Tongji University School of Medicine 7 articles published in JoVE Cancer Research Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2 Shiyi Liu*1, Zitao Wang*1, Ronghui Zhu1, Feiyan Wang2, Yanxiang Cheng1, Yeqiang Liu2 1Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, 2Department of Pathology, Shanghai Skin Disease Hospital, Tongji University School of Medicine A detailed protocol of differential expression analysis methods for RNA sequencing was provided: limma, EdgeR, DESeq2. Immunology and Infection Flow Cytometric Analysis of Lymphocyte Infiltration in Central Nervous System during Experimental Autoimmune Encephalomyelitis Zhe Ji1,2, Chenghua Zhou1, Hongshen Niu3, Jinshen Wang1, Lei Shen3 1Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, 2Department of Microbiology and Immunology, Tongji University School of Medicine, 3Shanghai Institute of Immunology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine This manuscript presents a protocol to induce active experimental autoimmune encephalomyelitis (EAE) in mice. A method for the isolation and characterization of the infiltrated lymphocytes in the central nervous system (CNS) is also presented to show how lymphocytes are involved in the development of CNS autoimmune disease. Environment Experimental Protocol for Detecting Mitochondrial Function in Hepatocytes Exposed to Organochlorine Pesticides Qian Liu1,2,3, Zhaoyan Jiang3, Aihua Gu1,2 1State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 2Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 3Center of Gallbladder Disease, Shanghai East Hospital, Institute of Gallstone Disease, Tongji University School of Medicine Understanding the influence of environmental organochlorine pesticides (OCPs) on mitochondrial function in hepatocytes is important in exploring the mechanism of OCPs causing metabolic disorders. This paper presents detailed methods on detecting hepatic mitochondrial function. Medicine Precision Measurements and Parametric Models of Vertebral Endplates Hang Feng1, Zhu Ziqi1, Yu Bin1, Xiaoming Liu1, Shenbei Duo1, Surendra Kumar Chaudhary1, Wu Tongde1, Xinhua Li1, Zhaoyu Ba1, Desheng Wu1 1Department of Spinal Surgery, Shanghai East Hospital, Tongji University School of Medicine A reverse engineering system is employed to record and obtain detailed and comprehensive geometry data of vertebral endplates. Parametric models of vertebral endplate are then developed, which are beneficial to designing personalized spinal implants, making clinical diagnoses, and developing accurate finite element models. Biochemistry Nitropeptide Profiling and Identification Illustrated by Angiotensin II Shan Feng1,2, Xiaofei Wen3, Xin Lu2,4,5,6 1Mass Spectrometry Core Facility, School of Life Sciences, Westlake University, 2Department of Biological Sciences, University of Notre Dame, 3Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, 4Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, 5Harper Cancer Research Institute, University of Notre Dame, 6Tumor Microenvironment and Metastasis Program, Indiana University Melvin and Bren Simon Cancer Center Proteomic profiling of tyrosine-nitrated proteins has been a challenging technique due to the low abundance of the 3-nitrotyrosine modification. Here we describe a novel approach for nitropeptide enrichment and profiling by using Angiotensin II as the model. This method can be extended for other in vitro or in vivo systems. Medicine Measuring the Carotid to Femoral Pulse Wave Velocity (Cf-PWV) to Evaluate Arterial Stiffness Hongwei Ji1, Jing Xiong1, Shikai Yu1, Chen Chi1, Bin Bai1, Jiadela Teliewubai1, Yuyan Lu1, Yi Zhang1, Yawei Xu1 1Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine This protocol describes a method to standardize the measurements of carotid-femoral pulse wave velocity to evaluate arterial stiffness. Behavior An Automated Rapid Iterative Negative Geotaxis Assay for Analyzing Adult Climbing Behavior in a Drosophila Model of Neurodegeneration Wenze Cao*1,2,3, Li Song*1,2,3, Jingjing Cheng1,2,3, Na Yi1,2,3, Luyi Cai1,2,3, Fu-de Huang4,5, Margaret Ho1,2,3 1Research Center for Translational Medicine, Tongji University School of Medicine, 2Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, 3Department of Anatomy and Neurobiology, Tongji University School of Medicine, 4Shanghai Advanced Research Institute, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 5Sino-Danish College, University of Chinese Academy of Sciences, Chinese Academy of Sciences This step-by-step protocol analyzes Drosophila negative geotaxis behavior using an automated multi-cylinder system that hosts hundreds of flies and synchronizes their action by an electric motor. Upon synchronization, fly negative geotaxis behavior is assayed, digitally recorded, and analyzed using the self-designed RflyDetection software.
