Simultaneous Measurement of Surface Proteins and Gene Expression from Single Cells

  • Jiadi Luo
  • Carla A. Erb
  • Kong ChenEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2111)


Single-cell transcriptomic analysis has become a new and powerful tool to study complex multicellular systems. Single-cell RNA sequencing provides an unbiased classification of heterogeneous cellular states at the transcriptional level, but it does not always correlate to cell-surface protein expression. A recently developed method called cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) simultaneously measures surface proteins and gene expression from single cells. Briefly, based on the existing single-cell sequencing technology, oligonucleotide-labeled antibodies and barcoded primer gel beads are used to bind to corresponding cell-surface proteins and mRNA, respectively. Further, libraries of labeled protein and RNA information are sequenced to integrate cellular protein and transcriptome reads together efficiently. CITE-seq is transforming comprehensive genomic studies into models of causal gene-protein investigation.

Key words

Single-cell RNA sequencing CITE-seq Surface proteins Gene expression ADT library 10× genomics 



This work was supported by NIH grant R01HL137709.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Division of Pulmonary, Allergy, and Critical Care Medicine, Department of MedicineUniversity of Pittsburgh Medical CenterPittsburghUSA

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