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Conventional two-dimensional as well as established three-dimensional cell culture systems exhibit a high modulus of elasticity, which largely do not represent the stiffness of human organs. This chapter describes a protocol to establish 3D cell cultures of human adipose tissue-derived mesenchymal stromal cells (hAT-MSC) on low stiffness silicon scaffolds. These feature a defined growing environment with a stiffness close to physiology, thus being useful for in vitro investigations for multiple applications.The modulation of gene express