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.
Gene Expression Omnibus
We acknowledge S. Jaini and K. Pandit of the NYGC Technology Innovation Lab for critical discussions and support; E. Papalexi for help with CBMCs isolation; M. Coppo, S. Fennessey, B. Baysa and S. Pescatore at NYGC for sequencing support; and C. Kocks for manuscript discussions. Multiparameter flow cytometer instrument time and reagents were generously provided by the Vaccine Research Center of the National Institutes of Health. C.H. was supported by a Deutsche Forschungsgemeinschaft research fellowship. R.S. was supported by an NIH New Innovator Award (DP2-HG-009623). Research reported here was partially supported by the National Human Genome Research Institute under Award Number UM1HG008901.