Journal Article

Simultaneous epitope and transcriptome measurement in single cells

Houck-Loomis, Brian, Chattopadhyay, Pratip K, Satija, Rahul, Hafemeister, Christoph, Stephenson, William, Stoeckius, Marlon, Swerdlow, Harold, Smibert, Peter

2017

Overview

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.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 13 / 38/91 / 631/1647/2217/2018 / 631/208/212/2019 / 631/337/475 / 631/61/514/1949 / 82 / 82/1 / 82/80 / Antibodies / Antigenic determinants / Bioinformatics / Biological Microscopy / Biological Techniques / Biomedical Engineering/Biotechnology / brief-communication / Cell surface / Epitope Mapping - methods / Epitopes / Epitopes - immunology / Flow cytometry / Gene expression / Gene Expression Profiling - methods / Gene sequencing / Genomics / High-Throughput Nucleotide Sequencing - methods / Life Sciences / Methods / Oligonucleotides / Physiological aspects / Properties / Proteins / Proteomics / Ribonucleic acid / RNA / Sequence Analysis, RNA - methods / T cells / Tissue Array Analysis - methods / Transcription factors / Transcriptome - physiology