PT  - JOURNAL ARTICLE
AU  - Karen Davey
AU  - Daniel Wong
AU  - Filip Konopacki
AU  - Eugene Kwa
AU  - Heike Fiegler
AU  - Christopher R. Sibley
TI  - A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
AID  - 10.1101/2020.01.06.895524
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.01.06.895524
4099  - http://biorxiv.org/content/early/2020/01/06/2020.01.06.895524.short
4100  - http://biorxiv.org/content/early/2020/01/06/2020.01.06.895524.full
AB  - 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.