Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Nat Commun. 2019 Jul 2;10(1):2907. doi: 10.1038/s41467-019-10756-2.


Single-nucleus RNA-seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate or are frozen, and opens the way to human genetics studies, clinical trials, and precise cell atlases of large organs. However, such applications are currently limited by batch effects, processing, and costs. Here, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter recovered profiles. We develop DemuxEM, a computational tool that detects inter-sample multiplets and assigns singlets to their sample of origin, and validate its accuracy using sex-specific gene expression, species-mixing and natural genetic variation. Our approach will facilitate tissue atlases of isogenic model organisms or from multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Aged
  • Aged, 80 and over
  • Animals
  • Antibodies / analysis*
  • Cell Nucleus / chemistry
  • Cell Nucleus / genetics*
  • Cell Nucleus / metabolism
  • DNA / genetics
  • Female
  • Genomics / methods*
  • Humans
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Neurons / chemistry
  • Neurons / cytology
  • Neurons / metabolism
  • Prefrontal Cortex / chemistry
  • Prefrontal Cortex / metabolism
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Single-Cell Analysis / methods*


  • Antibodies
  • RNA, Messenger
  • DNA