Virtual microfluidics for digital quantification and single-cell sequencing

Nature Methods

Volumn 13, Issue 9, 2016, Pages 759-762

  Xu, Liyi ^a,b   Brito, Ilana L ^a,b   Alm, Eric J ^a,b   Blainey, Paul C ^a,b  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL CELL; BACTERIAL GENOME; BACTERIUM CULTURE; CHIMERA; DIGITAL MULTIPLE DISPLACEMENT AMPLIFICATION; DNA TEMPLATE; GENE AMPLIFICATION; GENE SEQUENCE; HUMAN; HYDROGEL; MICROBIOME; MICROFLUIDICS; NONHUMAN; NUCLEIC ACID AMPLIFICATION; PRIORITY JOURNAL; SINGLE CELL ANALYSIS; CHEMISTRY; COMPUTER INTERFACE; DNA CONTAMINATION; DNA SEQUENCE; ESCHERICHIA COLI; FLUORESCENCE MICROSCOPY; GENETICS; HIGH THROUGHPUT SEQUENCING; INFORMATION PROCESSING; PROCEDURES; STAPHYLOCOCCUS AUREUS; WORKFLOW;

HYDROGEL;

AUTOMATIC DATA PROCESSING; DNA CONTAMINATION; ESCHERICHIA COLI; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HYDROGELS; MICROFLUIDICS; MICROSCOPY, FLUORESCENCE; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SEQUENCE ANALYSIS, DNA; SINGLE-CELL ANALYSIS; STAPHYLOCOCCUS AUREUS; USER-COMPUTER INTERFACE; WORKFLOW;

EID: 84980398168     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3955     Document Type: Article

References (35)

1. Blainey, P.C. & Quake, S.R. Nat. Methods 11, 19-21 (2014).
2. Marshall, I.P.G., Blainey, P.C., Spormann, A.M. & Quake, S.R.A. Appl. Environ. Microbiol. 78, 8555-8563 (2012).
3. Wang, J., Fan, H.C., Behr, B. & Quake, S.R. Cell 150, 402-412 (2012).
4. Huggett, J.F., Cowen, S. & Foy, C.A. Clin. Chem. 61, 79-88 (2015).
5. Sykes, P.J. et al. Biotechniques 13, 444-449 (1992).
6. Vogelstein, B. & Kinzler, K.W. Proc. Natl. Acad. Sci. USA 96, 9236-9241 (1999).
7. Blainey, P.C. & Quake, S.R. Nucleic Acids Res. 39, e19 (2011).
8. Raghunathan, A. et al. Appl. Environ. Microbiol. 71, 3342-3347 (2005).
9. Zhang, K. et al. Nat. Biotechnol. 24, 680-686 (2006).
10. Fu, Y. et al. Proc. Natl. Acad. Sci. USA 112, 11923-11928 (2015).
11. Pamp, S.J., Harrington, E.D., Quake, S.R., Relman, D.A. & Blainey, P.C. Genome Res. 22, 1107-1119 (2012).
12. Dodsworth, J.A. et al. Nat. Comm. 4, 1854 (2013).
13. Hess, M. et al. Science 331, 463-467 (2011).
14. Love, K.R., Bagh, S., Choi, J. & Love, J.C. Trends Biotechnol. 31, 280-286 (2013).
15. Thorsen, T., Maerkl, S.J. & Quake, S.R. Science 298, 580-584 (2002).
16. Landry, Z.C., Giovanonni, S.J., Quake, S.R. & Blainey, P.C. Methods Enzymol. 531, 61-90 (2013).
17. de Bourcy, C.F.A. et al. PLoS ONE 9, e105585 (2014).
18. Marcy, Y. et al. PLoS Genet. 3, 1702-1708 (2007).
19. Thorsen, T., Roberts, R.W., Arnold, F.H. & Quake, S.R. Phys. Rev. Lett. 86, 4163-4166 (2001).
20. Mazutis, L. et al. Nat. Protoc. 8, 870-891 (2013).
21. Hindson, C.M. et al. Nat. Methods 10, 1003-1005 (2013).
22. Morinishi, L.S. & Blainey, P. J. Vis. Exp. 103, e52925 (2015).
23. Blainey, P.C. FEMS Microbiol. Rev. 37, 407-427 (2013).
24. Podar, M., Keller, M. & Hugenholtz, P. in Uncultivated Microorganisms, Vol. 10 (ed. Epstein, S.S.) 241-256 (Springer, Berlin Heidelberg, 2009).
25. Mitra, R.D. & Church, G.M. Nucleic Acids Res. 27, e34 (1999).
26. Allen, L.Z. et al. PLoS ONE 6, e17722 (2011).
27. Raeber, G.P., Lutolf, M.P. & Hubbell, J.A. Biophys. J. 89, 1374-1388 (2005).
28. Wu, Y., Joseph, S. & Aluru, N.R. J. Phys. Chem. B 113, 3512-3520 (2009).
29. Phelps, E.A. et al. Adv. Mater. 24, 64-70 (2011).
30. Dean, F.B. et al. Proc. Natl. Acad. Sci. USA 99, 5261-5266 (2002).
31. Marcy, Y. et al. Proc. Natl. Acad. Sci. USA 104, 11889-11894 (2007).
32. Woyke, T. et al. PLoS ONE 6, e26161 (2011).
33. Lasken, R.S. & Stockwell, T.B. BMC Biotechnol. 7, 19 (2007).
34. Segata, N. et al. Nat. Methods 9, 811-814 (2012).
35. Wu, M. & Scott, A.J. Bioinformatics 28, 1033-1034 (2012).