|
|||||
|
|
A meta-analysis of kidney microarray datasets: investigation of cytokine gene detection and correlation with rt-PCR and detection thresholds |
|
| Authors: | Walter D Park Mark D Stegall |
| Institution: | 1. Department 3 - Genetics, Max-Planck-Institut für Entwicklungsbiologie, Spemannstr. 35/III, 72076, Tübingen, Germany 2. Department of Internal Medicine III - Cardiology, University of Heidelberg, Im Neuenheimer Feld 350, 69120, Heidelberg, Germany 3. Max Planck Institute for Molecular Genetics, Ihnestr,63-73, 14195, Berlin, Germany 4. Department of Biochemistry, Laboratory for Alzheimer's and Parkinson's Disease Research, Adolf-Butenandt-Institute, LMU, Schillerstr. 44, 80336, München, Germany 5. Team 31 - Vertebrate Development and Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, CB10 1SA, Cambridge, UK 6. Center for Brain Research - Division of Neuronal Cell Biology, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria 7. Centre for Cellular and Molecular Dynamics, Department of Anatomy and Developmental Biology, University College London, Gower St., WC1E 6BT, London, UK 8. 3. Physikalisches Institut, Universit?t Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany 9. Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, 06520-8103, New Haven, CT, USA 10. Institut für Klinische Pharmakologie und Toxikologie, Charité –, Universit?tsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200, Berlin, Germany 11. NMI – Natural and Medical Science Institute at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany 12. Institute of Physiology Dept. II and Tübingen Hearing Research Centre THRC, University of Tübingen, Elfriede-Aulhorn-Str. 5, 72076, Tübingen, Germany 13. Institute of Pathology, Rikshospitalet, Sognsvannveien 20, 0027, Oslo, Norway 14. Current Biology, Elsevier London, 84 Theobald's Rd., London, WC1X 8RR, UK 15. Institute of Zoology, University of Zurich, Winterthurerstr. 190, 8057, Zürich, Switzerland 16. Oregon Hearing Research Center and Vollum Institute, Oregon Health & Science University, 3181 SW Sam Jackson Pk. Rd., 97239, Portland, OR, USA 17. Division of Developmental Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, UK 18. Laboratory for Magnetic Brain Stimulation, Behavioral Neurology Unit, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA, 02215, USA 19. Howard Hughes Medical Institute, University of Utah, 15 North 2030 East, Salt Lake City, UT, 84112, USA 20. MDC - Max-Delbrück-Centrum für Molekulare Medizin, Berlin-Buch, Robert-R?ssle-Str. 10, 13092, Berlin, Germany 21. Cellzome AG, Meyerhofstr. 1, 69117, Heidelberg, Germany 22. Ingenium Pharmaceuticals AG, Fraunhoferstr. 13, 82152, Martinsried, Germany 23. Abt. Kinderheilkunde I, Children's Hospital, University of Tübingen, Hoppe-Seyler-Str. 1, 72076, Tübingen, Germany 24. IMP - Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030, Vienna, Austria 25. Department of Medicine, University of Pennsylvania School of Medicine, 1230 Biomedical Research Building II/III, 421 Curie Blvd., Philadelphia, PA, 19104, USA 26. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Mayer Building 630, 44 Binney St., Boston, MA, 02115, USA 27. Team 30 - Vertebrate functional proteomics laboratory, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SA, UK 28. Department of Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany |
| Abstract: | BackgroundLarge-scale mutagenesis screens in the zebrafish employing the mutagen ENU have isolated several hundred mutant loci that represent putative developmental control genes. In order to realize the potential of such screens, systematic genetic mapping of the mutations is necessary. Here we report on a large-scale effort to map the mutations generated in mutagenesis screening at the Max Planck Institute for Developmental Biology by genome scanning with microsatellite markers.ResultsWe have selected a set of microsatellite markers and developed methods and scoring criteria suitable for efficient, high-throughput genome scanning. We have used these methods to successfully obtain a rough map position for 319 mutant loci from the Tübingen I mutagenesis screen and subsequent screening of the mutant collection. For 277 of these the corresponding gene is not yet identified. Mapping was successful for 80 % of the tested loci. By comparing 21 mutation and gene positions of cloned mutations we have validated the correctness of our linkage group assignments and estimated the standard error of our map positions to be approximately 6 cM.ConclusionBy obtaining rough map positions for over 300 zebrafish loci with developmental phenotypes, we have generated a dataset that will be useful not only for cloning of the affected genes, but also to suggest allelism of mutations with similar phenotypes that will be identified in future screens. Furthermore this work validates the usefulness of our methodology for rapid, systematic and inexpensive microsatellite mapping of zebrafish mutations. |
| Keywords: | |
| 本文献已被 SpringerLink 等数据库收录！ | |