title: Designing Cell-Type-Specific Genome-wide Experiments.
abstract: Multicellular organisms depend on cell-type-specific division of labor for survival. Specific cell types have their unique developmental program and respond differently to environmental challenges, yet are orchestrated by the same genetic blueprint. A key challenge in biology is thus to understand how genes are expressed in the right place, at the right time, and to the right level. Further, this exquisite control of gene expression is perturbed in many diseases. As a consequence, coordinated physiological responses to the environment are compromised. Recently, innovative tools have been developed that are able to capture genome-wide gene expression using cell-type-specific approaches. These novel techniques allow us to understand gene regulation in vivo with unprecedented resolution and give us mechanistic insights into how multicellular organisms adapt to changing environments. In this article, we discuss the considerations needed when designing your own cell-type-specific experiment from the isolation of your starting material through selecting the appropriate controls and validating the data.
authors.affiliation: Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-University of Munich, Butenandtstrasse 5, 81377 Munich, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Martinsried, Germany.
authors.forename: Ava
authors.initials: A
authors.lastname: Handley
authors.affiliation: Department of Molecular Biology, Biomedical Center, Ludwig-Maximilians-University of Munich, Schillerstrasse 44, 80336 Munich, Germany.
authors.forename: Tamás
authors.initials: T
authors.lastname: Schauer
authors.affiliation: Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-University of Munich, Butenandtstrasse 5, 81377 Munich, Germany; International Max Planck Research School for Molecular and Cellular Life Sciences, Am Klopferspitz 18, 82152 Martinsried, Germany; Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany.
authors.forename: Andreas G
authors.initials: AG
authors.lastname: Ladurner
authors.affiliation: Department of Physiological Chemistry, Biomedical Center, Ludwig-Maximilians-University of Munich, Butenandtstrasse 5, 81377 Munich, Germany. Electronic address: carla.margulies@med.lmu.de.
authors.forename: Carla E
authors.initials: CE
authors.lastname: Margulies
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009928:Organ Specificity / Q000235:genetics*; D015203:Reproducibility of Results; D059010:Single-Cell Analysis / Q000379:methods*