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Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment (2007) / Chapter Skim
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Appendix B: Minimum Information About a Microarray Experiment for Toxicogenomics
Pages 262-269

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From page 262...
... The breadth, depth, and uniformity of the information a database contains are critical to its utility. To address the last issue, MIAME/Tox content areas for experiment descriptions include information that are recommended to be provided by maximum use of controlled vocabularies or ontologies (such as species taxonomy, cell types, anatomy terms, histopa 1 Source: Based on MIAME/Tox 1.1, Draft, August 2003, from MIAME 2002.
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From page 263...
... MIAME/TOX CHECKLIST Minimum information to be recorded about toxicogenomics experiments is defined in subsequent sections and should include the following data domains: • Agent description, formulation, purity, solubility, vehicle, separation methods, chemical structure, active moieties, safety and toxicity, storage, halflife. • Experimental design parameters, genetic background and animal husbandry information or cell line and culture information, exposure parameters, dosing regimen, and dose groups.
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From page 264...
... Gene expression measurement data and Specifications of data processing MIAME/Tox recommends the following details on each of these sections.
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From page 265...
... • sample source provider • descriptors relevant to the particular sample, such as - strain - sex - genetic background - genetic modifications - age - weights - development stage - organism part (tissue) of the organism's anatomy from which the biological material is derived (if samples are cells)
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From page 266...
... Sample manipulations: laboratory protocols and relevant parameters, such as: • facilities details • animal husbandry and housing details • cell culture conditions • growth conditions (passage level and frequency) • metabolic competency of cell strains • treatment (stressor)
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From page 267...
... Nucleic Acid Extraction Protocol Applied to the Biological Material • Type of nucleic acid RNA, mRNA, or genomic DNA is extracted • extraction method • amplification methods if any. Labeling Protocol for Each Labeling Prepared from the Extract, Including • amount of nucleic acids labeled • label used (e.g., A-Cy3, G-Cy5, 33P, ….)
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From page 268...
... Measurement Data and Specifications of Data Processing This section remains identical to the MIAME 1.1 document On the Behalf of EMBL-EBI, NIEHS NCT, NIEHS NTP and ILSI HESI Susanna-Assunta Sansone1, EMBL -- The European Bioinformatics Institute; Michael D Waters, NIEHS National Center for Toxicogenomics; Syril D
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From page 269...
... National Center for Toxicogenomics, National Institute of Environmental Health Sciences [online]
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Key Terms

  • niehs national
  • biological materials
  • experimental design
  • sciences institute
  • european bioinformatics

  • extract preparation
  • bioinformatics institute
  • biological material
  • ilsi health
  • microarray data

  • scientific journals
  • measurement data
  • embl ebi
  • ilsi hesi
  • relevant parameters

  • laboratory protocols
  • international life
  • design description
  • national toxicology
  • microarray experiment

  • nucleic acid
  • toxicology program
  • section remains
  • cal assays
  • remains identical

  • toxicogenomic experimental
  • array design
  • genomic dna
  • acids labeled
  • acid extraction


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