PT  - JOURNAL ARTICLE
AU  - Jack Harrington
AU  - Luis Blay Esteban
AU  - Jonathan Butement
AU  - Andres F. Vallejo
AU  - Simon I. R. Lane
AU  - Bhavwanti Sheth
AU  - Maaike S. A. Jongen
AU  - Rachel Parker
AU  - Patrick S. Stumpf
AU  - Rosanna C. G. Smith
AU  - Ben D. MacArthur
AU  - Matthew J. J. Rose-Zerilli
AU  - Marta E. Polak
AU  - Tim Underwood
AU  - Jonathan West
TI  - Dual Dean entrainment with volume ratio modulation for efficient co-encapsulation: Extreme single-cell indexing
AID  - 10.1101/2021.04.08.439026
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.04.08.439026
4099  - http://biorxiv.org/content/early/2021/04/09/2021.04.08.439026.short
4100  - http://biorxiv.org/content/early/2021/04/09/2021.04.08.439026.full
AB  - The future of single cell diversity screens involves ever-larger sample sizes, dictating the need for higher throughput methods with low analytical noise to accurately describe the nature of the cellular system. Current approaches are limited by the Poisson statistic, requiring dilute cell suspensions and associated losses in throughput. In this contribution, we apply Dean entrainment to both cell and bead inputs, defining different volume packets to effect efficient co-encapsulation. Volume ratio scaling was explored to identify optimal conditions. This enabled the co-encapsulation of single cells with reporter beads at rates of ~1 million cells/hour, while increasing assay signal-to-noise with cell multiplet rates of ~2.5% and capturing ~70% of cells. The method, called Pirouette-seq, extends our capacity to investigate biological systems.TOC Abstract Pirouette-seq involves cell and reporter bead inertial ordering for efficient co-encapsulation, achieving a throughput of 1 million cells/hour, a 2.5% multiplet rate and a 70% cell capture efficiency.Competing Interest StatementThe authors have declared no competing interest.