Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing
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s41587-022-01452-6.pdf
Description
Published version
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13.09 MB
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Author(s)
Simmons, Sean K
Lithwick-Yanai, Gila
Adiconis, Xian
Oberstrass, Florian
Iremadze, Nika
Geiger-Schuller, Kathryn
Thakore, Pratiksha I
Frangieh, Chris J
Barad, Omer
Almogy, Gilad
Date Issued
2022
Journal
Nature Biotechnology
Publisher
Springer Science and Business Media LLC
Citation
Simmons, Sean K, Lithwick-Yanai, Gila, Adiconis, Xian, Oberstrass, Florian, Iremadze, Nika et al. 2022. "Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing." Nature Biotechnology.
Version
Final published version
Abstract
AbstractHere we introduce a mostly natural sequencing-by-synthesis (mnSBS) method for single-cell RNA sequencing (scRNA-seq), adapted to the Ultima genomics platform, and systematically benchmark it against current scRNA-seq technology. mnSBS uses mostly natural, unmodified nucleotides and only a low fraction of fluorescently labeled nucleotides, which allows for high polymerase processivity and lower costs. We demonstrate successful application in four scRNA-seq case studies of different technical and biological types, including 5′ and 3′ scRNA-seq, human peripheral blood mononuclear cells from a single individual and in multiplex, as well as Perturb-Seq. Benchmarking shows that results from mnSBS-based scRNA-seq are very similar to those using Illumina sequencing, with minor differences in results related to the position of reads relative to annotated gene boundaries, owing to single-end reads of Ultima being closer to gene ends than reads from Illumina. The method is thus compatible with state-of-the-art scRNA-seq libraries independent of the sequencing technology. We expect mnSBS to be of particular utility for cost-effective large-scale scRNA-seq projects.
MIT Department
Massachusetts Institute of Technology. Department of Biology
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Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1038/S41587-022-01452-6
