Massively parallel digital transcriptional profiling of single cells

Grace X. Y. Zheng, Jessica M. Terry, Phillip Belgrader, Paul Ryvkin, Zachary W. Bent, Ryan Wilson, Solongo B. Ziraldo, Tobias D. Wheeler, Geoff P. McDermott, Junjie Zhu, Mark T. Gregory, Joe Shuga, Luz Montesclaros, Jason G. Underwood, Donald A. Masquelier, Stefanie Y. Nishimura, Michael Schnall-Levin, Paul W. Wyatt, Christopher M. Hindson, Rajiv Bharadwaj, Alexander Wong, Kevin D. Ness, Lan W. Beppu, H. Joachim Deeg, Christopher McFarland, Keith R. Loeb, William J. Valente, Nolan G. Ericson, Emily A. Stevens, Jerald P. Radich, Tarjei S. Mikkelsen, Benjamin J. Hindson () and Jason H. Bielas ()
Additional contact information
Grace X. Y. Zheng: 10x Genomics Inc.
Jessica M. Terry: 10x Genomics Inc.
Phillip Belgrader: 10x Genomics Inc.
Paul Ryvkin: 10x Genomics Inc.
Zachary W. Bent: 10x Genomics Inc.
Ryan Wilson: 10x Genomics Inc.
Solongo B. Ziraldo: 10x Genomics Inc.
Tobias D. Wheeler: 10x Genomics Inc.
Geoff P. McDermott: 10x Genomics Inc.
Junjie Zhu: 10x Genomics Inc.
Mark T. Gregory: Translational Research Program, Fred Hutchinson Cancer Research Center
Joe Shuga: 10x Genomics Inc.
Luz Montesclaros: 10x Genomics Inc.
Jason G. Underwood: 10x Genomics Inc.
Donald A. Masquelier: 10x Genomics Inc.
Stefanie Y. Nishimura: 10x Genomics Inc.
Michael Schnall-Levin: 10x Genomics Inc.
Paul W. Wyatt: 10x Genomics Inc.
Christopher M. Hindson: 10x Genomics Inc.
Rajiv Bharadwaj: 10x Genomics Inc.
Alexander Wong: 10x Genomics Inc.
Kevin D. Ness: 10x Genomics Inc.
Lan W. Beppu: Fred Hutchinson Cancer Research Center
H. Joachim Deeg: Fred Hutchinson Cancer Research Center
Christopher McFarland: Seattle Cancer Care Alliance Clinical Immunogenetics Laboratory
Keith R. Loeb: Fred Hutchinson Cancer Research Center
William J. Valente: Translational Research Program, Fred Hutchinson Cancer Research Center
Nolan G. Ericson: Translational Research Program, Fred Hutchinson Cancer Research Center
Emily A. Stevens: Fred Hutchinson Cancer Research Center
Jerald P. Radich: Fred Hutchinson Cancer Research Center
Tarjei S. Mikkelsen: 10x Genomics Inc.
Benjamin J. Hindson: 10x Genomics Inc.
Jason H. Bielas: Translational Research Program, Fred Hutchinson Cancer Research Center

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: 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 tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system’s technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system’s ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.

Date: 2017
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DOI: 10.1038/ncomms14049

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