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
2019-05-20
发表期刊NATURE COMMUNICATIONS
ISSN2041-1723
卷号10
发表状态已发表
DOI10.1038/s41467-019-10216-x
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.
收录类别SCI ; SCIE
语种英语
资助项目Shanghai Natural Science Foundation Program[17ZR1449400]
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
WOS关键词WILD-TYPE P53 ; GENOME-WIDE ; C/EBP ; EXPRESSION ; SEQ ; BETA ; TRANSCRIPTOME ; DOXORUBICIN ; CIRCUITS ; PROTEIN
原始文献类型Article
引用统计
文献类型期刊论文
条目标识符https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/40863
专题生命科学与技术学院_PI研究组_马涵慧组
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.
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.
MLA Duan, Bin,et al."Model-based understanding of single-cell CRISPR screening".NATURE COMMUNICATIONS 10(2019).
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