Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering

Andres F Vallejo; James Davies; Amit Grover; Ching-Hsuan Tsai; Robert Jepras; Marta E Polak; Jonathan West

doi:10.1016/j.isci.2021.102147

Resolving cellular systems by ultra-sensitive and economical single-cell transcriptome filtering

iScience. 2021 Feb 5;24(3):102147. doi: 10.1016/j.isci.2021.102147. eCollection 2021 Mar 19.

Authors

Andres F Vallejo¹, James Davies¹, Amit Grover², Ching-Hsuan Tsai³, Robert Jepras², Marta E Polak^{1

4}, Jonathan West^{4

5}

Affiliations

¹ Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD Southampton, UK.
² GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK.
³ GlaxoSmithKline, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.
⁴ Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.
⁵ Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.

Abstract

Single-cell transcriptomics suffer from sensitivity limits that restrict low abundance transcript identification, affects clustering and can hamper downstream analyses. Here, we describe Constellation sequencing (Constellation-Seq), a molecular transcriptome filter that delivers two orders of magnitude sensitivity gains by maximizing read utility while reducing the data sparsity and sequencing costs. The technique reliably measures changes in gene expression and was demonstrated by resolving rare dendritic cell populations from a peripheral blood mononuclear cell sample sample and exploring their biology with extreme resolution. The simple and powerful method is fully compatible with standard scRNA-Seq library preparation protocols and can be used for hypothesis testing, marker validation or investigating pathways.

Keywords: Biological Sciences; Omics; Transcriptomics.

Abstract

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