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A stand-alone microfluidic system consists of a reusable flow control part and a disposable microwell array for high throughput cell analysis is proposed. The flow control part is realized with addressable microvalve array driven by compactly-fabricated solenoid actuators and EOF micropumps. Disposable 16 microwell array with 4 reagent injection ports was fabricated using a PDMS structure. The disposable fluidic chip can be easily replaced to different functional fluidic networks depended on their actual uses. The prototype system with 25 (52) on-chip hydraulic valves that are driven by 10 (2×5) solenoid actuators was fabricated. Precise reagent injection of ten-nanoliter order to each microwell was successfully carried out.