气候变化领域集成服务门户(CCPortal): Microbial single-cell RNA sequencing by split-pool barcoding

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DOI	10.1126/science.aba5257
	Microbial single-cell RNA sequencing by split-pool barcoding
	Kuchina A.; Brettner L.M.; Paleologu L.; Roco C.M.; Rosenberg A.B.; Carignano A.; Kibler R.; Hirano M.; DePaolo R.W.; Seelig G.
发表日期	2021
ISSN	0036-8075
卷号	371 期号:6531
英文摘要	Single-cell RNA sequencing (scRNA-seq) has become an essential tool for characterizing gene expression in eukaryotes, but current methods are incompatible with bacteria. Here, we introduce microSPLiT (microbial split-pool ligation transcriptomics), a high-throughput scRNA-seq method for Gram-negative and Gram-positive bacteria that can resolve heterogeneous transcriptional states. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating an atlas of changes in metabolism and lifestyle. We retrieved detailed gene expression profiles associated with known, but rare, states such as competence and prophage induction and also identified unexpected gene expression states, including the heterogeneous activation of a niche metabolic pathway in a subpopulation of cells. MicroSPLiT paves the way to high-throughput analysis of gene expression in bacterial communities that are otherwise not amenable to single-cell analysis, such as natural microbiota. © 2021 American Association for the Advancement of Science. All rights reserved.
英文关键词	bacterium; cell; gene expression; microbial activity; RNA; article; gene expression profiling; Gram positive bacterium; growth curve; high throughput analysis; lifestyle; microbial community; microflora; nonhuman; prophage induction; single cell analysis; single cell RNA seq; transcriptomics; Bacillus phage; Bacillus subtilis; biosynthesis; culture medium; Escherichia coli; fermentation; gene expression regulation; genetic transcription; genetics; gluconeogenesis; glycolysis; growth, development and aging; heat shock response; ion transport; metabolism; movement (physiology); operon; physiological stress; physiology; procedures; virus activation; Bacillus subtilis; Bacteria (microorganisms); Eukaryota; Microbiota; Negibacteria; Posibacteria; antiinfective agent; bacterial RNA; carbon; inositol; metal; transcriptome; Anti-Bacterial Agents; Bacillus Phages; Bacillus subtilis; Carbon; Culture Media; Escherichia coli; Fermentation; Gene Expression Regulation, Bacterial; Gluconeogenesis; Glycolysis; Heat-Shock Response; Inositol; Ion Transport; Metabolic Networks and Pathways; Metals; Movement; Operon; RNA, Bacterial; RNA-Seq; Single-Cell Analysis; Stress, Physiological; Transcription, Genetic; Transcriptome; Virus Activation
语种	英语
来源期刊	Science
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/244411
作者单位	Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, United States; Department of Bioengineering, University of Washington, Seattle, WA, United States; Center for Microbiome Sciences and Therapeutics, School of Medicine, University of Washington, Seattle, WA, United States; Department of Microbiology, University of Washington, Seattle, WA, United States; Department of Biology, University of Washington, Seattle, WA, United States; Biological Physics, Structure, and Design, University of Washington, Seattle, WA, United States; Department of Medicine, Division of Gastroenterology, School of Medicine, University of Washington, Seattle, WA, United States; Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, United States; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, United States
推荐引用方式 GB/T 7714	Kuchina A.,Brettner L.M.,Paleologu L.,et al. Microbial single-cell RNA sequencing by split-pool barcoding[J],2021,371(6531).
APA	Kuchina A..,Brettner L.M..,Paleologu L..,Roco C.M..,Rosenberg A.B..,...&Seelig G..(2021).Microbial single-cell RNA sequencing by split-pool barcoding.Science,371(6531).
MLA	Kuchina A.,et al."Microbial single-cell RNA sequencing by split-pool barcoding".Science 371.6531(2021).