A self-driven carbon-doped high-density microwell array for single cell analysis

Single cell analysis preserves the heterogeneity information of target cell population in search of rare biomarkers for disease diagnosis. Microfluidic technology facilitates single cell analysis through its high integrability with multi-functionalities, high sensitivity, precision and dynamic range for digital assays. However, demonstrated microfluidic devices for single cell analysis suffer from low throughput, the need of external instruments and complicated control system. Herein, we present a self-driven high-density microwell array for quantitative analysis of single-cell metabolic activity. 38,400-microwell array (density: 25,000/cm2) is achieved through two features: (1) Two-layered vertical design of microchannels to provide more space for microwell integration; and (2) Doping of carbon powder in microwell wall to block stray light transmission and improve signal-to-noise ratio, decreasing the interval between microwells down to 30 µm. Moreover, the chip is powered by pre-stored negative pressure without the need of external pump. Our microwell array significantly reduces the assay time from over 24–3 h in Escherichia coli quantitative analysis (6-order dynamic range). We also demonstrated the viability assay and metabolic heterogeneity of single bacteria, envisioning that the microwell array could be applied for other target cells and extended to different molecular techniques such as digital PCR. •A high-density microwell array device for single cell analysis.•25,000/cm2 was achieved through microchannel design and carbon-doping.•Single E. coli quantitative assay using chemifluorescence reaction within 3 hr.•Viability assay and metabolic heterogeneity of single E. coli through the time-lapse imaging.•The high-throughput microwell array with broad dynamic range has potential in other digital assays such as digital PCR.