A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

Abstract Single cell transcriptome profiling has emerged as a breakthrough technology for the high-resolution understanding of complex cellular systems. Here we report a flexible, cost-effective and user-friendly droplet-based microfluidics system, called the Nadia Instrument, that can allow 3′ mRNA...

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Autores principales:	Karen Davey, Daniel Wong, Filip Konopacki, Eugene Kwa, Tony Ly, Heike Fiegler, Christopher R. Sibley
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/dfa3724a323b417181e7120eaceedce5
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spelling	oai:doaj.org-article:dfa3724a323b417181e7120eaceedce52021-12-02T18:03:27ZA flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle10.1038/s41598-021-86070-z2045-2322https://doaj.org/article/dfa3724a323b417181e7120eaceedce52021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-86070-zhttps://doaj.org/toc/2045-2322Abstract Single cell transcriptome profiling has emerged as a breakthrough technology for the high-resolution understanding of complex cellular systems. Here we report a flexible, cost-effective and user-friendly droplet-based microfluidics system, called the Nadia Instrument, that can allow 3′ mRNA capture of ~ 50,000 single cells or individual nuclei in a single run. The precise pressure-based system demonstrates highly reproducible droplet size, low doublet rates and high mRNA capture efficiencies that compare favorably in the field. Moreover, when combined with the Nadia Innovate, the system can be transformed into an adaptable setup that enables use of different buffers and barcoded bead configurations to facilitate diverse applications. Finally, by 3′ mRNA profiling asynchronous human and mouse cells at different phases of the cell cycle, we demonstrate the system's ability to readily distinguish distinct cell populations and infer underlying transcriptional regulatory networks. Notably this provided supportive evidence for multiple transcription factors that had little or no known link to the cell cycle (e.g. DRAP1, ZKSCAN1 and CEBPZ). In summary, the Nadia platform represents a promising and flexible technology for future transcriptomic studies, and other related applications, at cell resolution.Karen DaveyDaniel WongFilip KonopackiEugene KwaTony LyHeike FieglerChristopher R. SibleyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Karen Davey Daniel Wong Filip Konopacki Eugene Kwa Tony Ly Heike Fiegler Christopher R. Sibley A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
description	Abstract Single cell transcriptome profiling has emerged as a breakthrough technology for the high-resolution understanding of complex cellular systems. Here we report a flexible, cost-effective and user-friendly droplet-based microfluidics system, called the Nadia Instrument, that can allow 3′ mRNA capture of ~ 50,000 single cells or individual nuclei in a single run. The precise pressure-based system demonstrates highly reproducible droplet size, low doublet rates and high mRNA capture efficiencies that compare favorably in the field. Moreover, when combined with the Nadia Innovate, the system can be transformed into an adaptable setup that enables use of different buffers and barcoded bead configurations to facilitate diverse applications. Finally, by 3′ mRNA profiling asynchronous human and mouse cells at different phases of the cell cycle, we demonstrate the system's ability to readily distinguish distinct cell populations and infer underlying transcriptional regulatory networks. Notably this provided supportive evidence for multiple transcription factors that had little or no known link to the cell cycle (e.g. DRAP1, ZKSCAN1 and CEBPZ). In summary, the Nadia platform represents a promising and flexible technology for future transcriptomic studies, and other related applications, at cell resolution.
format	article
author	Karen Davey Daniel Wong Filip Konopacki Eugene Kwa Tony Ly Heike Fiegler Christopher R. Sibley
author_facet	Karen Davey Daniel Wong Filip Konopacki Eugene Kwa Tony Ly Heike Fiegler Christopher R. Sibley
author_sort	Karen Davey
title	A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
title_short	A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
title_full	A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
title_fullStr	A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
title_full_unstemmed	A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
title_sort	flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/dfa3724a323b417181e7120eaceedce5
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A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle

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