Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)
Identifieur interne : 002196 ( Pmc/Corpus ); précédent : 002195; suivant : 002197Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)
Auteurs : Eric W. Deutsch ; Catherine A. Ball ; Jules J. Berman ; G Steven Bova ; Alvis Brazma ; Roger E. Bumgarner ; David Campbell ; Helen C. Causton ; Jeffrey H. Christiansen ; Fabrice Daian ; Delphine Dauga ; Duncan R. Davidson ; Gregory Gimenez ; Young Ah Goo ; Sean Grimmond ; Thorsten Henrich ; Bernhard G. Herrmann ; Michael H. Johnson ; Martin Korb ; Jason C. Mills ; Asa J. Oudes ; Helen E. Parkinson ; Laura E. Pascal ; Nicolas Pollet ; John Quackenbush ; Mirana Ramialison ; Martin Ringwald ; David Salgado ; Susanna-Assunta Sansone ; Gavin Sherlock ; Christian J. Stoeckert ; Jason Swedlow ; Ronald C. Taylor ; Laura Walashek ; Anthony Warford ; David G. Wilkinson ; Yi Zhou ; Leonard I. Zon ; Alvin Y. Liu ; Lawrence D. TrueSource :
- Nature biotechnology [ 1087-0156 ] ; 2008.
Abstract
One purpose of the biomedical literature is to report results in sufficient detail so that the methods of data collection and analysis can be independently replicated and verified. Here we present for consideration a minimum information specification for gene expression localization experiments, called the “Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)”. It is modelled after the MIAME (Minimum Information About a Microarray Experiment) specification for microarray experiments. Data specifications like MIAME and MISFISHIE specify the information
Url:
DOI: 10.1038/nbt1391
PubMed: 18327244
PubMed Central: 4367930
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PMC:4367930Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)</title><author><name sortKey="Deutsch, Eric W" sort="Deutsch, Eric W" uniqKey="Deutsch E" first="Eric W" last="Deutsch">Eric W. Deutsch</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation></author><author><name sortKey="Ball, Catherine A" sort="Ball, Catherine A" uniqKey="Ball C" first="Catherine A" last="Ball">Catherine A. Ball</name><affiliation><nlm:aff id="A2">Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94305, USA</nlm:aff></affiliation></author><author><name sortKey="Berman, Jules J" sort="Berman, Jules J" uniqKey="Berman J" first="Jules J" last="Berman">Jules J. Berman</name><affiliation><nlm:aff id="A3">Association for Pathology Informatics, 9650 Rockville Pike, Bethesda, MD 20814, USA</nlm:aff></affiliation></author><author><name sortKey="Bova, G Steven" sort="Bova, G Steven" uniqKey="Bova G" first="G Steven" last="Bova">G Steven Bova</name><affiliation><nlm:aff id="A4">Johns Hopkins University School of Medicine, PELICAN Laboratory, Departments of Pathology , Health Information Sciences, Genetic Medicine, Oncology, and Urology, Baltimore, MD, USA</nlm:aff></affiliation></author><author><name sortKey="Brazma, Alvis" sort="Brazma, Alvis" uniqKey="Brazma A" first="Alvis" last="Brazma">Alvis Brazma</name><affiliation><nlm:aff id="A5">EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Bumgarner, Roger E" sort="Bumgarner, Roger E" uniqKey="Bumgarner R" first="Roger E" last="Bumgarner">Roger E. Bumgarner</name><affiliation><nlm:aff id="A6">Department of Microbiology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Campbell, David" sort="Campbell, David" uniqKey="Campbell D" first="David" last="Campbell">David Campbell</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation></author><author><name sortKey="Causton, Helen C" sort="Causton, Helen C" uniqKey="Causton H" first="Helen C" last="Causton">Helen C. Causton</name><affiliation><nlm:aff id="A7">MRC CSC Microarray Centre, Imperial College School of Medicine, London, W12 ONN, UK</nlm:aff></affiliation></author><author><name sortKey="Christiansen, Jeffrey H" sort="Christiansen, Jeffrey H" uniqKey="Christiansen J" first="Jeffrey H" last="Christiansen">Jeffrey H. Christiansen</name><affiliation><nlm:aff id="A8">MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, UK EH4 2XU</nlm:aff></affiliation></author><author><name sortKey="Daian, Fabrice" sort="Daian, Fabrice" uniqKey="Daian F" first="Fabrice" last="Daian">Fabrice Daian</name><affiliation><nlm:aff id="A9">Institut de Biologie du Développement de Marseille, UMR 6216, CNRS/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France</nlm:aff></affiliation></author><author><name sortKey="Dauga, Delphine" sort="Dauga, Delphine" uniqKey="Dauga D" first="Delphine" last="Dauga">Delphine Dauga</name><affiliation><nlm:aff id="A9">Institut de Biologie du Développement de Marseille, UMR 6216, CNRS/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France</nlm:aff></affiliation></author><author><name sortKey="Davidson, Duncan R" sort="Davidson, Duncan R" uniqKey="Davidson D" first="Duncan R" last="Davidson">Duncan R. Davidson</name><affiliation><nlm:aff id="A8">MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, UK EH4 2XU</nlm:aff></affiliation></author><author><name sortKey="Gimenez, Gregory" sort="Gimenez, Gregory" uniqKey="Gimenez G" first="Gregory" last="Gimenez">Gregory Gimenez</name><affiliation><nlm:aff id="A9">Institut de Biologie du Développement de Marseille, UMR 6216, CNRS/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France</nlm:aff></affiliation></author><author><name sortKey="Goo, Young Ah" sort="Goo, Young Ah" uniqKey="Goo Y" first="Young Ah" last="Goo">Young Ah Goo</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Grimmond, Sean" sort="Grimmond, Sean" uniqKey="Grimmond S" first="Sean" last="Grimmond">Sean Grimmond</name><affiliation><nlm:aff id="A11">Institute for Molecular Bioscience, University of Queensland, St. Lucia, Qld, Australia</nlm:aff></affiliation></author><author><name sortKey="Henrich, Thorsten" sort="Henrich, Thorsten" uniqKey="Henrich T" first="Thorsten" last="Henrich">Thorsten Henrich</name><affiliation><nlm:aff id="A12">EMBL Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany</nlm:aff></affiliation></author><author><name sortKey="Herrmann, Bernhard G" sort="Herrmann, Bernhard G" uniqKey="Herrmann B" first="Bernhard G" last="Herrmann">Bernhard G. Herrmann</name><affiliation><nlm:aff id="A13">Institute for medical Genetics, Charité-CBF, and Dept. Developmental Genetics, Max-Planck-Institute for molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany</nlm:aff></affiliation></author><author><name sortKey="Johnson, Michael H" sort="Johnson, Michael H" uniqKey="Johnson M" first="Michael H" last="Johnson">Michael H. Johnson</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation></author><author><name sortKey="Korb, Martin" sort="Korb, Martin" uniqKey="Korb M" first="Martin" last="Korb">Martin Korb</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation></author><author><name sortKey="Mills, Jason C" sort="Mills, Jason C" uniqKey="Mills J" first="Jason C" last="Mills">Jason C. Mills</name><affiliation><nlm:aff id="A14">Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA</nlm:aff></affiliation></author><author><name sortKey="Oudes, Asa J" sort="Oudes, Asa J" uniqKey="Oudes A" first="Asa J" last="Oudes">Asa J. Oudes</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Parkinson, Helen E" sort="Parkinson, Helen E" uniqKey="Parkinson H" first="Helen E" last="Parkinson">Helen E. Parkinson</name><affiliation><nlm:aff id="A5">EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Pascal, Laura E" sort="Pascal, Laura E" uniqKey="Pascal L" first="Laura E" last="Pascal">Laura E. Pascal</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Pollet, Nicolas" sort="Pollet, Nicolas" uniqKey="Pollet N" first="Nicolas" last="Pollet">Nicolas Pollet</name><affiliation><nlm:aff id="A15">CNRS UMR 8080, Université Paris-Sud, 91405 Orsay, France</nlm:aff></affiliation></author><author><name sortKey="Quackenbush, John" sort="Quackenbush, John" uniqKey="Quackenbush J" first="John" last="Quackenbush">John Quackenbush</name><affiliation><nlm:aff id="A16">Dana-Farber Cancer Institute, 44 Binney Street, M232, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Ramialison, Mirana" sort="Ramialison, Mirana" uniqKey="Ramialison M" first="Mirana" last="Ramialison">Mirana Ramialison</name><affiliation><nlm:aff id="A12">EMBL Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany</nlm:aff></affiliation></author><author><name sortKey="Ringwald, Martin" sort="Ringwald, Martin" uniqKey="Ringwald M" first="Martin" last="Ringwald">Martin Ringwald</name><affiliation><nlm:aff id="A17">The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA</nlm:aff></affiliation></author><author><name