Increasing efficiency, throughput and purity of Drop-seq through detection and sorting of correctly configured droplets

Patricia Schwilling; Jonas Pfeil; Marc Güttler; Othmar Marti

doi:10.1117/12.3000349

12 March 2024 Increasing efficiency, throughput and purity of Drop-seq through detection and sorting of correctly configured droplets

Patricia Schwilling, Jonas Pfeil, Marc Güttler, Othmar Marti

Author Affiliations +

Proceedings Volume 12853, High-Speed Biomedical Imaging and Spectroscopy IX; 128530B (2024) https://doi.org/10.1117/12.3000349
Event: SPIE BiOS, 2024, San Francisco, California, United States

Conference Poster

Abstract

Drop-seq was first published in 2015, posing a revolution in single-cell RNA sequencing with an open-source, cost-effective, high-throughput analysis of gene transcripts. In this method, a highly diluted suspension of cells and barcoded beads is encapsulated in a water-in-oil droplet following double-Poisson statistics, aiming for a maximum encapsulation rate of one cell together with one bead, while keeping erroneous encapsulations of multiple cells or multiple beads together with one or more beads or cells, respectively, at a minimum. This decreases the efficiency and increases the cost per cell as more reagents are used. In this work, we present an approach to increase the number of desired encapsulation events, while decreasing erroneous encapsulations. Therefore, we use a special microfluidic analysis device in combination with a custom-made dielectrophoretic (DEP) sorting microchannel, enabling the detection and elimination of erroneous bead encapsulations, providing the opportunity to increase the concentration of beads to increase the number of desired encapsulation events (1 bead + 1 cell) considerably, while decreasing relevant erroneously encapsulations.

(2024) Published by SPIE. Downloading of the abstract is permitted for personal use only.

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Patricia Schwilling, Jonas Pfeil, Marc Güttler, and Othmar Marti "Increasing efficiency, throughput and purity of Drop-seq through detection and sorting of correctly configured droplets", Proc. SPIE 12853, High-Speed Biomedical Imaging and Spectroscopy IX, 128530B (12 March 2024); https://doi.org/10.1117/12.3000349

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