دورية أكاديمية
Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing.
| العنوان: | Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing. |
|---|---|
| المؤلفون: | Simmons SK; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Lithwick-Yanai G; Ultima Genomics, Newark, CA, USA., Adiconis X; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Oberstrass F; Ultima Genomics, Newark, CA, USA., Iremadze N; Ultima Genomics, Newark, CA, USA., Geiger-Schuller K; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Genentech, South San Francisco, CA, USA., Thakore PI; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Genentech, South San Francisco, CA, USA., Frangieh CJ; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA., Barad O; Ultima Genomics, Newark, CA, USA., Almogy G; Ultima Genomics, Newark, CA, USA., Rozenblatt-Rosen O; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Genentech, South San Francisco, CA, USA., Regev A; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Biology, MIT, Cambridge, MA, USA.; Genentech, South San Francisco, CA, USA., Lipson D; Ultima Genomics, Newark, CA, USA., Levin JZ; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA. jlevin@broadinstitute.org.; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. jlevin@broadinstitute.org. |
| المصدر: | Nature biotechnology [Nat Biotechnol] 2023 Feb; Vol. 41 (2), pp. 204-211. Date of Electronic Publication: 2022 Sep 15. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural |
| اللغة: | English |
| بيانات الدورية: | Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: New York Ny : Nature America Publishing Original Publication: New York, NY : Nature Pub. Co., [1996- |
| مواضيع طبية MeSH: | Gene Expression Profiling*/methods , Leukocytes, Mononuclear*, Humans ; Sequence Analysis, RNA/methods ; Single-Cell Gene Expression Analysis ; Single-Cell Analysis/methods ; Nucleotides |
| مستخلص: | Here 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. (© 2022. The Author(s).) |
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| معلومات مُعتمدة: | R44 HG010558 United States HG NHGRI NIH HHS; R44 HG011060 United States HG NHGRI NIH HHS; F32 AI138458 United States AI NIAID NIH HHS; RM1 HG006193 United States HG NHGRI NIH HHS; United States HHMI Howard Hughes Medical Institute |
| المشرفين على المادة: | 0 (Nucleotides) |
| تواريخ الأحداث: | Date Created: 20220915 Date Completed: 20230217 Latest Revision: 20230314 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC9931582 |
| DOI: | 10.1038/s41587-022-01452-6 |
| PMID: | 36109685 |
| قاعدة البيانات: | MEDLINE |
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Full Text Finder | تدمد: | 1546-1696 |
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| DOI: | 10.1038/s41587-022-01452-6 |