Simultaneous epitope and transcriptome measurement in single cells

Using established high-throughput single-cell RNA-seq platforms, CITE-seq combines highly multiplexed, antibody-based protein marker quantification with unbiased transcriptome profiling for thousands of single cells. 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.