Quantitation of mRNA Transcripts and Proteins Using the BD Rhapsody™ Single-Cell Analysis System

  • Eleen Y. ShumEmail author
  • Elisabeth M. Walczak
  • Christina Chang
  • H. Christina Fan
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1129)


In this review, we describe the BD Rhapsody™ Single-Cell Analysis System, a platform that allows high-throughput capture of nucleic acids from single cells using a simple cartridge workflow and a multitier barcoding system. The resulting captured information can be used to generate various types of next-generation sequencing (NGS) libraries, including whole transcriptome analysis for discovery biology and targeted RNA analysis for high sensitivity transcript detection. The BD Rhapsody system can be used with emerging applications, such as BD™ AbSeq assays, to profile gene expression in both mRNA and protein level to provide ultra-high resolution analysis of single cells.


Single cells Microwell array Barcoded beads Magnetic beads Next-generation sequencing Molecular barcoding Unique molecular identifiers UMI Transcriptome Targeted RNA-seq Antibody 


  1. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell. 2009;136:215–33. Scholar
  2. Birey F, Andersen J, Makinson CD, et al. Assembly of functionally integrated human forebrain spheroids. Nature. 2017;545:54–9. Scholar
  3. Crick FH. On protein synthesis. Symp Soc Exp Biol. 1958;12:138–63.PubMedGoogle Scholar
  4. Fan HC, Fu GK, Fodor SPA. Combinatorial labeling of single cells for gene expression cytometry. Science. 2015;347:1258367. Scholar
  5. Fu GK, Hu J, Wang P-H, Fodor SPA. Counting individual DNA molecules by the stochastic attachment of diverse labels. Proc Natl Acad Sci. 2011;108:9026–31. Scholar
  6. Gygi SP, Rochon Y, Franza BR, Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol. 1999;19:1720–30.CrossRefGoogle Scholar
  7. Hochstrasser M. Ubiquitin, proteasomes, and the regulation of intracellular protein degradation. Curr Opin Cell Biol. 1995;7:215–23. Scholar
  8. Klein AM, Mazutis L, Akartuna I, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell. 2015;161:1187–201. Scholar
  9. Macosko EZ, Basu A, Satija R, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015;161:1202–14. Scholar
  10. Peterson VM, Zhang KX, Kumar N, et al. Multiplexed quantification of proteins and transcripts in single cells. Nat Biotechnol. 2017;35:936–9. Scholar
  11. Shahi P, Kim SC, Haliburton JR, et al. Abseq: ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding. Sci Rep. 2017;7:44447. Scholar
  12. Stoeckius M, Hafemeister C, Stephenson W, et al. Simultaneous epitope and transcriptome measurement in single cells. Nat Methods. 2017;14:865–8. Scholar
  13. van der Maaten L, Hinton G. Visualizing data using t-SNE. J Mach Learn Res. 2008;9:2579–605.Google Scholar
  14. Wassarman PM. Advances in developmental biochemistry, vol. 3B. Amsterdam: Elsevier; 1995.Google Scholar
  15. Wu AR, Neff NF, Kalisky T, et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat Methods. 2013;11:41–6. Scholar
  16. Zheng GXY, Terry JM, Belgrader P, et al. Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017;8:14049. Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Eleen Y. Shum
    • 1
    Email author
  • Elisabeth M. Walczak
    • 1
  • Christina Chang
    • 1
  • H. Christina Fan
    • 1
  1. 1.BD BiosciencesSan JoseUSA

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