The data originates from lung tumor samples obtained at the University Hospital Bern. Patient-derived alveolar epithelial type 2 cells (AEC2) were isolated and cultured into organoids. Grown organoids where dissociated and seeded onto a novel alveoli-on-chip system submerged in medium. After 24 h of either no mechanical stimulus (control) or cyclic breathing stretch (stretch), RNA was isolated and sequenced. The RNA-seq data underwent quality control, alignment to the reference genome, read counting, DGE and GSEA. All analyses were run in R version 4.2.1.