Model-based understanding of single-cell CRISPR screening

doi:10.1038/s41467-019-10216-x

	Model-based understanding of single-cell CRISPR screening
	Duan, Bin 7,8; Zhou, Chi 8; Zhu, Chengyu 8; Yu, Yifei 8; Li, Gaoyang 5,6; Zhang, Shihua 4; Zhang, Chao 8; Ye, Xiangyun 3; Ma, Hanhui 2; Qu, Shen 8
刊名	NATURE COMMUNICATIONS
	2019-05-20
卷号	10 页码:11
ISSN号	2041-1723
DOI	10.1038/s41467-019-10216-x
英文摘要	The recently developed single-cell CRISPR screening techniques, independently termed Perturb-Seq, CRISP-seq, or CROP-seq, combine pooled CRISPR screening with single-cell RNA-seq to investigate functional CRISPR screening in a single-cell granularity. Here, we present MUSIC, an integrated pipeline for model-based understanding of single-cell CRISPR screening data. Comprehensive tests applied to all the publicly available data revealed that MUSIC accurately quantifies and prioritizes the individual gene perturbation effect on cell phenotypes with tolerance for the substantial noise that exists in such data analysis. MUSIC facilitates the single-cell CRISPR screening from three perspectives, i.e., prioritizing the gene perturbation effect as an overall perturbation effect, in a functional topic-specific way, and quantifying the relationships between different perturbations. In summary, MUSIC provides an effective and applicable solution to elucidate perturbation function and biologic circuits by a model-based quantitative analysis of single-cell-based CRISPR screening data.
资助项目	National Key Research and Development Program of China[2017YFC0908500] ; National Key Research and Development Program of China[2016YFC1303205] ; National Natural Science Foundation of China[61572361] ; Shanghai Rising-Star Program[16QA1403900] ; Shanghai Natural Science Foundation Program[17ZR1449400] ; Fundamental Research Funds for the Central Universities
WOS研究方向	Science & Technology - Other Topics
语种	英语
出版者	NATURE PUBLISHING GROUP
WOS记录号	WOS:000468274900002
内容类型	期刊论文
源URL	[http://ir.amss.ac.cn/handle/2S8OKBNM/34711]
专题	中国科学院数学与系统科学研究院
通讯作者	Wang, Ping; Sun, Shuyang; Liu, Qi
作者单位	1.Shanghai Jiao Tong Univ, Shanghai Peoples Hosp 9, Dept Oral & Maxillofacial Head Neck Oncol, Coll Stomatol,Sch Med, Shanghai, Peoples R China 2.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China 3.Shanghai Jiao Tong Univ, Shanghai Chest Hosp, Shanghai, Peoples R China 4.Acad Math & Syst Sci, Inst Appl Math, Beijing, Peoples R China 5.Tongji Univ, Sch Med, Shanghai, Peoples R China 6.Tongji Univ, Shanghai Peoples Hosp 10, Ctr Canc, Shanghai, Peoples R China 7.Ninghai First Hosp, Dept Ophthalmol, Ninghai, Zhejiang, Peoples R China 8.Tongji Univ, Dept Endocrinol & Metab, Shanghai Peoples Hosp 10, Bioinformat Dept,Coll Life Sci, Shanghai, Peoples R China
推荐引用方式 GB/T 7714	Duan, Bin,Zhou, Chi,Zhu, Chengyu,et al. Model-based understanding of single-cell CRISPR screening[J]. NATURE COMMUNICATIONS,2019,10:11.
APA	Duan, Bin.,Zhou, Chi.,Zhu, Chengyu.,Yu, Yifei.,Li, Gaoyang.,...&Liu, Qi.(2019).Model-based understanding of single-cell CRISPR screening.NATURE COMMUNICATIONS,10,11.
MLA	Duan, Bin,et al."Model-based understanding of single-cell CRISPR screening".NATURE COMMUNICATIONS 10(2019):11.