Abstract
The isolation of individual cells has gained tremendous importance with the advent of new methods for highly parallel single-cell analysis. A prerequisite for effective clonal cultivation or single-cell analysis is the efficient isolation of individual cells from liquid cell suspensions. This review provides an overview of technologies that are used to automate the isolation of single cells for subsequent cultivation or analysis. First, currently available technologies are classified based on their major technical characteristics. Then, the most prominent technologies such as limiting dilution, FACS, single-cell printing, hydrodynamic trapping, droplet microfluidics, and cell manipulation by external forces are described in detail. Furthermore, the individual features of each technology with focus on throughput, isolation efficiency, level of automation, flexibility in terms of cell types, and their suitability for specific downstream processing and analysis methods are discussed. In contrast to previous works, this review provides a classification approach for single-cell isolation technologies according to performance requirements, makes specific reference to methods for the isolation of microbial cells, and discusses sample input requirements, which is an important aspect in particular for diagnostic purposes.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- CLD:
-
Cell line development
- DEP:
-
Dielectrophoresis
- FACS:
-
Fluorescence-activated cell sorting
- LD:
-
Limiting dilution
- MNC:
-
Mononuclear cells
- OET:
-
Optoelectronic tweezer
- OT:
-
Optical tweezer
- SCD:
-
Single-cell dispensing
References
Abate AR et al (2010) High-throughput injection with microfluidics using picoinjectors. Proc Natl Acad Sci USA 107(45):19163–19166. Available at http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2984161&tool=pmcentrez&rendertype=abstract. Accessed 2 Dec 2014
Agresti JJ et al (2010) Ultrahigh-throughput screening in drop-based microfluidics for directed evolution. Proc Natl Acad Sci USA 107:4004–4009
Anis YH, Holl MR, Meldrum DR (2010) Automated selection and placement of single cells using vision-based feedback control. IEEE Trans Autom Sci Eng 7(3):598–606
Ashkin A, Dziedzic JM, Yamane T (1987) Optical trapping and manipulation of single cells using infrared laser beams. Nature 330(6150):769–771
Chabert M, Viovy J-L (2008) Microfluidic high-throughput encapsulation and hydrodynamic self-sorting of single cells. Proc Natl Acad Sci USA 105(9):3191–3196. Available at http://www.ncbi.nlm.nih.gov/pubmed/18316742
Chiou PY, Ohta AT, Wu MC (2005) Massively parallel manipulation of single cells and microparticles using optical images. Nature 436(7049):370–372
Di Carlo D, Wu LY, Lee LP (2006) Dynamic single cell culture array. Lab Chip 6(11):1445. Available at http://xlink.rsc.org/?DOI=b605937f
Duffy DC et al (1998) Rapid prototyping of microfluidic systems in poly(dimethylsiloxane). Anal Chem 70(23):4974–4984
Elder D (2017) ICH Q6A Specifications: test procedures and acceptance criteria for new drug substances and new drug products: chemical substances. ICH Quality Guidelines: An Implementation Guide, 433–466
European Medicines Agency (2016) Guideline on development, production, characterisation and specification for monoclonal antibodies and related products. EMA/CHMP/BWP/532517/2008. Available at http://www.ema.europa.eu/docs/en_GB/document_library/Scientific_guideline/2016/08/WC500211640.pdf
Evans K et al (2015) Assurance of monoclonality in one round of cloning through cell sorting for single cell deposition coupled with high resolution cell imaging. Biotechnol Prog 31(5):1172–1178
Fieder J, Schulz P, Gorr I, Bradl H, Wenger T (2017) A single-step FACS sorting strategy in conjunction with fluorescent vital dye imaging efficiently assures clonality of biopharmaceutical production cell lines. Biotechnology journal 12(6):1700002
Freshney RI (2015) Culture of animal cells: a manual of basic technique and specialized applications. John Wiley & Sons
Fröhlich J, König H (2000) New techniques for isolation of single prokaryotic cells. FEMS Microbiol Rev 24(5):567–572
Gagnon ZR (2011) Cellular dielectrophoresis: applications to the characterization, manipulation, separation and patterning of cells. Electrophoresis 32(18):2466–2487
Gawad C, Koh W, Quake SR (2016) Single-cell genome sequencing: current state of the science. Nat Rev Genet 17:175. Available at http://www.nature.com/doifinder/10.1038/nrg.2015.16
Gierahn TM et al (2017) Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Nat Methods 14(4):395–398
