Simultaneous Epitope and Transcriptome Measurement in Single Cells

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2017 Aug 1

PMID 28759029

Citations 1370

Authors

Marlon Stoeckius

Christoph Hafemeister

William Stephenson

Brian Houck-Loomis

Pratip K Chattopadhyay

Harold Swerdlow

Rahul Satija

Peter Smibert

Affiliations

Soon will be listed here.

Abstract

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.

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References

Breton G, Lee J, Liu K, Nussenzweig M . Defining human dendritic cell progenitors by multiparametric flow cytometry. Nat Protoc. 2015; 10(9):1407-22. PMC: 4607256. DOI: 10.1038/nprot.2015.092. View

Macosko E, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M . Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015; 161(5):1202-1214. PMC: 4481139. DOI: 10.1016/j.cell.2015.05.002. View

Baranauskas A, Paliksa S, Alzbutas G, Vaitkevicius M, Lubiene J, Letukiene V . Generation and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variants. Protein Eng Des Sel. 2012; 25(10):657-68. DOI: 10.1093/protein/gzs034. View

Ponten F, Gry M, Fagerberg L, Lundberg E, Asplund A, Berglund L . A global view of protein expression in human cells, tissues, and organs. Mol Syst Biol. 2009; 5:337. PMC: 2824494. DOI: 10.1038/msb.2009.93. View

Shahi P, Kim S, Haliburton J, Gartner Z, Abate A . Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding. Sci Rep. 2017; 7:44447. PMC: 5349531. DOI: 10.1038/srep44447. View

Albayrak C, Jordi C, Zechner C, Lin J, Bichsel C, Khammash M . Digital Quantification of Proteins and mRNA in Single Mammalian Cells. Mol Cell. 2016; 61(6):914-24. DOI: 10.1016/j.molcel.2016.02.030. View

Yuan J, Sims P . An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq. Sci Rep. 2016; 6:33883. PMC: 5037380. DOI: 10.1038/srep33883. View

Paul F, Arkin Y, Giladi A, Jaitin D, Kenigsberg E, Keren-Shaul H . Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Cell. 2015; 163(7):1663-77. DOI: 10.1016/j.cell.2015.11.013. View

Wilson N, Kent D, Buettner F, Shehata M, Macaulay I, Calero-Nieto F . Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations. Cell Stem Cell. 2015; 16(6):712-24. PMC: 4460190. DOI: 10.1016/j.stem.2015.04.004. View

10.

Wendt K, Wilk E, Buyny S, Buer J, Schmidt R, Jacobs R . Gene and protein characteristics reflect functional diversity of CD56dim and CD56bright NK cells. J Leukoc Biol. 2006; 80(6):1529-41. DOI: 10.1189/jlb.0306191. View

11.

Adler M, Wacker R, Niemeyer C . Sensitivity by combination: immuno-PCR and related technologies. Analyst. 2008; 133(6):702-18. DOI: 10.1039/b718587c. View

12.

Darmanis S, Gallant C, Marinescu V, Niklasson M, Segerman A, Flamourakis G . Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells. Cell Rep. 2016; 14(2):380-9. PMC: 4713867. DOI: 10.1016/j.celrep.2015.12.021. View

13.

Zheng G, Terry J, Belgrader P, Ryvkin P, Bent Z, Wilson R . Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017; 8:14049. PMC: 5241818. DOI: 10.1038/ncomms14049. View

14.

Frei A, Bava F, Zunder E, Hsieh E, Chen S, Nolan G . Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat Methods. 2016; 13(3):269-75. PMC: 4767631. DOI: 10.1038/nmeth.3742. View

15.

Stahlberg A, Thomsen C, Ruff D, Aman P . Quantitative PCR analysis of DNA, RNAs, and proteins in the same single cell. Clin Chem. 2012; 58(12):1682-91. DOI: 10.1373/clinchem.2012.191445. View

16.

Fan H, Fu G, Fodor S . Expression profiling. Combinatorial labeling of single cells for gene expression cytometry. Science. 2015; 347(6222):1258367. DOI: 10.1126/science.1258367. View

17.

Cao J, Packer J, Ramani V, Cusanovich D, Huynh C, Daza R . Comprehensive single-cell transcriptional profiling of a multicellular organism. Science. 2017; 357(6352):661-667. PMC: 5894354. DOI: 10.1126/science.aam8940. View

18.

Genshaft A, Li S, Gallant C, Darmanis S, Prakadan S, Ziegler C . Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction. Genome Biol. 2016; 17(1):188. PMC: 5027636. DOI: 10.1186/s13059-016-1045-6. View

19.

Poli A, Michel T, Theresine M, Andres E, Hentges F, Zimmer J . CD56bright natural killer (NK) cells: an important NK cell subset. Immunology. 2009; 126(4):458-65. PMC: 2673358. DOI: 10.1111/j.1365-2567.2008.03027.x. View

20.

Ferlazzo G, Munz C . NK cell compartments and their activation by dendritic cells. J Immunol. 2004; 172(3):1333-9. DOI: 10.4049/jimmunol.172.3.1333. View