@article {Zheng065912, author = {Grace X.Y. Zheng and Jessica M. Terry and Phillip Belgrader and Paul Ryvkin and Zachary W. Bent and Ryan Wilson and Solongo B. Ziraldo and Tobias D. Wheeler and Geoff P. McDermott and Junjie Zhu and Mark T. Gregory and Joe Shuga and Luz Montesclaros and Donald A. Masquelier and Stefanie Y. Nishimura and Michael Schnall-Levin and Paul W Wyatt and Christopher M. Hindson and Rajiv Bharadwaj and Alexander Wong and Kevin D. Ness and Lan W. Beppu and H. Joachim Deeg and Christopher McFarland and Keith R. Loeb and William J. Valente and Nolan G. Ericson and Emily A. Stevens and Jerald P. Radich and Tarjei S. Mikkelsen and Benjamin J. Hindson and Jason H. Bielas}, title = {Massively parallel digital transcriptional profiling of single cells}, elocation-id = {065912}, year = {2016}, doi = {10.1101/065912}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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 \~{}{\textonequarter} 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.}, URL = {https://www.biorxiv.org/content/early/2016/07/26/065912}, eprint = {https://www.biorxiv.org/content/early/2016/07/26/065912.full.pdf}, journal = {bioRxiv} }