spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content

Joachim Jonghe, Tomasz S. Kaminski, David B. Morse, Marcin Tabaka, Anna L. Ellermann, Timo N. Kohler, Gianluca Amadei, Charlotte E. Handford, Gregory M. Findlay, Magdalena Zernicka-Goetz, Sarah A. Teichmann and Florian Hollfelder ()
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Joachim Jonghe: University of Cambridge
Tomasz S. Kaminski: University of Cambridge
David B. Morse: University of Cambridge
Marcin Tabaka: International Centre for Translational Eye Research
Anna L. Ellermann: University of Cambridge
Timo N. Kohler: University of Cambridge
Gianluca Amadei: University of Cambridge
Charlotte E. Handford: University of Cambridge
Gregory M. Findlay: Francis Crick Institute
Magdalena Zernicka-Goetz: University of Cambridge
Sarah A. Teichmann: Wellcome Sanger Institute, Wellcome Genome Campus
Florian Hollfelder: University of Cambridge

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: Abstract Droplet microfluidic methods have massively increased the throughput of single-cell sequencing campaigns. The benefit of scale-up is, however, accompanied by increased background noise when processing challenging samples and the overall RNA capture efficiency is lower. These drawbacks stem from the lack of strategies to enrich for high-quality material or specific cell types at the moment of cell encapsulation and the absence of implementable multi-step enzymatic processes that increase capture. Here we alleviate both bottlenecks using fluorescence-activated droplet sorting to enrich for droplets that contain single viable cells, intact nuclei, fixed cells or target cell types and use reagent addition to droplets by picoinjection to perform multi-step lysis and reverse transcription. Our methodology increases gene detection rates fivefold, while reducing background noise by up to half. We harness these properties to deliver a high-quality molecular atlas of mouse brain development, despite starting with highly damaged input material, and provide an atlas of nascent RNA transcription during mouse organogenesis. Our method is broadly applicable to other droplet-based workflows to deliver sensitive and accurate single-cell profiling at a reduced cost.

Date: 2023
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DOI: 10.1038/s41467-023-40322-w

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