PT - JOURNAL ARTICLE AU - Jinzhou Yuan AU - Peter A. Sims TI - An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq AID - 10.1101/070193 DP - 2016 Jan 01 TA - bioRxiv PG - 070193 4099 - http://biorxiv.org/content/early/2016/08/18/070193.short 4100 - http://biorxiv.org/content/early/2016/08/18/070193.full AB - 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. We report an automated microwell array platform for single cell RNA-Seq with significantly improved performance over previous implementations. We demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. We evaluate the level of cross-contamination in our platform by both tracking fluorescent cell lysate in sealed microwells and with a human-mouse mixed species RNA-Seq experiment. Finally, we apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue.