Fig. 2

Experimental perturbation and RNA-Seq analysis. a Experimental design. Triplicate biological replicates were subjected to no treatment (hSAEC) or TGFβ treatment (hSAEC-EMT). Cells were stimulated with TNFα for 0, 1 or 12 h prior to RNA extraction. b Flow diagram for RNA-Seq GLM data analysis. Abbreviations: NGS, next generation sequencing; QA/QC, quality assurance/quality control; GLM, generalized linear model; DGE, differential gene expression. c Multidimensional unsupervised clustering analysis of RNA-Seq data sets. Shown is the similarity of each replicate based on TGF treatment or time post TNF and their clustering by group. Abbreviations: CE, control (unstimulated) epithelial cells; CM, control mesenchymal cells