sortKey="Salgado, David" sort="Salgado, David" uniqKey="Salgado D" first="David" last="Salgado">David Salgado</name><affiliation><nlm:aff id="A9">Institut de Biologie du Développement de Marseille, UMR 6216, CNRS/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France</nlm:aff></affiliation></author><author><name sortKey="Sansone, Susanna Assunta" sort="Sansone, Susanna Assunta" uniqKey="Sansone S" first="Susanna-Assunta" last="Sansone">Susanna-Assunta Sansone</name><affiliation><nlm:aff id="A5">EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Sherlock, Gavin" sort="Sherlock, Gavin" uniqKey="Sherlock G" first="Gavin" last="Sherlock">Gavin Sherlock</name><affiliation><nlm:aff id="A18">Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5120, USA</nlm:aff></affiliation></author><author><name sortKey="Stoeckert, Christian J" sort="Stoeckert, Christian J" uniqKey="Stoeckert C" first="Christian J" last="Stoeckert">Christian J. Stoeckert</name><affiliation><nlm:aff id="A19">Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA</nlm:aff></affiliation></author><author><name sortKey="Swedlow, Jason" sort="Swedlow, Jason" uniqKey="Swedlow J" first="Jason" last="Swedlow">Jason Swedlow</name><affiliation><nlm:aff id="A20">Division of Gene Regulation and Expression, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland</nlm:aff></affiliation></author><author><name sortKey="Taylor, Ronald C" sort="Taylor, Ronald C" uniqKey="Taylor R" first="Ronald C" last="Taylor">Ronald C. Taylor</name><affiliation><nlm:aff id="A21">Computational Biology & Bioinformatics Group, Pacific Northwest National Laboratory, PO Box 999, MS K7-90, Richland, WA 99352, USA</nlm:aff></affiliation></author><author><name sortKey="Walashek, Laura" sort="Walashek, Laura" uniqKey="Walashek L" first="Laura" last="Walashek">Laura Walashek</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Warford, Anthony" sort="Warford, Anthony" uniqKey="Warford A" first="Anthony" last="Warford">Anthony Warford</name><affiliation><nlm:aff id="A22">Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 IHH, UK</nlm:aff></affiliation></author><author><name sortKey="Wilkinson, David G" sort="Wilkinson, David G" uniqKey="Wilkinson D" first="David G" last="Wilkinson">David G. Wilkinson</name><affiliation><nlm:aff id="A23">Division of Developmental Neurobiology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK</nlm:aff></affiliation></author><author><name sortKey="Zhou, Yi" sort="Zhou, Yi" uniqKey="Zhou Y" first="Yi" last="Zhou">Yi Zhou</name><affiliation><nlm:aff id="A24">Stem Cell Program, Division of Hematology/Oncology, Children’s Hospital Boston and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Zon, Leonard I" sort="Zon, Leonard I" uniqKey="Zon L" first="Leonard I" last="Zon">Leonard I. Zon</name><affiliation><nlm:aff id="A24">Stem Cell Program, Division of Hematology/Oncology, Children’s Hospital Boston and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Liu, Alvin Y" sort="Liu, Alvin Y" uniqKey="Liu A" first="Alvin Y" last="Liu">Alvin Y. Liu</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="True, Lawrence D" sort="True, Lawrence D" uniqKey="True L" first="Lawrence D" last="True">Lawrence D. True</name><affiliation><nlm:aff id="A25">Department of Pathology, University of Washington, Seattle, WA 98195-6100, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18327244</idno><idno type="pmc">4367930</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4367930</idno><idno type="RBID">PMC:4367930</idno><idno type="doi">10.1038/nbt1391</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">002196</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002196</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)</title><author><name sortKey="Deutsch, Eric W" sort="Deutsch, Eric W" uniqKey="Deutsch E" first="Eric W" last="Deutsch">Eric W. Deutsch</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation></author><author><name sortKey="Ball, Catherine A" sort="Ball, Catherine A" uniqKey="Ball C" first="Catherine A" last="Ball">Catherine A. Ball</name><affiliation><nlm:aff id="A2">Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94305, USA</nlm:aff></affiliation></author><author><name sortKey="Berman, Jules J" sort="Berman, Jules J" uniqKey="Berman J" first="Jules J" last="Berman">Jules J. Berman</name><affiliation><nlm:aff id="A3">Association for Pathology Informatics, 9650 Rockville Pike, Bethesda, MD 20814, USA</nlm:aff></affiliation></author><author><name sortKey="Bova, G Steven" sort="Bova, G Steven" uniqKey="Bova G" first="G Steven" last="Bova">G Steven Bova</name><affiliation><nlm:aff id="A4">Johns Hopkins University School of Medicine, PELICAN Laboratory, Departments of Pathology , Health Information Sciences, Genetic Medicine, Oncology, and Urology, Baltimore, MD, USA</nlm:aff></affiliation></author><author><name sortKey="Brazma, Alvis" sort="Brazma, Alvis" uniqKey="Brazma A" first="Alvis" last="Brazma">Alvis Brazma</name><affiliation><nlm:aff id="A5">EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Bumgarner, Roger E" sort="Bumgarner, Roger E" uniqKey="Bumgarner R" first="Roger E" last="Bumgarner">Roger E. Bumgarner</name><affiliation><nlm:aff id="A6">Department of Microbiology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Campbell, David" sort="Campbell, David" uniqKey="Campbell D" first="David" last="Campbell">David Campbell</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation></author><author><name sortKey="Causton, Helen C" sort="Causton, Helen C" uniqKey="Causton H" first="Helen C" last="Causton">Helen C. Causton</name><affiliation><nlm:aff id="A7">MRC CSC Microarray Centre, Imperial College School of Medicine, London, W12 ONN, UK</nlm:aff></affiliation></author><author><name sortKey="Christiansen, Jeffrey H" sort="Christiansen, Jeffrey H" uniqKey="Christiansen J" first="Jeffrey H" last="Christiansen">Jeffrey H. Christiansen</name><affiliation><nlm:aff id="A8">MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, UK EH4 2XU</nlm:aff></affiliation></author><author><name sortKey="Daian, Fabrice" sort="Daian, Fabrice" uniqKey="Daian F" first="Fabrice" last="Daian">Fabrice Daian</name><affiliation><nlm:aff id="A9">Institut de Biologie du Développement de Marseille, UMR 6216, CNRS/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France</nlm:aff></affiliation></author><author><name sortKey="Dauga, Delphine" sort="Dauga, Delphine" uniqKey="Dauga D" first="Delphine" last="Dauga">Delphine Dauga</name><affiliation><nlm:aff id="A9">Institut de Biologie du Développement de Marseille, UMR 6216, CNRS/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France</nlm:aff></affiliation></author><author><name sortKey="Davidson, Duncan R" sort="Davidson, Duncan R" uniqKey="Davidson D" first="Duncan R" last="Davidson">Duncan R. Davidson</name><affiliation><nlm:aff id="A8">MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, UK EH4 2XU</nlm:aff></affiliation></author><author><name sortKey="Gimenez, Gregory" sort="Gimenez, Gregory" uniqKey="Gimenez G" first="Gregory" last="Gimenez">Gregory Gimenez</name><affiliation><nlm:aff id="A9">Institut de Biologie du Développement de Marseille, UMR 6216, CNRS/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France</nlm:aff></affiliation></author><author><name sortKey="Goo, Young Ah" sort="Goo, Young Ah" uniqKey="Goo Y" first="Young Ah" last="Goo">Young Ah Goo</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Grimmond, Sean" sort="Grimmond, Sean" uniqKey="Grimmond S" first="Sean" last="Grimmond">Sean Grimmond</name><affiliation><nlm:aff id="A11">Institute for Molecular Bioscience, University of Queensland, St. Lucia, Qld, Australia</nlm:aff></affiliation></author><author><name sortKey="Henrich, Thorsten" sort="Henrich, Thorsten" uniqKey="Henrich T" first="Thorsten" last="Henrich">Thorsten Henrich</name><affiliation><nlm:aff id="A12">EMBL Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany</nlm:aff></affiliation></author><author><name sortKey="Herrmann, Bernhard G" sort="Herrmann, Bernhard G" uniqKey="Herrmann B" first="Bernhard G" last="Herrmann">Bernhard G. Herrmann</name><affiliation><nlm:aff id="A13">Institute for medical Genetics, Charité-CBF, and Dept. Developmental Genetics, Max-Planck-Institute for molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany</nlm:aff></affiliation></author><author><name sortKey="Johnson, Michael H" sort="Johnson, Michael H" uniqKey="Johnson M" first="Michael H" last="Johnson">Michael H. Johnson</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation></author><author><name sortKey="Korb, Martin" sort="Korb, Martin" uniqKey="Korb M" first="Martin" last="Korb">Martin Korb</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation></author><author><name sortKey="Mills, Jason C" sort="Mills, Jason C" uniqKey="Mills J" first="Jason C" last="Mills">Jason C. Mills</name><affiliation><nlm:aff id="A14">Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA</nlm:aff></affiliation></author><author><name sortKey="Oudes, Asa J" sort="Oudes, Asa J" uniqKey="Oudes A" first="Asa J" last="Oudes">Asa J. Oudes</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Parkinson, Helen E" sort="Parkinson, Helen E" uniqKey="Parkinson H" first="Helen E" last="Parkinson">Helen E. Parkinson</name><affiliation><nlm:aff id="A5">EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Pascal, Laura E" sort="Pascal, Laura E" uniqKey="Pascal L" first="Laura E" last="Pascal">Laura E. Pascal</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Pollet, Nicolas" sort="Pollet, Nicolas" uniqKey="Pollet N" first="Nicolas" last="Pollet">Nicolas Pollet</name><affiliation><nlm:aff id="A15">CNRS UMR 8080, Université Paris-Sud, 91405 Orsay, France</nlm:aff></affiliation></author><author><name sortKey="Quackenbush, John" sort="Quackenbush, John" uniqKey="Quackenbush J" first="John" last="Quackenbush">John Quackenbush</name><affiliation><nlm:aff id="A16">Dana-Farber Cancer Institute, 44 Binney Street, M232, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Ramialison, Mirana" sort="Ramialison, Mirana" uniqKey="Ramialison M" first="Mirana" last="Ramialison">Mirana Ramialison</name><affiliation><nlm:aff id="A12">EMBL Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany</nlm:aff></affiliation></author><author><name sortKey="Ringwald, Martin" sort="Ringwald, Martin" uniqKey="Ringwald M" first="Martin" last="Ringwald">Martin Ringwald</name><affiliation><nlm:aff id="A17">The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA</nlm:aff></affiliation></author><author><name sortKey="Salgado, David" sort="Salgado, David" uniqKey="Salgado D" first="David" last="Salgado">David Salgado</name><affiliation><nlm:aff id="A9">Institut de Biologie du Développement de Marseille, UMR 6216, CNRS/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France</nlm:aff></affiliation></author><author><name sortKey="Sansone, Susanna Assunta" sort="Sansone, Susanna Assunta" uniqKey="Sansone S" first="Susanna-Assunta" last="Sansone">Susanna-Assunta Sansone</name><affiliation><nlm:aff id="A5">EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</nlm:aff></affiliation></author><author><name sortKey="Sherlock, Gavin" sort="Sherlock, Gavin" uniqKey="Sherlock G" first="Gavin" last="Sherlock">Gavin Sherlock</name><affiliation><nlm:aff id="A18">Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5120, USA</nlm:aff></affiliation></author><author><name sortKey="Stoeckert, Christian J" sort="Stoeckert, Christian J" uniqKey="Stoeckert C" first="Christian J" last="Stoeckert">Christian J. Stoeckert</name><affiliation><nlm:aff id="A19">Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA</nlm:aff></affiliation></author><author><name sortKey="Swedlow, Jason" sort="Swedlow, Jason" uniqKey="Swedlow J" first="Jason" last="Swedlow">Jason Swedlow</name><affiliation><nlm:aff id="A20">Division of Gene Regulation and Expression, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland</nlm:aff></affiliation></author><author><name sortKey="Taylor, Ronald C" sort="Taylor, Ronald C" uniqKey="Taylor R" first="Ronald C" last="Taylor">Ronald C. Taylor</name><affiliation><nlm:aff id="A21">Computational Biology & Bioinformatics Group, Pacific Northwest National Laboratory, PO Box 999, MS K7-90, Richland, WA 99352, USA</nlm:aff></affiliation></author><author><name sortKey="Walashek, Laura" sort="Walashek, Laura" uniqKey="Walashek L" first="Laura" last="Walashek">Laura Walashek</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="Warford, Anthony" sort="Warford, Anthony" uniqKey="Warford A" first="Anthony" last="Warford">Anthony Warford</name><affiliation><nlm:aff id="A22">Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 IHH, UK</nlm:aff></affiliation></author><author><name sortKey="Wilkinson, David G" sort="Wilkinson, David