Perspective abstract
Nature Biotechnology 26, 305 - 312 (2008)
Published online: 7 March 2008 | doi:10.1038/nbt1391
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)
Eric W Deutsch1, Catherine A Ball2, Jules J Berman3, G Steven Bova4, Alvis Brazma5, Roger E Bumgarner6, David Campbell1, Helen C Causton7, Jeffrey H Christiansen8, Fabrice Daian9, Delphine Dauga9, Duncan R Davidson8, Gregory Gimenez9, Young Ah Goo1,10, Sean Grimmond11, Thorsten Henrich12, Bernhard G Herrmann13, Michael H Johnson1, Martin Korb13, Jason C Mills14, Asa J Oudes1,10, Helen E Parkinson5, Laura E Pascal1,10, Nicolas Pollet15, John Quackenbush16, Mirana Ramialison12, Martin Ringwald17, David Salgado9, Susanna-Assunta Sansone5, Gavin Sherlock18, Christian J Stoeckert, Jr19, Jason Swedlow20, Ronald C Taylor21, Laura Walashek1,10, Anthony Warford22, David G Wilkinson23, Yi Zhou24, Leonard I Zon24, Alvin Y Liu1,10 & Lawrence D True25
Abstract
One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guidelines for gene expression localization experiments: the minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). MISFISHIE is modeled after the Minimum Information About a Microarray Experiment (MIAME) specification for microarray experiments. Both guidelines define what information should be reported without dictating a format for encoding that information. MISFISHIE describes six types of information to be provided for each experiment: experimental design, biomaterials and treatments, reporters, staining, imaging data and image characterizations. This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.
- Institute for Systems Biology, 1441 N 34th Street, Seattle, Washington 98103, USA.
- Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive West, Stanford, California 94305, USA.
- Association for Pathology Informatics, 9650 Rockville Pike, Bethesda, Maryland 20814, USA.
- Johns Hopkins University School of Medicine, PELICAN Laboratory, Departments of Pathology, Health Information Sciences, Genetic Medicine, Oncology, and Urology, Baltimore, Maryland, 21287 USA.
- European Molecular Biology Laboratory (EMBL)–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
- Department of Microbiology, University of Washington, Seattle, Washington 98195, USA.
- Medical Research Council (MRC) Clinical Sciences Centre Microarray Centre, Imperial College School of Medicine, London W12 ONN, UK.
- MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
- Institut de Biologie du Développement de Marseille, UMR 6216, Centre National de la Recherche Scientifique (CNRS)/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France.
- Department of Urology, University of Washington, Seattle, Washington 98195, USA.
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland 4027, Australia.
- EMBL Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
- Institute for Medical Genetics, Charité-Campus Benjamin Franklin, and Department of Developmental Genetics, Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
- CNRS UMR 8080, Université Paris-Sud, 91405 Orsay, France.
- Dana-Farber Cancer Institute, 44 Binney Street, M232, Boston, Massachusetts 02115, USA.
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609, USA.
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305-5120, USA.
- Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
- Division of Gene Regulation and Expression, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, UK.
- Computational Biology & Bioinformatics Group, Pacific Northwest National Laboratory, PO Box 999, MS K7-90, Richland, Washington 99352, USA.
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 IHH, UK.
- Division of Developmental Neurobiology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
- Stem Cell Program, Division of Hematology/Oncology, Children's Hospital Boston and Harvard Medical School, 300 Longwood Ave., Boston, Massachusetts 02115, USA.
- Department of Pathology, University of Washington, Seattle, Washington 98195-6100, USA.
Correspondence to: Eric W Deutsch1 e-mail: edeutsch@systemsbiology.org
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