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

Karen Davey, Daniel Wong, Filip Konopacki, Eugene Kwa, Heike Fiegler, View ORCID ProfileChristopher R. Sibley
doi: https://doi.org/10.1101/2020.01.06.895524
Karen Davey
1Department of Medicine, Division of Brain Sciences, Imperial College London, Burlington Danes, London, United Kingdom
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Daniel Wong
2Dolomite Bio, Unit 3, Anglian Business Park, Royston, United Kingdom
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Filip Konopacki
2Dolomite Bio, Unit 3, Anglian Business Park, Royston, United Kingdom
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Eugene Kwa
1Department of Medicine, Division of Brain Sciences, Imperial College London, Burlington Danes, London, United Kingdom
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Heike Fiegler
2Dolomite Bio, Unit 3, Anglian Business Park, Royston, United Kingdom
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Christopher R. Sibley
1Department of Medicine, Division of Brain Sciences, Imperial College London, Burlington Danes, London, United Kingdom
3Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, 1 George Square, Edinburgh University, EH8 9JZ, United Kingdom
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  • ORCID record for Christopher R. Sibley
  • For correspondence: chris.sibley@ed.ac.uk
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Summary

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 identified 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 06, 2020.
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A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
Karen Davey, Daniel Wong, Filip Konopacki, Eugene Kwa, Heike Fiegler, Christopher R. Sibley
bioRxiv 2020.01.06.895524; doi: https://doi.org/10.1101/2020.01.06.895524
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A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
Karen Davey, Daniel Wong, Filip Konopacki, Eugene Kwa, Heike Fiegler, Christopher R. Sibley
bioRxiv 2020.01.06.895524; doi: https://doi.org/10.1101/2020.01.06.895524

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