气候变化领域集成服务门户(CCPortal): Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states

CCPortal

DOI	10.1073/pnas.2113568118
	Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states
	Isakova A.; Neff N.; Quake S.R.
发表日期	2021
ISSN	0027-8424
卷号	118 期号:51
英文摘要	The ability to interrogate total RNA content of single cells would enable better mapping of the transcriptional logic behind emerging cell types and states. However, current single-cell RNA-sequencing (RNA-seq) methods are unable to simultaneously monitor all forms of RNA transcripts at the single-cell level, and thus deliver only a partial snapshot of the cellular RNAome. Here we describe Smart-seq-total, a method capable of assaying a broad spectrum of coding and noncoding RNA from a single cell. Smart-seq-total does not require splitting the RNA content of a cell and allows the incorporation of unique molecular identifiers into short and long RNA molecules for absolute quantification. It outperforms current poly(A)-independent total RNA-seq protocols by capturing transcripts of a broad size range, thus enabling simultaneous analysis of protein-coding, long-noncoding, microRNA, and other noncoding RNA transcripts from single cells. We used Smart-seq-total to analyze the total RNAome of human primary fibroblasts, HEK293T, and MCF7 cells, as well as that of induced murine embryonic stem cells differentiated into embryoid bodies. By analyzing the coexpression patterns of both noncoding RNA and mRNA from the same cell, we were able to discover new roles of noncoding RNA throughout essential processes, such as cell cycle and lineage commitment during embryonic development. Moreover, we show that independent classes of short-noncoding RNA can be used to determine cell-type identity. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Cell cycle; Differentiation; Noncoding RNA; Single-cell RNA-seq
语种	英语
scopus关键词	histone; RNA; animal; classification; embryonic stem cell; fibroblast; gene expression regulation; genetics; HEK293 cell line; human; MCF-7 cell line; metabolism; mouse; procedures; sequence analysis; single cell analysis; Animals; Embryonic Stem Cells; Fibroblasts; Gene Expression Regulation; HEK293 Cells; Histones; Humans; MCF-7 Cells; Mice; RNA; Sequence Analysis, RNA; Single-Cell Analysis
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/250905
作者单位	Department of Bioengineering, Stanford University, Stanford, CA 94305, United States; Chan Zuckerberg Biohub, San Francisco, CA 94158, United States; Department of Applied Physics, Stanford University, Stanford, CA 94305, United States
推荐引用方式 GB/T 7714	Isakova A.,Neff N.,Quake S.R.. Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states[J],2021,118(51).
APA	Isakova A.,Neff N.,&Quake S.R..(2021).Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states.Proceedings of the National Academy of Sciences of the United States of America,118(51).
MLA	Isakova A.,et al."Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states".Proceedings of the National Academy of Sciences of the United States of America 118.51(2021).