JoVE Journal

Genetics

JoVE Genetics includes experimental approaches to study gene function, gene expression and regulation, epigenetics, genetic disorders, population genetics, and evolution.

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Retrospective MicroRNA Sequencing: Complementary DNA Library Preparation Protocol Using Formalin-fixed Paraffin-embedded RNA Specimens

Olivier Loudig^1,2,3, Christina Liu^1,2, Thomas Rohan³, Iddo Z. Ben-Dov⁴

¹Department of Research, Hackensack University Medical Center, ²Department of Medical Sciences, Seton Hall University, ³Department of Epidemiology and Population Health, Albert Einstein College of Medicine, ⁴Department of Nephrology and Hypertension, Hadassah - Hebrew University Medical Center

Investigation of RNA Synthesis Using 5-Bromouridine Labelling and Immunoprecipitation

Rikke H. Kofoed¹, Cristine Betzer¹, Søren Lykke-Andersen², Ewa Molska², Poul H. Jensen¹

¹DANDRITE - Danish Research Institute of Translational Neuroscience, Dept. of Biomedicine, Aarhus University, ²Dept. of Molecular Biology and Genetics, Aarhus University

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Tuesday Simmons¹, Daniel F. Caddell¹, Siwen Deng¹, Devin Coleman-Derr^1,2

¹Department of Plant and Microbial Biology, University of California, Berkeley, ²Plant Gene Expression Center, USDA ARS

Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance

Jose Antonio Escudero^1,2, R Craig MacLean³, Alvaro San Millan⁴

¹Department of Animal Health, Universidad Complutense de Madrid, ²Visavet Health Surveillance Centre, Universidad Complutense de Madrid, ³Department of Zoology, University of Oxford, ⁴Department of Microbiology, Hospital Universitario Ramon y Cajal (IRYCIS) and CIBERESP

A Rapid and Facile Pipeline for Generating Genomic Point Mutants in C. elegans Using CRISPR/Cas9 Ribonucleoproteins

Harriet Prior*¹, Lauren MacConnachie*¹, Jose L. Martinez¹, Georgina C.B. Nicholl¹, Asim A. Beg¹

¹Department of Pharmacology, University of Michigan

Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System

Joseph C. Siefert^1,2, Emily A. Clowdus^1,2, Duane Goins¹, Amnon Koren³, Christopher L. Sansam^1,2

¹Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, ²Department of Cell Biology, University of Oklahoma Health Sciences Center, ³Department of Molecular Biology and Genetics, Cornell University

A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel

Ling Huang*¹, Xiaohui Deng*¹, Ronghua Li¹, Yanshi Xia¹, Guihua Bai², Kadambot H.M. Siddique³, Peiguo Guo¹

¹College of Life Sciences, Guangzhou University, ²Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service, ³The UWA Institute of Agriculture, University of Western Australia

Using Mouse Oocytes to Assess Human Gene Function During Meiosis I

Diego Marin*^1,2, Alexandra L. Nguyen*³, Richard T. Scott, Jr.^1,2, Karen Schindler³

¹IVI-RMA New Jersey, ²Jefferson College of Biomedical Sciences, Thomas Jefferson University, ³Department of Genetics, Rutgers, The State University of New Jersey

RNA Pull-down Procedure to Identify RNA Targets of a Long Non-coding RNA

Manon Torres¹, Denis Becquet¹, Séverine Guillen¹, Bénédicte Boyer¹, Mathias Moreno¹, Marie-Pierre Blanchard², Jean-Louis Franc¹, Anne-Marie François-Bellan¹

¹CNRS, CRN2M-UMR7286, Faculté de Médecine Nord, Aix-Marseille Université, ²Plate-forme d'imagerie MRI, UMS3426, CNRS 141, Institut de Génétique Humaine

Highly Efficient Gene Disruption of Murine and Human Hematopoietic Progenitor Cells by CRISPR/Cas9

Lorenzo Brunetti*^1,2,3, Michael C. Gundry*^1,2,4, Ayumi Kitano⁴, Daisuke Nakada^1,2,4, Margaret A. Goodell^1,2,4,5

¹Stem Cells & Regenerative Medicine Center, Baylor College of Medicine, ²Center for Cell and Gene Therapy, Baylor College of Medicine, ³Centro di Ricerca Emato-Oncologica (CREO), University of Perugia, ⁴Department of Molecular & Human Genetics, Baylor College of Medicine, ⁵Texas Children's Hospital & Houston Methodist Hospital

Production and Purification of Baculovirus for Gene Therapy Application

Md Nasimuzzaman^1,2, Johannes C.M. van der Loo^1,2,3, Punam Malik^1,2

¹Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, ²University of Cincinnati College of Medicine, ³Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Allison A. Dilliott^1,2, Sali M.K. Farhan³, Mahdi Ghani⁴, Christine Sato⁴, Eric Liang⁵, Ming Zhang⁴, Adam D. McIntyre¹, Henian Cao¹, Lemuel Racacho^6,7, John F. Robinson¹, Michael J. Strong^1,8, Mario Masellis^9,10, Dennis E. Bulman^6,7, Ekaterina Rogaeva⁴, Anthony Lang^10,11, Carmela Tartaglia^4,10, Elizabeth Finger^12,13, Lorne Zinman⁹, John Turnbull¹⁴, Morris Freedman^10,15, Rick Swartz⁹, Sandra E. Black^9,16, Robert A. Hegele^1,2