Goding JW (1980) Antibody production by hybridomas. J Immunol Methods 39(4):285–308
Gross A et al (2013) Single-cell printer: automated, on demand, and label free. J Lab Autom 18:504–518. Available at http://jla.sagepub.com/lookup/doi/10.1177/2211068213497204
Gross A et al (2015) Technologies for single-cell isolation. Int J Mol Sci 16(8):16897–16919
Grün D, van Oudenaarden A (2015) Design and analysis of single-cell sequencing experiments. Cell 163(4):799–810. Available at http://linkinghub.elsevier.com/retrieve/pii/S0092867415013537
Guo MT et al (2012) Droplet microfluidics for high-throughput biological assays. Lab Chip 12:2146
Gustavsson AK et al (2012) Sustained glycolytic oscillations in individual isolated yeast cells. FEBS J 279:2837–2847
Hawksworth DL, Lücking R (2017) Fungal diversity revisited: 2.2 to 3.8 million species. Microbiol Spectr 5(4). Available at http://www.asmscience.org/content/journal/microbiolspec/10.1128/microbiolspec.FUNK-0052-2016
He M et al (2005) Selective encapsulation of single cells and subcellular organelles into picoliter- and femtoliter-volume droplets. Anal Chem 77(6):1539–1544
Hu H, Eustace D, Merten CA (2015) Efficient cell pairing in droplets using dual-color sorting. Lab Chip 15(20):3989–3993. Available at http://xlink.rsc.org/?DOI=C5LC00686D
Hughes MP (2002) Strategies for dielectrophoretic separation in laboratory-on-a-chip systems. Electrophoresis 23:2569–2582. Review
Hümmer D et al (2015) Single cells in confined volumes: microchambers and microdroplets. Lab Chip 16:447–458. Available at http://pubs.rsc.org/en/content/articlehtml/2015/lc/c5lc01314c
Hymer WC, Kuff EL (1964) Isolation of nuclei from mammalian tissues through the use of Triton X-100. J Histochem Cytochem 12(5):359
Joensson HN, Andersson Svahn H (2012) Droplet microfluidics-a tool for single-cell analysis. Angew Chem Int Ed 51:12176–12192
Johansen PL et al (2016) Optical micromanipulation of nanoparticles and cells inside living zebrafish. Nat Commun 7:1–8. https://doi.org/10.1038/ncomms10974
Kemna EWM et al (2012) High-yield cell ordering and deterministic cell-in-droplet encapsulation using Dean flow in a curved microchannel. Lab Chip 12(16):2881
Kemna EW, Segerink LI, Wolbers F, Vermes I, van den Berg A (2013) Label-free, high-throughput, electrical detection of cells in droplets. Analyst, 138(16):4585–459
Kim J et al (2014) A high-efficiency microfluidic device for size-selective trapping and sorting. Lab Chip 14(14):2480–2490. Available at http://xlink.rsc.org/?DOI=C4LC00219A
Klein AM et al (2015) Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 161(5):1187–1201. Available at http://linkinghub.elsevier.com/retrieve/pii/S0092867415005000
Kumano I et al (2012) Hydrodynamic trapping of Tetrahymena thermophila for the long-term monitoring of cell behaviors. Lab Chip 12(18):3451. Available at http://xlink.rsc.org/?DOI=c2lc40367f
Lake BB et al (2017) A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. Sci Rep 7(1):1–8. https://doi.org/10.1038/s41598-017-04426-w
Landenberger B et al (2012) Microfluidic sorting of arbitrary cells with dynamic optical tweezers. Lab Chip 12(17):3177. Available at http://xlink.rsc.org/?DOI=c2lc21099a
Landry ZC, Giovanonni SJ, Quake SR, Blainey PC (2013) Optofluidic cell selection from complex microbial communities for single-genome analysis. In Methods in enzymology (Vol. 531, pp. 61–90). Academic Press
Leung ML et al (2015) SNES: single nucleus exome sequencing. Genome Biol 16(1):55. Available at http://genomebiology.com/2015/16/1/55
Levin PA, Angert ER (2015) Small but mighty: cell size and bacteria. Cold Spring Harb Perspect Biol 7(7):a019216
Macosko EZ et al (2015) Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161(5):1202–1214. Available at http://www.sciencedirect.com/science/article/pii/S0092867415005498
Manaresi N et al (2003) A CMOS chip for individual cell manipulation and detection. IEEE J Solid State Circuits 38(12):2297–2305
Mazutis L et al (2013) Single-cell analysis and sorting using droplet-based microfluidics. Nat Protoc 8(5):870–891. Available at http://www.ncbi.nlm.nih.gov/pubmed/23558786. Accessed 13 July 2014
Mishra A et al (2014) Optoelectrical microfluidics as a promising tool in biology. Trends Biotechnol 32(8):414–421. https://doi.org/10.1016/j.tibtech.2014.06.002
Müller S, Nebe-Von-Caron G (2010) Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities. FEMS Microbiol Rev 34(4):554–587
Narayanamurthy V et al (2017) Microfluidic hydrodynamic trapping for single cell analysis: mechanisms, methods and applications. Anal Methods 9(25):3751–3772. Available at http://xlink.rsc.org/?DOI=C7AY00656J
