Highly multiplexed simultaneous detection of RNAs and proteins in single cells

Nat Methods. 2016 Mar;13(3):269-75. doi: 10.1038/nmeth.3742. Epub 2016 Jan 25.


To enable the detection of expression signatures specific to individual cells, we developed PLAYR (proximity ligation assay for RNA), a method for highly multiplexed transcript quantification by flow and mass cytometry that is compatible with standard antibody staining. When used with mass cytometry, PLAYR allowed for the simultaneous quantification of more than 40 different mRNAs and proteins. In primary cells, we quantified multiple transcripts, with the identity and functional state of each analyzed cell defined on the basis of the expression of a separate set of transcripts or proteins. By expanding high-throughput deep phenotyping of cells beyond protein epitopes to include RNA expression, PLAYR opens a new avenue for the characterization of cellular metabolism.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Flow Cytometry / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • High-Throughput Screening Assays / methods*
  • Humans
  • Jurkat Cells
  • Protein Array Analysis / methods*
  • Proteins / analysis
  • Proteins / metabolism*
  • RNA / analysis
  • RNA / metabolism*


  • Proteins
  • RNA