An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq

Recent developments have enabled rapid, inexpensive RNA sequencing of thousands of individual cells from a single specimen, raising the possibility of unbiased and comprehensive expression profiling from complex tissues. Microwell arrays are a particularly attractive microfluidic platform for single cell analysis due to their scalability, cell capture efficiency, and compatibility with imaging.

Researchers from Columbia University Medical Center report an automated microwell array platform for single cell RNA-Seq with significantly improved performance over previous implementations. They demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. They evaluate the level of cross-contamination in their platform by both tracking fluorescent cell lysate in sealed microwells and with a human-mouse mixed species RNA-Seq experiment. Finally, the researchers apply their system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue.


Schematic depiction (not drawn to scale) of the work flow (left column) and multiple check points (right column) of the automated microwell array platform. The check points can be used to assess the quality of a run and acquire additional phenotypic information on the same cells to be sequenced.

Yuan J, Sims PA. (2016) An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq. bioRXiv [Epub ahead of print]. [abstract]

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