Massively parallel digital transcriptional profiling of single cells

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.…

• UD
  U.S. Department of Defense

  Awards: W81XWH, W81XWH-10-1-0563
• EM
  Ellison Medical Foundation

  Award: AG-NS-0577-09
• CF
  Canary Foundation
• NC
  National Cancer Institute

  Award: U10CA180861
• NI
  National Institute of Environmental Health Sciences

  Award: R01ES019319
• CD
  Congressionally Directed Medical Research Programs

  Award: W81XWH-10-1-0563