Data analysis guidelines for single-cell RNA-seq in biomedical studies and clinical applications
作者全名："Su, Min; Pan, Tao; Chen, Qiu-Zhen; Zhou, Wei-Wei; Gong, Yi; Xu, Gang; Yan, Huan-Yu; Li, Si; Shi, Qiao-Zhen; Zhang, Ya; He, Xiao; Jiang, Chun-Jie; Fan, Shi-Cai; Li, Xia; Cairns, Murray J.; Wang, Xi; Li, Yong-Sheng"
作者地址："[Su, Min; Chen, Qiu-Zhen; Gong, Yi; Yan, Huan-Yu; Shi, Qiao-Zhen; Wang, Xi] Nanjing Med Univ, State Key Lab Reprod Med, Nanjing 211166, Peoples R China; [Pan, Tao; Xu, Gang; Li, Si; Zhang, Ya; Li, Yong-Sheng] Hainan Med Univ, Affiliated Hosp 1, Coll Biomed Informat & Engn, Haikou 571199, Hainan, Peoples R China; [Zhou, Wei-Wei; Li, Xia] Harbin Med Univ, Coll Bioinformat Sci & Technol, Harbin 150081, Heilongjiang, Peoples R China; [Gong, Yi] Nanjing Med Univ, Dept Immunol, Nanjing 211166, Peoples R China; [He, Xiao] Chongqing Med Univ, Dept Lab Med, Women & Childrens Hosp, Chongqing 401174, Peoples R China; [Jiang, Chun-Jie] Baylor Coll Med, Houston, TX 77030 USA; [Fan, Shi-Cai] Univ Elect Sci & Technol China, Shenzhen Inst Adv Study, Shenzhen 518110, Guangdong, Peoples R China; [Cairns, Murray J.] Univ Newcastle, Fac Hlth & Med, Sch Biomed Sci & Pharm, Univ Dr,, Callaghan, NSW 2308, Australia; [Cairns, Murray J.] Hunter Med Res Inst, Precis Med Res Program, New Lambton Hts, NSW 2305, Australia"
通信作者："Wang, X (通讯作者)，Nanjing Med Univ, State Key Lab Reprod Med, Nanjing 211166, Peoples R China.; Li, YS (通讯作者)，Hainan Med Univ, Affiliated Hosp 1, Coll Biomed Informat & Engn, Haikou 571199, Hainan, Peoples R China.; Li, X (通讯作者)，Harbin Med Univ, Coll Bioinformat Sci & Technol, Harbin 150081, Heilongjiang, Peoples R China.; Cairns, MJ (通讯作者)，Univ Newcastle, Fac Hlth & Med, Sch Biomed Sci & Pharm, Univ Dr,, Callaghan, NSW 2308, Australia.; Cairns, MJ (通讯作者)，Hunter Med Res Inst, Precis Med Res Program, New Lambton Hts, NSW 2305, Australia."
来源：MILITARY MEDICAL RESEARCH
ESI学科分类：CLINICAL MEDICINE
WOS号：WOS:000912673400001
JCR分区：Q1
影响因子：21.1
年份：2022
卷号：9
期号：1
开始页：
结束页：
文献类型：Review
关键词：Single-cell RNA-sequencing (scRNA-seq); Data analysis; Biomedical research; Clinical applications
摘要："The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity for high-throughput scRNA-seq, including clinical samples, the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field. Here, we review the workflow for typical scRNA-seq data analysis, covering raw data processing and quality control, basic data analysis applicable for almost all scRNA-seq data sets, and advanced data analysis that should be tailored to specific scientific questions. While summarizing the current methods for each analysis step, we also provide an online repository of software and wrapped-up scripts to support the implementation. Recommendations and caveats are pointed out for some specific analysis tasks and approaches. We hope this resource will be helpful to researchers engaging with scRNA-seq, in particular for emerging clinical applications."
基金机构："National Key Research and Development Program of China [2022YFC2702502]; National Natural Science Foundation of China [32170742, 31970646, 32060152]; Start Fund for Specially Appointed Professor of Jiangsu Province, Hainan Province Science and Technology Special Fund [ZDYF2021SHFZ051]; Hainan Provincial Natural Science Foundation of China [820MS053]; Start Fund for High-level Talents of Nanjing Medical University [NMUR2020009]; Marshal Initiative Funding of Hainan Medical University [JBGS202103]; Hainan Province Clinical Medical Center [QWYH202175]; Bioinformatics for Major Diseases Science Innovation Group of Hainan Medical University; Shenzhen Science and Technology Program, China [JCYJ20210324140407021]"
基金资助正文："This work was supported by the National Key Research and Development Program of China (2022YFC2702502), the National Natural Science Foundation of China (32170742, 31970646, and 32060152), the Start Fund for Specially Appointed Professor of Jiangsu Province, Hainan Province Science and Technology Special Fund (ZDYF2021SHFZ051), Hainan Provincial Natural Science Foundation of China (820MS053), the Start Fund for High-level Talents of Nanjing Medical University (NMUR2020009), Marshal Initiative Funding of Hainan Medical University (JBGS202103), Hainan Province Clinical Medical Center (QWYH202175), Bioinformatics for Major Diseases Science Innovation Group of Hainan Medical University, and Shenzhen Science and Technology Program, China (JCYJ20210324140407021)."
