Abstract: A cell analysis system includes a multi-layer microfluidic device that includes a layer of microfluidic channels, a layer of microwells, a membrane with nanochannels, and a layer of extraction chambers. The microwells and the membrane are configured to allow culturing of cells that are adhered to the membrane or suspended in the microwells, and the membrane is configured to allow diffusion of substances across the membrane into the layer of extraction chambers. The cell analysis system includes a top conductive layer and a bottom conductive layer on the opposite sides of the multi-layer microfluidic device. The cell analysis system also includes a function generator configured to apply an electroporation pulse between the top conductive layer and the bottom conductive layer.