G" uniqKey="Wilkinson D" first="David G" last="Wilkinson">David G. Wilkinson</name><affiliation><nlm:aff id="A23">Division of Developmental Neurobiology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK</nlm:aff></affiliation></author><author><name sortKey="Zhou, Yi" sort="Zhou, Yi" uniqKey="Zhou Y" first="Yi" last="Zhou">Yi Zhou</name><affiliation><nlm:aff id="A24">Stem Cell Program, Division of Hematology/Oncology, Children’s Hospital Boston and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Zon, Leonard I" sort="Zon, Leonard I" uniqKey="Zon L" first="Leonard I" last="Zon">Leonard I. Zon</name><affiliation><nlm:aff id="A24">Stem Cell Program, Division of Hematology/Oncology, Children’s Hospital Boston and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA</nlm:aff></affiliation></author><author><name sortKey="Liu, Alvin Y" sort="Liu, Alvin Y" uniqKey="Liu A" first="Alvin Y" last="Liu">Alvin Y. Liu</name><affiliation><nlm:aff id="A1">Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A10">Department of Urology, University of Washington, Seattle, WA 98195, USA</nlm:aff></affiliation></author><author><name sortKey="True, Lawrence D" sort="True, Lawrence D" uniqKey="True L" first="Lawrence D" last="True">Lawrence D. True</name><affiliation><nlm:aff id="A25">Department of Pathology, University of Washington, Seattle, WA 98195-6100, USA</nlm:aff></affiliation></author></analytic><series><title level="j">Nature biotechnology</title><idno type="ISSN">1087-0156</idno><idno type="eISSN">1546-1696</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">One purpose of the biomedical literature is to report results in sufficient detail so that the methods of data collection and analysis can be independently replicated and verified. Here we present for consideration a minimum information specification for gene expression localization experiments, called the “Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)”. It is modelled after the MIAME (Minimum Information About a Microarray Experiment) specification for microarray experiments. Data specifications like MIAME and MISFISHIE specify the information <italic>content</italic> without dictating a <italic>format</italic> for encoding that information. The MISFISHIE specification describes six types of information that should 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 initially developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9604648</journal-id><journal-id journal-id-type="pubmed-jr-id">20305</journal-id><journal-id journal-id-type="nlm-ta">Nat Biotechnol</journal-id><journal-id journal-id-type="iso-abbrev">Nat. Biotechnol.</journal-id><journal-title-group><journal-title>Nature biotechnology</journal-title></journal-title-group><issn pub-type="ppub">1087-0156</issn><issn pub-type="epub">1546-1696</issn></journal-meta><article-meta><article-id pub-id-type="pmid">18327244</article-id><article-id pub-id-type="pmc">4367930</article-id><article-id pub-id-type="doi">10.1038/nbt1391</article-id><article-id pub-id-type="manuscript">NIHMS336668</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Deutsch</surname><given-names>Eric W</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Ball</surname><given-names>Catherine A</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Berman</surname><given-names>Jules J</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Bova</surname><given-names>G Steven</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Brazma</surname><given-names>Alvis</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Bumgarner</surname><given-names>Roger E</given-names></name><xref ref-type="aff" rid="A6">6</xref></contrib><contrib contrib-type="author"><name><surname>Campbell</surname><given-names>David</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Causton</surname><given-names>Helen C</given-names></name><xref ref-type="aff" rid="A7">7</xref></contrib><contrib contrib-type="author"><name><surname>Christiansen</surname><given-names>Jeffrey H</given-names></name><xref ref-type="aff" rid="A8">8</xref></contrib><contrib contrib-type="author"><name><surname>Daian</surname><given-names>Fabrice</given-names></name><xref ref-type="aff" rid="A9">9</xref></contrib><contrib contrib-type="author"><name><surname>Dauga</surname><given-names>Delphine</given-names></name><xref