Systematic investigation of complex cellular systems using micro and nano devices has distinctive advantages over traditional approaches. The capabilities of performing time-varying stimulation and real-time monitoring of cells are invaluable for investigating dynamic biological systems, such as gene regulatory networks. In this work, we report a generic microfluidic platform, which is capable of long term cell cultivation, for investigating the complex dynamics of a transcription factor, nuclear factor kappa B (NF-κB). The temporal responses of NF-κB mediated gene expression were measured at the single cell level and the results were compared to a computational model. Our microfluidic platforms combining with advanced biotechnologies and computational techniques provide powerful tools for investigating complex biological networks.