Model-based understanding of single-cell CRISPR screening

doi:10.1038/s41467-019-10216-x

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	Model-based understanding of single-cell CRISPR screening
	Duan, Bin 1,2; Zhou, Chi 1; Zhu, Chengyu 1; Yu, Yifei 1; Li, Gaoyang 3,4; Zhang, Shihua5 ; Zhang, Chao 1; Ye, Xiangyun 6; Ma, Hanhui 7; Qu, Shen 1; Zhang, Zhiyuan 8; Wang, Ping 3,4; Sun, Shuyang 8; Liu, Qi 1,2
	2019-05-20
发表期刊	NATURE COMMUNICATIONS
ISSN	2041-1723
卷号	10 页码:11
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.
DOI	10.1038/s41467-019-10216-x
语种	英语
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
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000468274900002
出版者	NATURE PUBLISHING GROUP
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/34712
专题	应用数学研究所
通讯作者	Wang, Ping; Sun, Shuyang; Liu, Qi
作者单位	1.Tongji Univ, Dept Endocrinol & Metab, Shanghai Peoples Hosp 10, Bioinformat Dept,Coll Life Sci, Shanghai, Peoples R China 2.Ninghai First Hosp, Dept Ophthalmol, Ninghai, Zhejiang, Peoples R China 3.Tongji Univ, Shanghai Peoples Hosp 10, Ctr Canc, Shanghai, Peoples R China 4.Tongji Univ, Sch Med, Shanghai, Peoples R China 5.Acad Math & Syst Sci, Inst Appl Math, Beijing, Peoples R China 6.Shanghai Jiao Tong Univ, Shanghai Chest Hosp, Shanghai, Peoples R China 7.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China 8.Shanghai Jiao Tong Univ, Shanghai Peoples Hosp 9, Dept Oral & Maxillofacial Head Neck Oncol, Coll Stomatol,Sch Med, 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.