TY - JOUR T1 - Massively parallel digital transcriptional profiling of single cells JF - bioRxiv DO - 10.1101/065912 SP - 065912 AU - Grace X.Y. Zheng AU - Jessica M. Terry AU - Phillip Belgrader AU - Paul Ryvkin AU - Zachary W. Bent AU - Ryan Wilson AU - Solongo B. Ziraldo AU - Tobias D. Wheeler AU - Geoff P. McDermott AU - Junjie Zhu AU - Mark T. Gregory AU - Joe Shuga AU - Luz Montesclaros AU - Donald A. Masquelier AU - Stefanie Y. Nishimura AU - Michael Schnall-Levin AU - Paul W Wyatt AU - Christopher M. Hindson AU - Rajiv Bharadwaj AU - Alexander Wong AU - Kevin D. Ness AU - Lan W. Beppu AU - H. Joachim Deeg AU - Christopher McFarland AU - Keith R. Loeb AU - William J. Valente AU - Nolan G. Ericson AU - Emily A. Stevens AU - Jerald P. Radich AU - Tarjei S. Mikkelsen AU - Benjamin J. Hindson AU - Jason H. Bielas Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/07/26/065912.abstract N2 - Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of up to tens of thousands of single cells per sample. Cell encapsulation in droplets takes place in ∼6 minutes, with ∼50% cell capture efficiency, up to 8 samples at a time. The speed and efficiency allow the processing of precious samples while minimizing stress to cells. To demonstrate the system′s technical performance and its applications, we collected transcriptome data from ∼¼ million single cells across 29 samples. First, we validate the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. Then, we profile 68k peripheral blood mononuclear cells (PBMCs) to demonstrate the system′s ability to characterize large immune populations. Finally, we use sequence variation in the transcriptome data to determine host and donor chimerism at single cell resolution in bone marrow mononuclear cells (BMMCs) of transplant patients. This analysis enables characterization of the complex interplay between donor and host cells and monitoring of treatment response. This high-throughput system is robust and enables characterization of diverse biological systems with single cell mRNA analysis. ER -