Universite de Paris 5 articles published in JoVE Engineering Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress Kevin Baudry1,2,3, Christine Paysant-Le Roux1,2, Stefano Colella4, Benoît Castandet1,2, Marie-Laure Martin1,2,5 1Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France, 2Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France, 3Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France, 4LSTM, Univ Montpellier, INRAE, IRD, CIRAD, Institut Agro, Montpellier, France, 5Universitté Paris-Saclay, AgroParisTech, INRAE, UMR MIA-Paris, Paris, France DiCoExpress is a script-based tool implemented in R to perform an RNA-Seq analysis from quality control to co-expression. DiCoExpress handles complete and unbalanced design up to 2 biological factors. This video tutorial guides the user through the different features of DiCoExpress. Neuroscience Magnetic Isolation of Microglial Cells from Neonate Mouse for Primary Cell Cultures Cindy Bokobza*1, Alice Jacquens*1,2, Manuela Zinni1, Valérie Faivre1, Jennifer Hua1, David Guenoun1, Caroline Userovici1, Shyamala Mani1, Vincent Degos1,2, Pierre Gressens1, Juliette Van Steenwinckel1 1NeuroDiderot, Inserm UMR-1141, Hôpital Robert Debré 48, Université de Paris, 2Department of anesthesia and critical care, APHP-Sorbonne university Primary microglia cultures are commonly used to evaluate new anti-inflammatory molecules. The present protocol describes a reproducible and relevant method to magnetically isolate microglia from neonate pups. Biology Primary Human Nasal Epithelial Cells: Biobanking in the Context of Precision Medicine Mairead Kelly1,2, Elise Dreano1,2, Aurelie Hatton1,2, Agathe Lepissier1,2, Anita Golec1,2, Isabelle Sermet-Gaudelus1,2,3, Iwona Pranke1,2,3 1Institut Necker Enfants Malades, 2Université de Paris, 3Centre de Référence Maladies Rares Mucoviscidose et Maladies apparentées, Assistance Publique Hôpitaux de Paris Here we describe the isolation, amplification, and differentiation of primary human nasal epithelial (HNE) cells at the air-liquid interface and a biobanking protocol allowing to successfully freeze and then thaw amplified HNE. The protocol analyzes electrophysiological properties of differentiated HNE cells and CFTR-related chloride secretion correction upon different modulator treatments. Developmental Biology 2D and 3D Human Induced Pluripotent Stem Cell-Based Models to Dissect Primary Cilium Involvement during Neocortical Development Lucile Boutaud*1, Marie Michael*1, Céline Banal2, Damelys Calderon1, Sarah Farcy1, Julie Pernelle1, Nicolas Goudin3, Camille Maillard1, Clémantine Dimartino1, Cécile Deleschaux1, Sébastien Dupichaud4, Corinne Lebreton1, Sophie Saunier1, Tania Attié-Bitach1,5, Nadia Bahi-Buisson1,6, Nathalie Lefort2, Sophie Thomas1 1Imagine Institute, INSERM UMR 1163, Université de Paris, 2Imagine Institute, iPSC Core Facility, INSERM UMR U1163, Université de Paris, 3Necker Bio-image Analysis platform of the SFR Necker, 4Imagine Institute, Cell Imaging Platform, INSERM-US24-CNRS UMS 3633 Structure Fédérative de Recherche Necker, INSERM UMR U1163, Université de Paris, 5Fédération de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, 6Pediatric Neurology, APHP- Necker Enfants Malades Hospital We present detailed protocols for the generation and characterization of 2D and 3D human induced pluripotent stem cell (hIPSC)-based models of neocortical development as well as complementary methodologies enabling qualitative and quantitative analysis of primary cilium (PC) biogenesis and function. Neuroscience Whole-Brain 3D Activation and Functional Connectivity Mapping in Mice using Transcranial Functional Ultrasound Imaging Adrien Bertolo*1, Mohamed Nouhoum*1, Silvia Cazzanelli*1, Jeremy Ferrier*3, Jean-Charles Mariani2, Andrea Kliewer4,2, Benoit Belliard1, Bruno-Félix Osmanski3, Thomas Deffieux*1, Sophie Pezet*1, Zsolt Lenkei*2, Mickael Tanter*1 1Physics for Medicine Paris, ESPCI Paris, INSERM, CNRS, PSL Research University, 2Institute of Psychiatry and Neurosciences of Paris, INSERM U1266, Université de Paris, 3Iconeus, 4Department of Pharmacology and Toxicology, Jena University Hospital - Friedrich Schiller University Jena This protocol describes the quantification of volumetric cerebral hemodynamic variations in the mouse brain using functional ultrasound (fUS). Procedures for 3D functional activation map following sensory stimulation as well as resting-state functional connectivity are provided as illustrative examples, in anesthetized and awake mice.