ref-type="aff" rid="A9">9</xref></contrib><contrib contrib-type="author"><name><surname>Davidson</surname><given-names>Duncan R</given-names></name><xref ref-type="aff" rid="A8">8</xref></contrib><contrib contrib-type="author"><name><surname>Gimenez</surname><given-names>Gregory</given-names></name><xref ref-type="aff" rid="A9">9</xref></contrib><contrib contrib-type="author"><name><surname>Goo</surname><given-names>Young Ah</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Grimmond</surname><given-names>Sean</given-names></name><xref ref-type="aff" rid="A11">11</xref></contrib><contrib contrib-type="author"><name><surname>Henrich</surname><given-names>Thorsten</given-names></name><xref ref-type="aff" rid="A12">12</xref></contrib><contrib contrib-type="author"><name><surname>Herrmann</surname><given-names>Bernhard G</given-names></name><xref ref-type="aff" rid="A13">13</xref></contrib><contrib contrib-type="author"><name><surname>Johnson</surname><given-names>Michael H</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Korb</surname><given-names>Martin</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib><contrib contrib-type="author"><name><surname>Mills</surname><given-names>Jason C</given-names></name><xref ref-type="aff" rid="A14">14</xref></contrib><contrib contrib-type="author"><name><surname>Oudes</surname><given-names>Asa J</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Parkinson</surname><given-names>Helen E</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Pascal</surname><given-names>Laura E</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Pollet</surname><given-names>Nicolas</given-names></name><xref ref-type="aff" rid="A15">15</xref></contrib><contrib contrib-type="author"><name><surname>Quackenbush</surname><given-names>John</given-names></name><xref ref-type="aff" rid="A16">16</xref></contrib><contrib contrib-type="author"><name><surname>Ramialison</surname><given-names>Mirana</given-names></name><xref ref-type="aff" rid="A12">12</xref></contrib><contrib contrib-type="author"><name><surname>Ringwald</surname><given-names>Martin</given-names></name><xref ref-type="aff" rid="A17">17</xref></contrib><contrib contrib-type="author"><name><surname>Salgado</surname><given-names>David</given-names></name><xref ref-type="aff" rid="A9">9</xref></contrib><contrib contrib-type="author"><name><surname>Sansone</surname><given-names>Susanna-Assunta</given-names></name><xref ref-type="aff" rid="A5">5</xref></contrib><contrib contrib-type="author"><name><surname>Sherlock</surname><given-names>Gavin</given-names></name><xref ref-type="aff" rid="A18">18</xref></contrib><contrib contrib-type="author"><name><surname>Stoeckert</surname><given-names>Christian J</given-names><suffix>Jr.</suffix></name><xref ref-type="aff" rid="A19">19</xref></contrib><contrib contrib-type="author"><name><surname>Swedlow</surname><given-names>Jason</given-names></name><xref ref-type="aff" rid="A20">20</xref></contrib><contrib contrib-type="author"><name><surname>Taylor</surname><given-names>Ronald C</given-names></name><xref ref-type="aff" rid="A21">21</xref></contrib><contrib contrib-type="author"><name><surname>Walashek</surname><given-names>Laura</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>Warford</surname><given-names>Anthony</given-names></name><xref ref-type="aff" rid="A22">22</xref></contrib><contrib contrib-type="author"><name><surname>Wilkinson</surname><given-names>David G</given-names></name><xref ref-type="aff" rid="A23">23</xref></contrib><contrib contrib-type="author"><name><surname>Zhou</surname><given-names>Yi</given-names></name><xref ref-type="aff" rid="A24">24</xref></contrib><contrib contrib-type="author"><name><surname>Zon</surname><given-names>Leonard I</given-names></name><xref ref-type="aff" rid="A24">24</xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Alvin Y</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A10">10</xref></contrib><contrib contrib-type="author"><name><surname>True</surname><given-names>Lawrence D</given-names></name><xref ref-type="aff" rid="A25">25</xref></contrib></contrib-group><aff id="A1"><label>1</label>Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA</aff><aff id="A2"><label>2</label>Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive West, Stanford, CA 94305, USA</aff><aff id="A3"><label>3</label>Association for Pathology Informatics, 9650 Rockville Pike, Bethesda, MD 20814, USA</aff><aff id="A4"><label>4</label>Johns Hopkins University School of Medicine, PELICAN Laboratory, Departments of Pathology , Health Information Sciences, Genetic Medicine, Oncology, and Urology, Baltimore, MD, USA</aff><aff id="A5"><label>5</label>EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK</aff><aff id="A6"><label>6</label>Department of Microbiology, University of Washington, Seattle, WA 98195, USA</aff><aff id="A7"><label>7</label>MRC CSC Microarray Centre, Imperial College School of Medicine, London, W12 ONN, UK</aff><aff id="A8"><label>8</label>MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh, UK EH4 2XU</aff><aff id="A9"><label>9</label>Institut de Biologie du Développement de Marseille, UMR 6216, CNRS/Université de la Méditerranée, Parc Scientifique de Luminy, Case 907, F-13288 Marseille Cedex 9, France</aff><aff id="A10"><label>10</label>Department of Urology, University of Washington, Seattle, WA 98195, USA</aff><aff id="A11"><label>11</label>Institute for Molecular Bioscience, University of Queensland, St. Lucia, Qld, Australia</aff><aff id="A12"><label>12</label>EMBL Heidelberg, Meyerhofstrasse 1, D-69117 Heidelberg, Germany</aff><aff id="A13"><label>13</label>Institute for medical Genetics, Charité-CBF, and Dept. Developmental Genetics, Max-Planck-Institute for molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany</aff><aff id="A14"><label>14</label>Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA</aff><aff id="A15"><label>15</label>CNRS UMR 8080, Université Paris-Sud, 91405 Orsay, France</aff><aff id="A16"><label>16</label>Dana-Farber Cancer Institute, 44 Binney Street, M232, Boston, MA 02115, USA</aff><aff id="A17"><label>17</label>The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA</aff><aff id="A18"><label>18</label>Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5120, USA</aff><aff id="A19"><label>19</label>Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA</aff><aff id="A20"><label>20</label>Division of Gene Regulation and Expression, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland</aff><aff id="A21"><label>21</label>Computational Biology & Bioinformatics Group, Pacific Northwest National Laboratory, PO Box 999, MS K7-90, Richland, WA 99352, USA</aff><aff id="A22"><label>22</label>Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 IHH, UK</aff><aff id="A23"><label>23</label>Division of Developmental Neurobiology, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK</aff><aff id="A24"><label>24</label>Stem Cell Program, Division of Hematology/Oncology, Children’s Hospital Boston and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA</aff><aff id="A25"><label>25</label>Department of Pathology, University of Washington, Seattle, WA 98195-6100, USA</aff><pub-date pub-type="nihms-submitted"><day>11</day><month>3</month><year>2015</year></pub-date><pub-date pub-type="ppub"><month>3</month><year>2008</year></pub-date><pub-date pub-type="pmc-release"><day>20</day><month>3</month><year>2015</year></pub-date><volume>26</volume><issue>3</issue><fpage>305</fpage><lpage>312</lpage><pmc-comment>elocation-id from pubmed: 10.1038/nbt1391</pmc-comment>
<abstract><p id="P1">One purpose of the biomedical literature is to report results in sufficient detail so that the methods of data collection and analysis can be independently replicated and verified. Here we present for consideration a minimum information specification for gene expression localization experiments, called the “Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE)”. It is modelled after the MIAME (Minimum Information About a Microarray Experiment) specification for microarray experiments. Data specifications like MIAME and MISFISHIE specify the information <italic>content</italic> without dictating a <italic>format</italic> for encoding that information. The MISFISHIE specification describes six types of information that should 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 initially developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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