¹Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, ²Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, ³Analytic and Translational Genetics Unit, Center for Genomic Medicine, Harvard Medical School, Massachusetts General Hospital, Stanley Centre for Psychiatric Research, Broad Institute of MIT and Harvard, ⁴Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, ⁵School of Medicine, Faculty of Health Sciences, Queen's University, ⁶Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, ⁷CHEO Research Institute, Faculty of Medicine, University of Ottawa, ⁸Department of Clinical Neurological Sciences, Western University, ⁹Division of Neurology, Department of Medicine, Sunnybrook Health Sciences Centre, University of Toronto, ¹⁰Division of Neurology, Department of Medicine, University of Toronto, ¹¹Morton and Gloria Shulman Movement Disorders Centre, Toronto Western Hospital, ¹²Department of Clinical Neurological Sciences, Schulich School of Medicine and Dentistry, Western University, ¹³Parkwood Institute, St. Joseph's Health Care, ¹⁴Department of Medicine, Division of Neurology, McMaster University, ¹⁵Division of Neurology, Department of Medicine, Baycrest Health Sciences, ¹⁶Canadian Partnership for Stroke Recovery Sunnybrook Site, Sunnybrook Health Science Centre, University of Toronto

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells

Alfonso Rodríguez-Gil¹, Tabea Riedlinger², Olesja Ritter², Vera V. Saul², M. Lienhard Schmitz²

¹Department of Oncohematology and Genetics. Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, ²Institute of Biochemistry, Medical Faculty, Friedrichstrasse 24, Member of the German Center for Lung Research, Justus-Liebig-University

Measuring Gene Expression in Bombarded Barley Aleurone Layers with Increased Throughput

Grace Uwase¹, Taylor P. Enrico¹, David S. Chelimo¹, Benjamin R. Keyser¹, Russell R. Johnson¹

¹Department of Biology, Colby College

Adapting 3' Rapid Amplification of CDNA Ends to Map Transcripts in Cancer

Chioniso Patience Masamha¹, Zachery Todd¹

¹Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Butler University

Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector

Mariliis Tark-Dame¹, Blaise Weber¹, Mara de Sain¹, Damar Tri Anggoro¹, Rechien Bader¹, Aimee Walmsley¹, Rurika Oka¹, Maike Stam¹

¹Swammerdam Institute for Life Sciences, University of Amsterdam

An Optogenetic Method to Control and Analyze Gene Expression Patterns in Cell-to-cell Interactions

Akihiro Isomura^1,2, Ryoichiro Kageyama^1,3,4,5

¹Institute for Frontier Life and Medical Sciences, Kyoto University, ²Japan Science and Technology Agency, PRESTO, ³Institute for Integrated Cell-Material Sciences, Kyoto University, ⁴Graduate School of Medicine, Kyoto University, ⁵Graduate School of Biostudies, Kyoto University

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome

Eric J. Foss¹, Uyen Lao¹, Antonio Bedalov^1,2

¹Division of Clinical Research, Fred Hutchinson Cancer Research Center, ²Departments of Medicine and Biochemistry, University of Washington

Investigation of Protein Recruitment to DNA Lesions Using 405 Nm Laser Micro-irradiation

Antoine Gaudreau-Lapierre*¹, Daniel Garneau*¹, Billel Djerir*¹, Frédéric Coulombe¹, Théo Morin¹, Alexandre Marechal¹

¹Department of Biology, Université de Sherbrooke

Manipulation of Ploidy in Caenorhabditis elegans

Erlyana K. Clarke¹, Katherine A. Rivera Gomez^1,2, Zaki Mustachi¹, Mikaela C. Murph^1,3, Mara Schvarzstein^1,2,3

¹Brooklyn College, Biology Department, City University of New York, ²The Graduate Center, Biology Department, City University of New York, ³Advanced Science Research Center, City University of New York

CRISPR/Cas9-mediated Targeted Integration In Vivo Using a Homology-mediated End Joining-based Strategy

Xuan Yao^1,2, Xing Wang^1,2, Junlai Liu^2,3,4, Linyu Shi¹, Pengyu Huang³, Hui Yang¹

¹Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, ²College of Life Sciences, University of Chinese Academy of Sciences, ³School of Life Science and Technology, Shanghai Tech University, ⁴Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens

Saman Saeidi*¹, Michael R. McKain*^1,2, Elizabeth A. Kellogg¹

¹Donald Danforth Plant Science Center, ²Department of Biological Sciences, The University of Alabama

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Kathrin Davari*¹, Johannes Lichti*¹, Caroline C. Friedel², Elke Glasmacher^1,3

¹Institute for Diabetes and Obesity (IDO), German Center for Diabetes Research (DZD), Helmholtz Zentrum München, ²Institute for Informatics, Ludwig-Maximilians-Universität München, ³Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Penzberg

A Simple, Rapid, and Quantitative Assay to Measure Repair of DNA-protein Crosslinks on Plasmids Transfected into Mammalian Cells

Lisa N. Chesner¹, Colin Campbell¹

¹Department of Pharmacology, University of Minnesota

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