气候变化领域集成服务门户(CCPortal): HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes

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DOI	10.1073/PNAS.2010738117
	HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes
	Marshall J.L.; Doughty B.R.; Subramanian V.; Guckelberger P.; Wang Q.; Chen L.M.; Rodriques S.G.; Zhang K.; Fulco C.P.; Nasser J.; Grinkevich E.J.; Noel T.; Mangiameli S.; Bergman D.T.; Greka A.; Lander E.S.; Chen F.; Engreitz J.M.
发表日期	2021
ISSN	00278424
起始页码	33404
结束页码	33413
卷号	117 期号:52
英文摘要	Single-cell quantification of RNAs is important for understanding cellular heterogeneity and gene regulation, yet current approaches suffer from low sensitivity for individual transcripts, limiting their utility for many applications. Here we present Hybridization of Probes to RNA for sequencing (HyPR-seq), a method to sensitively quantify the expression of hundreds of chosen genes in single cells. HyPR-seq involves hybridizing DNA probes to RNA, distributing cells into nanoliter droplets, amplifying the probes with PCR, and sequencing the amplicons to quantify the expression of chosen genes. HyPR-seq achieves high sensitivity for individual transcripts, detects nonpolyadenylated and low-abundance transcripts, and can profile more than 100,000 single cells. We demonstrate how HyPR-seq can profile the effects of CRISPR perturbations in pooled screens, detect time-resolved changes in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-type frequencies in tissue using low-abundance marker genes. By directing sequencing power to genes of interest and sensitively quantifying individual transcripts, HyPR-seq reduces costs by up to 100-fold compared to whole-transcriptome single-cell RNA-sequencing, making HyPR-seq a powerful method for targeted RNA profiling in single cells. © 2020 National Academy of Sciences. All rights reserved.
英文关键词	Enhancers; Gene regulation; Genomics; Single cell
语种	英语
scopus关键词	messenger RNA; RNA; animal; CRISPR Cas system; cytology; DNA probe; gene expression; genetics; high throughput sequencing; human; intron; K-562 cell line; kidney; metabolism; mouse; nucleic acid hybridization; polyadenylation; procedures; single cell analysis; THP-1 cell line; time factor; Animals; CRISPR-Cas Systems; DNA Probes; Gene Expression; High-Throughput Nucleotide Sequencing; Humans; Introns; K562 Cells; Kidney; Mice; Nucleic Acid Hybridization; Polyadenylation; RNA; RNA, Messenger; Single-Cell Analysis; THP-1 Cells; Time Factors
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/179676
作者单位	Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States; Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, 14195, Germany; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, United States; Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA 02115, United States; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, United States; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, United States; Basic Science and Engineering Initiative,...
推荐引用方式 GB/T 7714	Marshall J.L.,Doughty B.R.,Subramanian V.,et al. HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes[J],2021,117(52).
APA	Marshall J.L..,Doughty B.R..,Subramanian V..,Guckelberger P..,Wang Q..,...&Engreitz J.M..(2021).HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes.Proceedings of the National Academy of Sciences of the United States of America,117(52).
MLA	Marshall J.L.,et al."HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes".Proceedings of the National Academy of Sciences of the United States of America 117.52(2021).