Review Article | Published:

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices

Nature Reviews Genetics volume 18, pages 345361 (2017) | Download Citation

This article has been updated


Recent advances in cellular profiling have demonstrated substantial heterogeneity in the behaviour of cells once deemed 'identical', challenging fundamental notions of cell 'type' and 'state'. Not surprisingly, these findings have elicited substantial interest in deeply characterizing the diversity, interrelationships and plasticity among cellular phenotypes. To explore these questions, experimental platforms are needed that can extensively and controllably profile many individual cells. Here, microfluidic structures — whether valve-, droplet- or nanowell-based — have an important role because they can facilitate easy capture and processing of single cells and their components, reducing labour and costs relative to conventional plate-based methods while also improving consistency. In this article, we review the current state-of-the-art methodologies with respect to microfluidics for mammalian single-cell 'omics' and discuss challenges and future opportunities.

Key points

  • There has been a renaissance in single-cell biology, facilitated in part by the rise of microfluidic devices that can facilitate easy capture, processing and profiling of single cells and their components, reducing labour and costs relative to conventional plate-based methods while also improving consistency.

  • The three most common classes of microfluidic device are defined by their fundamental elements: valves, droplets or nanowells. Valve-based microfluidic devices afford control but have limited scale; droplet-based devices have high throughput but limited control; and nanowell-based methods have intermediate scale and control, but greater simplicity in operation. These factors influence the costs and benefits of porting any existing assay to each microfluidic device.

  • Each of these three classes has been used to profile several cellular 'omics' — including the genome, epigenome, transcriptome and proteome — achieving different levels of throughput and efficiency, while leaving opportunities for future development.

  • Emerging efforts are beginning to focus on measuring multiple cellular properties at once, such as the transcriptome and the proteome or the transcriptome and the epigenome, to obtain a more comprehensive picture of cellular phenotype and its drivers.

  • Such comprehensive profiling is especially important when studying single cells owing to technical and biological noise sources, which limit the utility of any given measurement from any given cell.

  • Sequencing is increasingly becoming the de facto method for profiling information from single cells given its bandwidth relative to the information content of a single cell and the growing ease of mapping information in a nucleic acid readout. Yet, given fixed sequencing bandwidth and the often limited utility of any one measurement, it is important to carefully consider how to most judiciously allocate reads over cells and their variables.

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Change history

  • 19 April 2017

    In the acknowledgements section of this article, the number of an NIH grant awarded to A.K.S. was corrected from U24AI11862 to U24AI118672.


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The authors thank J. C. Love, A. S Genshaft, K. E. Kolb, C. G. K. Ziegler and S. L. Carroll for helpful comments and suggestions. This work was supported by the Searle Scholars Program (A.K.S.), the Beckman Young Investigator Program (A.K.S.), a US National Institutes of Health (NIH) New Innovator Award DP2OD020839 (A.K.S.), NIH grants U24AI118672 (A.K.S.), P50HG006193 (A.K.S.), P01GM096971 (D.A.W.), P01HL120839 (D.A.W.) and R01EB014703 (D.A.W.), US National Science Foundation (NSF) Materials Research Science and Engineering Center grant DMR-1420570 (D.A.W.) and NSF grant DMR-1310266 (D.A.W.).

Author information


  1. Institute for Medical Engineering & Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts 02139, USA.

    • Sanjay M. Prakadan
    •  & Alex K. Shalek
  2. Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA.

    • Sanjay M. Prakadan
    •  & Alex K. Shalek
  3. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.

    • Sanjay M. Prakadan
    •  & Alex K. Shalek
  4. School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA.

    • David A. Weitz
  5. Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.

    • David A. Weitz


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Competing interests

D.A.W. is a founder of 1-CellBio, a company that provides equipment for preparing samples for single-cell sequencing, as well as Hunter BioDiscovery and SphereBio, companies that employ single-cell analysis for diagnostic and therapeutic applications. D.A.W. and A.K.S. have both filed patents on work that can be used to prepare samples for single-cell sequencing. S.M.P. declares no competing interests.

Corresponding authors

Correspondence to Alex K. Shalek or David A. Weitz.


Spatial encoding

Stratifying analytes (cells or multiple cellular products) by physical confinement on a microfluidic chip.

Spectral encoding

Stratifying analytes (multiple cellular products) using different colours of fluorescence.

Temporal encoding

Stratifying analytes (cells or multiple cellular products) by measuring them sequentially.

Exome sequencing

Selective amplification and sequencing of the protein- coding regions of the genome using exon-specific priming.

Direct deterministic phasing

(DDP). The chromosomes of individual cells are partitioned, isolated and amplified using multiple displacement amplification. The products are then flushed and analysed by molecular haplotyping.


An enzyme that catalyses the movement of a transposable DNA element into another DNA sequence (for example, a genome) by a cut and paste mechanism. A hyperactive variant of the Tn5 transposase is now commonly used to insert adaptor sequences for next-generation sequencing library preparation. If performed on native chromosomes, the transposase can only bind to exposed DNA, revealing accessible DNA regions.

Zero inflation

Owing to inefficiencies in detection, the distribution of counts for several detected genes can be artificially inflated by the abundance of 'zeros' (detection failures) during normalization.

Micrococcal nuclease

(MNase). An endo-exo nuclease derived from Staphylococcus aureus. When applied to single-stranded and double-stranded DNA, MNase will digest all accessible DNA, enabling the study of which DNA regions are occluded with chromatin.

Mass cytometry

Cells are tagged with antibodies that have been labelled with rare earth metal isotopes, nebulized and passed through a quadrapole mass spectrometer for detection. The abundance of a rare earth metal can thus be used as a proxy for the level of the protein in the single cell. Importantly, whereas the number of proteins that can be detected at once with fluorescent labels is limited owing to overlap between emission spectra, mass cytometry can detect tens of proteins in parallel because individual isotopes of rare earth metals have well-defined, non-overlapping masses.

Directed evolution

A technique in which a series of genetic variants is introduced into a cell population, which are then screened with a fitness assay to isolate a desired phenotype. The genetic variants responsible for the greatest fitness are identified by sequencing the surviving cell population for the target gene.

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