RNA Sequencing and Data Analysis of the Effects of Biophysical Cues on Cellular Transcriptome

Cells have been shown to respond to the biophysical microenvironment that surrounds them. Previous phenomenological studies suggest that microenvironmental stiffness, the composition and density of adhesion ligands, and the stress relaxation properties [1, 2] can couple and interact to regulate various cell behaviors, such as morphological changes, proliferation, migration, and stem cell differentiation and fate. In order to recapitulate how cell responds to these cues, a 3D alginate culture system can be engineered to independently control the different biophysical features of the microenvironment by tuning the molecular weight distribution, the crosslinking density, and the density of cell adhesion ligands [3]. However, a deep and comprehensive understanding of how external biophysical conditions affect the cellular transcriptome which in turn regulates downstream cell responses is lacking.