Search Results - "Journal of visualized experiments"

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2 by Liu, Shiyi, Wang, Zitao, Zhu, Ronghui, Wang, Feiyan, Cheng, Yanxiang, Liu, Yeqiang

“…RNA sequencing (RNA-seq) is one of the most widely used technologies in transcriptomics as it can reveal the relationship between the genetic alteration and…”
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Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases by AlRyalat, Saif Aldeen S., Malkawi, Lna W., Momani, Shaher M.

“…Literature databases (i.e., PubMed, Scopus, and Web of Science) differ in terms of their coverage, focus, and the tool they provide. PubMed focuses mainly on…”
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Evaluation of Oxidative Stress in Biological Samples Using the Thiobarbituric Acid Reactive Substances Assay by Aguilar Diaz De Leon, Jesús, Borges, Chad R.

“…Despite its limited analytical specificity and ruggedness, the thiobarbituric acid reactive substances (TBARS) assay has been widely used as a generic metric…”
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Novel Object Recognition Test for the Investigation of Learning and Memory in Mice by Lueptow, Lindsay M.

“…The object recognition test (ORT) is a commonly used behavioral assay for the investigation of various aspects of learning and memory in mice. The ORT is…”
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Quantifying Microglia Morphology from Photomicrographs of Immunohistochemistry Prepared Tissue Using ImageJ by Young, Kimberly, Morrison, Helena

“…Microglia are brain phagocytes that participate in brain homeostasis and continuously survey their environment for dysfunction, injury, and disease. As the…”
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Detection of total reactive oxygen species in adherent cells by 2', 7'-dichlorodihydrofluorescein diacetate staining by Kim, Hyeoncheol, Xue, Xiang

“…Oxidative stress is an important event under both physiological and pathological conditions. In this study, we demonstrate how to quantify oxidative stress by…”
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Use of the Open Field Maze to Measure Locomotor and Anxiety-like Behavior in Mice by Seibenhener, Michael L., Wooten, Michael C.

“…Animal models have proven to be invaluable to researchers trying to answer questions regarding the mechanisms of behavior. The Open Field Maze is one of the…”
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Novel Object Recognition and Object Location Behavioral Testing in Mice on a Budget by Denninger, Jiyeon K, Smith, Bryon M, Kirby, Elizabeth D

“…Ethologically relevant behavioral testing is a critical component of any study that uses mouse models to study the cognitive effects of various physiological…”
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Preparation of Acute Brain Slices Using an Optimized N-Methyl-D-glucamine Protective Recovery Method by Ting, Jonathan T., Lee, Brian R., Chong, Peter, Soler-Llavina, Gilberto, Cobbs, Charles, Koch, Christof, Zeng, Hongkui, Lein, Ed

“…This protocol is a practical guide to the N-methyl-D-glucamine (NMDG) protective recovery method of brain slice preparation. Numerous recent studies have…”
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Assisted Selection of Biomarkers by Linear Discriminant Analysis Effect Size (LEfSe) in Microbiome Data by Chang, Fang, He, Shishi, Dang, Chenyuan

“…There is growing attention toward closed biological genomes in the environment and in health. To explore and reveal the intergroup differences among different…”
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Sample Preparation and Imaging of Exosomes by Transmission Electron Microscopy by Jung, Min Kyo, Mun, Ji Young

“…Exosomes are nano-sized extracellular vesicles secreted by body fluids and are known to represent the characteristics of cells that secrete them. The contents…”
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Differentiation of the SH-SY5Y Human Neuroblastoma Cell Line by Shipley, Mackenzie M., Mangold, Colleen A., Szpara, Moriah L.

“…Having appropriate in vivo and in vitro systems that provide translational models for human disease is an integral aspect of research in neurobiology and the…”
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In vitro Cell Migration and Invasion Assays by Justus, Calvin R., Leffler, Nancy, Ruiz-Echevarria, Maria, Yang, Li V.

“…Migration is a key property of live cells and critical for normal development, immune response, and disease processes such as cancer metastasis and…”
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Pentylenetetrazole-Induced Kindling Mouse Model by Shimada, Tadayuki, Yamagata, Kanato

“…Pentylenetetrazole (PTZ) is a GABA-A receptor antagonist. An intraperitoneal injection of PTZ into an animal induces an acute, severe seizure at a high dose,…”
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The Soft Agar Colony Formation Assay by Borowicz, Stanley, Van Scoyk, Michelle, Avasarala, Sreedevi, Karuppusamy Rathinam, Manoj Kumar, Tauler, Jordi, Bikkavilli, Rama Kamesh, Winn, Robert A.

“…Anchorage-independent growth is the ability of transformed cells to grow independently of a solid surface, and is a hallmark of carcinogenesis. The soft agar…”
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Study of In Vivo Glucose Metabolism in High-fat Diet-fed Mice Using Oral Glucose Tolerance Test (OGTT) and Insulin Tolerance Test (ITT) by Nagy, Csörsz, Einwallner, Elisa

“…Obesity represents the most important single risk factor in the pathogenesis of type 2 diabetes, a disease which is characterized by a resistance to…”
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Extraction of Structural Extracellular Polymeric Substances from Aerobic Granular Sludge by Felz, Simon, Al-Zuhairy, Salah, Aarstad, Olav Andreas, van Loosdrecht, Mark C.M., Lin, Yue Mei

“…To evaluate and develop methodologies for the extraction of gel-forming extracellular polymeric substances (EPS), EPS from aerobic granular sludge (AGS) was…”
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The Forced Swim Test as a Model of Depressive-like Behavior by Yankelevitch-Yahav, Roni, Franko, Motty, Huly, Avrham, Doron, Ravid

“…The goal of the present protocol is to describe the forced swim test (FST), which is one of the most commonly used assays for the study of depressive-like…”
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Assessment of Spontaneous Alternation, Novel Object Recognition and Limb Clasping in Transgenic Mouse Models of Amyloid-β and Tau Neuropathology by Miedel, Christian J., Patton, Jennifer M., Miedel, Andrew N., Miedel, Edward S., Levenson, Jonathan M.

“…Here we describe a staged, behavioral testing approach that can be used to screen for compounds that exhibit in vivo efficacy on cognitive and functional motor…”
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Viral Concentration Determination Through Plaque Assays: Using Traditional and Novel Overlay Systems by Baer, Alan, Kehn-Hall, Kylene

“…Plaque assays remain one of the most accurate methods for the direct quantification of infectious virons and antiviral substances through the counting of…”
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