Simultaneous epitope and transcriptome measurement in single cells

Nat Methods. 2017 Sep;14(9):865-868. doi: 10.1038/nmeth.4380. Epub 2017 Jul 31.


High-throughput single-cell RNA sequencing has transformed our understanding of complex cell populations, but it does not provide phenotypic information such as cell-surface protein levels. Here, we describe cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), a method in which oligonucleotide-labeled antibodies are used to integrate cellular protein and transcriptome measurements into an efficient, single-cell readout. CITE-seq is compatible with existing single-cell sequencing approaches and scales readily with throughput increases.

Publication types

  • Evaluation Study

MeSH terms

  • Epitope Mapping / methods*
  • Epitopes / immunology*
  • Gene Expression Profiling / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Sequence Analysis, RNA / methods*
  • Tissue Array Analysis / methods*
  • Transcriptome / physiology*


  • Epitopes