Microfluidic devices provide powerful platforms for single-cell transcriptome analysis for many advantages such as highly parallel processing and low consumption of reagents. We have elaborated an integrated system with individual controller for effective single-cell transcriptome analysis. Inside this integrated microfluidic device, the cells are individually manipulated and isolated in an array using micro sieve structures, then transferred into different nanoliter reaction chambers for parallel processing of single-cell transcriptome analysis. The result demonstrates that this platform has the potential for assessment of genetic stability in cancer diagnosis.