title: Massively parallel digital transcriptional profiling of single cells.
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.
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Grace X Y
authors.initials: GX
authors.lastname: Zheng
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Terry
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Phillip
authors.initials: P
authors.lastname: Belgrader
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Ryvkin
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Zachary W
authors.initials: ZW
authors.lastname: Bent
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Ryan
authors.initials: R
authors.lastname: Wilson
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Solongo B
authors.initials: SB
authors.lastname: Ziraldo
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Tobias D
authors.initials: TD
authors.lastname: Wheeler
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Geoff P
authors.initials: GP
authors.lastname: McDermott
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Junjie
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Mark T
authors.initials: MT
authors.lastname: Gregory
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Joe
authors.initials: J
authors.lastname: Shuga
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Luz
authors.initials: L
authors.lastname: Montesclaros
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.|Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Jason G
authors.initials: JG
authors.lastname: Underwood
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Donald A
authors.initials: DA
authors.lastname: Masquelier
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Stefanie Y
authors.initials: SY
authors.lastname: Nishimura
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Schnall-Levin
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Paul W
authors.initials: PW
authors.lastname: Wyatt
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Hindson
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Rajiv
authors.initials: R
authors.lastname: Bharadwaj
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Wong
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Kevin D
authors.initials: KD
authors.lastname: Ness
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Lan W
authors.initials: LW
authors.lastname: Beppu
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: H Joachim
authors.initials: HJ
authors.lastname: Deeg
authors.affiliation: Seattle Cancer Care Alliance Clinical Immunogenetics Laboratory, Seattle, Washington 98109, USA.
authors.forename: Christopher
authors.identifier: 0000-0003-0546-9652
authors.initials: C
authors.lastname: McFarland
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.|Department of Pathology, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Keith R
authors.initials: KR
authors.lastname: Loeb
authors.affiliation: Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.|Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington 98195, USA.|Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA.
authors.forename: William J
authors.initials: WJ
authors.lastname: Valente
authors.affiliation: Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Nolan G
authors.initials: NG
authors.lastname: Ericson
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Emily A
authors.initials: EA
authors.lastname: Stevens
authors.affiliation: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Jerald P
authors.initials: JP
authors.lastname: Radich
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Tarjei S
authors.initials: TS
authors.lastname: Mikkelsen
authors.affiliation: 10x Genomics Inc., Pleasanton, California, 94566, USA.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Hindson
authors.affiliation: Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.|Department of Pathology, University of Washington, Seattle, Washington 98195, USA.|Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington 98195, USA.|Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
authors.forename: Jason H
authors.initials: JH
authors.lastname: Bielas
mesh_terms: D002460:Cell Line; D005260:Female; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000737:chemistry / Q000378:metabolism*; D008297:Male; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D059010:Single-Cell Analysis; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger