A549 and MDA-MB-231 cells were cultured in 2D and Matrigel based 3D culture for 4 days. Total RNA was extracted using Trizol. RNA-SEQ was carried out to profile the gene expression in both culture conditions. Overall design: The goal of this experiment was to profie the genes that are regulated by extracellular matrix in cancer cells. Gene expression was probed globally using RNA-SEQ.