CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins

doi:10.1016/j.csbj.2022.07.026

	CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins
	Mei, Hong1 ; Gu, Qian1,2,3 ; Wang, Wei1 ; Meng, Yu1,2,3 ; Jiang, Lichun1 ; Liu, Jia1,2,3,4,5
	2022-01
发表期刊	COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (IF:4.4[JCR-2023],5.0[5-Year])
ISSN	2001-0370
EISSN	2001-0370
卷号	20 页码:3833-3838
发表状态	已发表
DOI	10.1016/j.csbj.2022.07.026
摘要	CRISPR-based genome-editing tools have emerged as an efficient tool for functional genomics studies. Online tools and databases have been developed to facilitate the design and selection of CRISPR single guide RNA (sgRNA) for gene modifications. However, to the best of our knowledge, none of these tools or database are designated to cell surface proteins. In a previous study, we described the development and application of surfaceome CRISPR libraries targeting to cell surface proteins on human cells. Here, we present the design and construction of an online tool and database (https://crispr-surfaceome.siais.shanghaitech.edu.cn/home), named CRISPR-Surfaceome, for the design of highly efficient sgRNA targeting to the surface proteins on human cells. To show case and validate the efficiencies of sgRNAs designed by this online tool, we chose ICAM-1 gene for knockout studies and found that all the 10 designed ICAM-1 sgRNAs could efficiently generate knockout cells, with more than 80% gene disruption rates. These ICAM-1 knockout cells were found to be resistant to the infection of rhinovirus (RV), which utilizes ICAM-1 as the receptor. Therefore, CRISPR-Surfaceome can serve the research community for the functional genomics studies on cell surface proteins, such as identification of pathogen receptors and discovery of drug targets. © 2022 The Authors
关键词	Cell membranes Cytology Database systems Proteins Cell surface proteins CRISPR Editing tools Functional genomics Genomic studies Human cells On-line tools Online database Single guide RNA Surfaceome
URL	查看原文
收录类别	SCI ; EI ; SCIE
语种	英语
资助项目	Shang-haiTech University[JYJC202126] ; ShanghaiTech University Startup Fund[2019F0301-000-01] ; China Postdoctoral Science Foundation[2017M621551]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS类目	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS记录号	WOS:000855026500003
出版者	Elsevier B.V.
EI入藏号	20223012420425
EI主题词	Genes
EI分类号	461.2 Biological Materials and Tissue Engineering ; 461.9 Biology ; 723.3 Database Systems ; 804.1 Organic Compounds
原始文献类型	Journal article (JA)
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/211715
专题	免疫化学研究所_PI研究组_刘佳组生命科学与技术学院_硕士生免疫化学研究所_公共科研平台_生物医学大数据平台
通讯作者	Jiang, Lichun; Liu, Jia
作者单位	1.ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai 201210, Peoples R China 2.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Shanghai Clin Res & Trial Ctr, Shanghai 201210, Peoples R China 5.ShanghaiTech Univ, Gene Editing Ctr, Sch Life Sci & Technol, Shanghai 201210, Peoples R China
第一作者单位	免疫化学研究所
通讯作者单位	免疫化学研究所; 生命科学与技术学院
第一作者的第一单位	免疫化学研究所
推荐引用方式 GB/T 7714	Mei, Hong,Gu, Qian,Wang, Wei,et al. CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins[J]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,2022,20:3833-3838.
APA	Mei, Hong,Gu, Qian,Wang, Wei,Meng, Yu,Jiang, Lichun,&Liu, Jia.(2022).CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins.COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,20,3833-3838.
MLA	Mei, Hong,et al."CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins".COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 20(2022):3833-3838.