left panel) or decreased expression (right panel) using ToppFun and selecting highly enriched GO: Biological Processes. p-values determined by the hypergeometric probability mass function and reported as a Benjamini and Hochberg corrected FDR < 0.05.
