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MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity.
Peirsman, Arne; Blondeel, Eva; Ahmed, Tasdiq; Anckaert, Jasper; Audenaert, Dominique; Boterberg, Tom; Buzas, Krisztina; Carragher, Neil; Castellani, Gastone; Castro, Flávia; Dangles-Marie, Virginie; Dawson, John; De Tullio, Pascal; De Vlieghere, Elly; Dedeyne, Sándor; Depypere, Herman; Diosdi, Akos; Dmitriev, Ruslan I; Dolznig, Helmut; Fischer, Suzanne; Gespach, Christian; Goossens, Vera; Heino, Jyrki; Hendrix, An; Horvath, Peter; Kunz-Schughart, Leoni A; Maes, Sebastiaan; Mangodt, Christophe; Mestdagh, Pieter; Michlíková, Sona; Oliveira, Maria José; Pampaloni, Francesco; Piccinini, Filippo; Pinheiro, Cláudio; Rahn, Jennifer; Robbins, Stephen M; Siljamäki, Elina; Steigemann, Patrick; Sys, Gwen; Takayama, Shuichi; Tesei, Anna; Tulkens, Joeri; Van Waeyenberge, Michiel; Vandesompele, Jo; Wagemans, Glenn; Weindorfer, Claudia; Yigit, Nurten; Zablowsky, Nina; Zanoni, Michele; Blondeel, Phillip.
Affiliation
  • Peirsman A; Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Blondeel E; Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Ahmed T; Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium.
  • Anckaert J; Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Audenaert D; Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Boterberg T; Wallace H Coulter Department of Biomedical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology and Emory School of Medicine, Atlanta, GA, USA.
  • Buzas K; OncoRNALab, Cancer Research Institute, Ghent, Belgium.
  • Carragher N; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
  • Castellani G; VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium.
  • Castro F; Department of Radiation Oncology, Ghent University Hospital, Ghent, Belgium.
  • Dangles-Marie V; Department of Immunology, University of Szeged, Faculty of Medicine-Faculty of Science and Informatics, Szeged, Hungary.
  • Dawson J; Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK.
  • De Tullio P; Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.
  • De Vlieghere E; i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.
  • Dedeyne S; Translational Research Department, Institut Curie, PSL Research University, and Faculty of Pharmacy, Paris, France.
  • Depypere H; Faculty of Pharmacy, Université Paris Descartes, Paris, France.
  • Diosdi A; Institute of Genetics and Cancer, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK.
  • Dmitriev RI; Center for Interdisciplinary Research on Medicines (CIRM), Metabolomics Group, Université de Liège, Liège, Belgium.
  • Dolznig H; Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Fischer S; Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Gespach C; Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Goossens V; Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Heino J; Menopause and Breast Clinic, Ghent University Hospital, Ghent, Belgium.
  • Hendrix A; Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center (BRC), Szeged, Hungary.
  • Horvath P; Tissue Engineering and Biomaterials Group, Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Kunz-Schughart LA; Institute of Medical Genetics, Medical University of Vienna, Vienna, Austria.
  • Maes S; Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Mangodt C; Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Mestdagh P; INSERM U938 Hospital Saint-Antoine Research Center CRSA, Team Céline Prunier, TGFbeta Signaling in Cellular Plasticity and Cancer, Sorbonne University, Paris, France.
  • Michlíková S; VIB Screening Core and Ghent University Expertise Centre for Bioassay Development and Screening (C-BIOS-VIB), Ghent University, Ghent, Belgium.
  • Oliveira MJ; Department of Life Technologies, University of Turku, Turku, Finland.
  • Pampaloni F; Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Piccinini F; Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Pinheiro C; Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center (BRC), Szeged, Hungary.
  • Rahn J; OncoRay - National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Carl Gustav Carus Faculty of Medicine at TU Dresden, and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.
  • Robbins SM; Plastic, Reconstructive and Aesthetic Surgery, Ghent University Hospital, Ghent, Belgium.
  • Siljamäki E; Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Steigemann P; Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Sys G; OncoRNALab, Cancer Research Institute, Ghent, Belgium.
  • Takayama S; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
  • Tesei A; OncoRay - National Center for Radiation Research in Oncology, University Hospital Carl Gustav Carus Dresden, Carl Gustav Carus Faculty of Medicine at TU Dresden, and Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany.
  • Tulkens J; i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal.
  • Van Waeyenberge M; Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany.
  • Vandesompele J; IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Meldola, Italy.
  • Wagemans G; Laboratory of Experimental Cancer Research, Cancer Research Institute, Ghent, Belgium.
  • Weindorfer C; Department of Human Structure and Repair, Ghent University, Ghent, Belgium.
  • Yigit N; Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
  • Zablowsky N; Departments of Oncology and Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
  • Zanoni M; Department of Life Technologies, University of Turku, Turku, Finland.
  • Blondeel P; Lead Discovery, Nuvisan ICB, Berlin, Germany.
Nat Methods ; 18(11): 1294-1303, 2021 11.
Article in En | MEDLINE | ID: mdl-34725485
ABSTRACT
Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase that assembles the experimental parameters of 3,058 published spheroid-related experiments. Interrogation of this knowledgebase identified heterogeneity in the methodological setup of spheroids. Empirical evaluation and interlaboratory validation of selected variations in spheroid methodology revealed diverse impacts on spheroid metrics. To facilitate interpretation, stimulate transparency and increase awareness, the Consortium defines the MISpheroID string, a minimum set of experimental parameters required to report spheroid research. Thus, MISpheroID combines a valuable resource and a tool for three-dimensional cellular models to mine experimental parameters and to improve reproducibility.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Biomarkers, Tumor / Spheroids, Cellular / Cell Proliferation / Knowledge Bases / Tumor Microenvironment / Neoplasms Type of study: Prognostic_studies Limits: Humans Language: En Journal: Nat Methods Journal subject: TECNICAS E PROCEDIMENTOS DE LABORATORIO Year: 2021 Document type: Article Affiliation country:
Fulltext
Add to My VHL
Print
XML
PubMed Links
Search on Google

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Biomarkers, Tumor / Spheroids, Cellular / Cell Proliferation / Knowledge Bases / Tumor Microenvironment / Neoplasms Type of study: Prognostic_studies Limits: Humans Language: En Journal: Nat Methods Journal subject: TECNICAS E PROCEDIMENTOS DE LABORATORIO Year: 2021 Document type: Article Affiliation country: