Model-based understanding of single-cell CRISPR screening
Duan, Bin1,2; Zhou, Chi1; Zhu, Chengyu1; Yu, Yifei1; Li, Gaoyang3,4; Zhang, Shihua5; Zhang, Chao1; Ye, Xiangyun6; Ma, Hanhui7; Qu, Shen1; Zhang, Zhiyuan8; Wang, Ping3,4; Sun, Shuyang8; Liu, Qi1,2
AbstractThe 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.
Funding ProjectNational 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 Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000468274900002
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Document Type期刊论文
Corresponding AuthorWang, Ping; Sun, Shuyang; Liu, Qi
Affiliation1.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
Recommended Citation
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.
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