Investigation Title Transcription profiling of liver from wistar and kyoto rats exposed to orotic acid to investigate fatty liver disease Comment[Submitted Name] The Influence of Pharmacogenetics on Fatty Liver Disease in the Wistar and Kyoto Rats: A Combined Transcriptomic and Metabonomic Experimental Design time series design transcription profiling by array Experimental Design Term Source REF OBI EFO Comment[SecondaryAccession] BII-S-6 Comment[ArrayExpressReleaseDate] 2009-03-11 Comment[AEMIAMESCORE] 4 Comment[Publication DOI] DOI: 10.1021/pr0601640 Comment[ArrayExpressAccession] E-BIID-1 Comment[MAGETAB TimeStamp_Version] 2011-06-28 11:45:14 Last Changed Rev: 14857 Experimental Factor Name compound time strain Experimental Factor Type compound time strain_or_line Experimental Factor Term Source REF Person Last Name Griffin Jeremy Person First Name Julian Nicholson Person Mid Initials K Person Email Person Phone Person Fax Person Address University of Cambridge Imperial College London Person Affiliation Department of Molecular Biology Biomedical Sciences Person Roles investigator;submitter investigator Person Roles Term Source REF Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2009-03-11 PubMed ID 17203948 Publication DOI 17203948 Publication Author List Griffin JL, Scott J, Nicholson JK. Publication Title The influence of pharmacogenetics on fatty liver disease in the wistar and kyoto rats: a combined transcriptomic and metabonomic study. Publication Status journal_article Publication Status Term Source REF The MGED Ontology Experiment Description Although fatty liver disease is caused by a number of toxicological insults and the metabolic syndrome, the exact mechanisms by which many of these pathophysiological stimulii induce fatty liver are unknown. The rapid and profound steatosis caused by orotic acid, resulting from an impairment in the production of ApoB, has been investigated in the Wistar strain rat using a combined transcriptomic and metabonomic/metabolomic approach. Analysis of liver tissue from rats exposed to orotic acid for 1, 3, and 14 days was performed by DNA microarrays and high resolution 1H NMR spectroscopy based metabonomics of both tissue extracts and intact tissue (n = 3). Data were analyzed using a combination of ANOVA and principal components analysis, used as a data reduction tool to visualize the most perturbed transcripts and metabolites. Orotic acid produced a profound 8-fold increase in total lipids, and in particular increases in resonances associated with polyunsaturated fats (CHCH and CH2CHCH groups). This was accompanied by increases in the concentrations of trimethylamine-oxide (TMAO), betaine, choline, and phosphocholine, as well as a relative decrease in glucose and glycogen. At the transcriptional level, perturbations were detected in both oxidative stress and osmoregulation/pH homeostasis. However, this contrasts with a previous transcriptomic/metabolic study of fatty liver disease in a combined data set of Wistar (out-bred) and Kyoto (in-bred) strains of rats, with only 4 transcripts being found to be in common between the two analyses. This emphasizes the need to understand how strain background interacts with a given toxic lesion or genetic modification. Keywords: metabolomics . metabolic profiling . pattern recognition . nonalcoholic steatohepatisis Protocol Name P-MTAB-3518 P-MTAB-3521 P-MTAB-3522 P-MTAB-3523 P-MTAB-3525 Protocol Type animal care nucleic acid extraction labeling hybridization data_transformation Protocol Description All animal procedures conformed to Home Office, UK, guidelines for animal welfare. Male Wistar rats (n ) 3 for each time point; control animals fed control diet for the same time period; Charles River UK Ltd.) were fed either standard laboratory chow, or chow supplemented with 1% orotic acid (Sigma Aldrich, UK) ad libitum.5-6 Rats were killed by cervical dislocation at days 0, 1, 3 and 14, and the left lateral lobe of the liver excised. Tissues were snap frozen and stored at -80 ᄀC. Total RNA was extracted by RNA Isolation Kit (Stratagene) from the livers of Wistar rats at day 0 (n ) 3), day 1 and 3 (n ) 2), and day 14 (n ) 3). Biotinylated cRNA was prepared following the guidelines described by Affymetrix. Biotinylated cRNA probes was hybridized following the guidelines described by Affymetrix. CEL were normalized using Affymetrix MAS 5.0 application Protocol Parameters compound;sacrifice method;diet availability;diet;dose; Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF OBI OBI OBI SDRF File E-BIID-1.sdrf.txt Term Source Name NEWT EFO NCBI Taxonomy BTO ArrayExpress CHEBI OBI EFO The MGED Ontology Term Source File NEWT UniProt Taxonomy Database http://www.ebi.ac.uk/efo/ http://www.ncbi.nlm.nih.gov/Taxonomy/ BRENDA tissue / enzyme source http://www.ebi.ac.uk/arrayexpress Chemical Entities of Biological Interest Ontology for Biomedical Investigations http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version