RT Journal Article
SR Electronic
T1 A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycle
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.01.06.895524
DO 10.1101/2020.01.06.895524
A1 Karen Davey
A1 Daniel Wong
A1 Filip Konopacki
A1 Eugene Kwa
A1 Heike Fiegler
A1 Christopher R. Sibley
YR 2020
UL http://biorxiv.org/content/early/2020/01/06/2020.01.06.895524.abstract
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.