An Automated Microwell Platform for Large-Scale Single Cell RNA-Seq.
Recent developments have enabled rapid, inexpensive RNA sequencing of thousands of individual cells from a single specimen, raising the possibility of unbiased and comprehensive expression profiling from complex tissues. Microwell arrays are a particularly attractive microfluidic platform for single cell analysis due to their scalability, cell capture efficiency, and compatibility with imaging. We report an automated microwell array platform for single cell RNA-Seq with significantly improved performance over previous implementations. We demonstrate cell capture efficiencies of >50%, compatibility with commercially available barcoded mRNA capture beads, and parallel expression profiling from thousands of individual cells. We evaluate the level of cross-contamination in our platform by both tracking fluorescent cell lysate in sealed microwells and with a human-mouse mixed species RNA-Seq experiment. Finally, we apply our system to comprehensively assess heterogeneity in gene expression of patient-derived glioma neurospheres and uncover subpopulations similar to those observed in human glioma tissue.
Department of Systems Biology, Columbia University Medical Center, New York, NY 10032 USA.
Jinzhou
J
Yuan
Department of Systems Biology, Columbia University Medical Center, New York, NY 10032 USA.|Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, NY 10032 USA.|Department of Biochemistry &Molecular Biophysics, Columbia University Medical Center, New York, NY 10032 USA.
Peter A
PA
Sims
Lab Chip. 2012 Jun 21;12(12):2229-39
22311152
Nat Methods. 2011 Nov 20;9(1):72-4
22101854
Proc Natl Acad Sci U S A. 2014 May 13;111(19):7048-53
24782542
Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1347-52
22232676
Cell Rep. 2012 Sep 27;2(3):666-73
22939981
Nat Methods. 2011 Apr;8(4 Suppl):S6-11
21451510
Nat Biotechnol. 2014 Oct;32(10):1053-8
25086649
Nat Biotechnol. 2006 Jun;24(6):703-7
16699501
Genome Res. 2011 Jul;21(7):1160-7
21543516
Science. 2014 Jun 20;344(6190):1396-401
24925914
Cell. 2015 May 21;161(5):1187-201
26000487
Science. 2015 Feb 6;347(6222):1258367
25657253
Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):4009-14
23412337
Nat Methods. 2014 Feb;11(2):163-6
24363023
Nat Biotechnol. 2011 Nov 13;29(12):1120-7
22081019
Cell. 2015 May 21;161(5):1202-14
26000488
Nat Cell Biol. 2012 Apr 22;14(5):477-87
22522171
PLoS One. 2012;7(3):e33844
22479456
Nat Methods. 2009 May;6(5):377-82
19349980
Oncogene. 2008 Mar 27;27(14):2091-6
17934519
Nat Methods. 2011 Jun 12;8(7):575-80
21666670
Nat Methods. 2014 Jan;11(1):25-7
24524134
Stem Cells. 2009 Apr;27(4):980-7
19353526
Anal Chem. 2006 May 1;78(9):3084-9
16642997
Mol Biol Cell. 2002 Jun;13(6):1977-2000
12058064
PLoS One. 2015 May 22;10(5):e0116328
26000628
Genome Biol. 2015 Jun 06;16:120
26047807
Cancer Cell. 2010 Jan 19;17(1):98-110
20129251
Nat Cell Biol. 2015 Mar;17(3):340-9
25664616