Neuman KC et al (1999) Characterization of photodamage to Escherichia coli in optical traps. Biophys J 77(5):2856–2863. https://doi.org/10.1016/S0006-3495(99)77117-1
Palermo GD et al (1995) Intracytoplasmic sperm injection: a novel treatment for all forms of male factor infertility. Fertil Steril 63(6):1231–1240. https://doi.org/10.1016/S0015-0282(16)57603-1
Park MC et al (2011) High-throughput single-cell quantification using simple microwell-based cell docking and programmable time-course live-cell imaging. Lab Chip 11(1):79–86. Available at http://xlink.rsc.org/?DOI=C0LC00114G
Peterman EJG, Gittes F, Schmidt CF (2003) Laser-induced heating in optical traps. Biophys J 84(2):1308–1316. https://doi.org/10.1016/S0006-3495(03)74946-7
Picot J, Guerin CL, Le Van Kim C, Boulanger CM (2012) Flow cytometry: retrospective, fundamentals and recent instrumentation. Cytotechnology 64(2):109–130
Prakadan SM, Shalek AK, Weitz DA (2017) Scaling by shrinking: empowering single-cell “omics” with microfluidic devices. Nat Rev Genet 18(6):345–361
Riba J et al (2016) Label-free isolation and deposition of single bacterial cells from heterogeneous samples for clonal culturing. Sci Rep 6(August):32837. Available at http://www.nature.com/articles/srep32837
Rinke C et al (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499(7459):431–437. Available at http://www.ncbi.nlm.nih.gov/pubmed/23851394
Rinke C et al (2014) Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics. Nat Protoc 9(5):1038–1048. Available at http://www.ncbi.nlm.nih.gov/pubmed/24722403. Accessed 30 Jan 2015
Schoendube J et al (2015) Single-cell printing based on impedance detection. Biomicrofluidics 9:14117. https://doi.org/10.1063/1.4907896
Shaw D, Yim M, Tsukuda J, Joly JC, Lin A, Snedecor B, Laird MW, Lang SE (2018) Development and characterization of an automated imaging workflow to generate clonally-derived cell lines for therapeutic proteins. Biotechnol Progress 34:584–592. https://doi.org/10.1002/btpr.2561
Szulwach KE et al (2015) Single-cell genetic analysis using automated microfluidics to resolve somatic mosaicism. PLoS One 10(8):e0135007. Available at http://plos.org/10.1371/journal.pone.0135007
Tan W-H, Takeuchi S (2007) A trap-and-release integrated microfluidic system for dynamic microarray applications. Proc Natl Acad Sci 104(4):1146–1151. Available at http://www.pnas.org/cgi/doi/10.1073/pnas.0606625104
Thorsen T, Maerkl SJ, Quake SR (2002) Microfluidic large-scale integration. Science 298(5593):580–584
Tornay R et al (2007) Electrical detection and ejection of beads in a one-cell-per-drop microdispenser. In: TRANSDUCERS and EUROSENSORS ’07 – 4th international conference on solid-state sensors, actuators and microsystems, (Figure 2), pp 695–698
Tsao CW (2016) Polymer microfluidics: simple, low-cost fabrication process bridging academic lab research to commercialized production. Micromachines 7(12):225
Ungai-Salánki R et al (2016) Automated single cell isolation from suspension with computer vision. Sci Rep 6(February):1–9. https://doi.org/10.1038/srep20375
Unger MA (2000) Monolithic microfabricated valves and pumps by multilayer soft lithography. Science 288(5463):113–116. Available at http://www.sciencemag.org/cgi/doi/10.1126/science.288.5463.113
Voldman J (2006) Electrical forces for microscale cell manipulation. Annu Rev Biomed Eng 8, 425–454
Yamaguchi S, Ueno A, Akiyama Y, Morishima K (2012) Cell patterning through inkjet printing of one cell per droplet. Biofabrication 4(4):045005
Yusof A et al (2011) Inkjet-like printing of single-cells. Lab Chip 11(14):2447–2454. Available at http://www.ncbi.nlm.nih.gov/pubmed/21655638. Accessed 26 Sept 2014
Zhou Y, Shaw D, Lam C, Tsukuda J, Yim M, Tang D, Misaghi S (2018) Beating the odds: the poisson distribution of all input cells during limiting dilution grossly underestimates whether a cell line is clonally-derived or not. Biotechnology progress 34(3):559–569
Zhu P, Wang L (2017) Passive and active droplet generation with microfluidics: a review. Lab on a Chip 17(1):34–75
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Nature Singapore Pte Ltd
About this entry
Cite this entry
Riba, J., Zimmermann, S., Koltay, P. (2018). Technologies for Automated Single Cell Isolation. In: Santra, T., Tseng, FG. (eds) Handbook of Single Cell Technologies. Springer, Singapore. https://doi.org/10.1007/978-981-10-4857-9_9-1
Download citation
DOI: https://doi.org/10.1007/978-981-10-4857-9_9-1
Received:
Accepted:
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-10-4857-9
Online ISBN: 978-981-10-4857-9
eBook Packages: Springer Reference EngineeringReference Module Computer Science and Engineering