Comment[ArrayExpressAccession] E-GEOD-31561 MAGE-TAB Version 1.1 Public Release Date 2013-02-19 Investigation Title Transcriptional analysis of organ-specific toxicity induced by a panPPAR agonist in mice: Identification of organ-specific toxicity biomarkers Comment[Submitted Name] Transcriptional analysis of organ-specific toxicity induced by a panPPAR agonist in mice: Identification of organ-specific toxicity biomarkers Experiment Description In this study, we aim to identify candidate biomarkers which may be useful as surrogate indicators of toxicity for pre-clinical development of panPPAR-agonist drug candidates. Gene expression microarray, histopathology and clinical chemistry data were generated from liver, heart, kidney and skeletal muscles of three groups of mice administered with three different dosages of an experimental pan-peroxisome proliferator-activated receptor (pan-PPAR) agonist, PPM-201, for 14 days. The histopathology and clinical chemistry data were compared with the gene expression analysis and candidate biomarker genes were identified. Nine wild type mice (strain: C57BL/6J) were randomly divided into three groups - Group-I, II and III. PPM-201 in the vehicle base was administered daily for 14 days at 6 mg/kg body weight dose rate to each mouse in Group-II and at 20mg/kg body weight dose rate to each mouse in Group-III while the mice in Group-I received only the vehicle base. On 15th day, the mice were sacrificed to harvest blood, heart, skeletal muscle, liver and kidney tissues for clinical chemistry, microarray and histopathology analysis. In the clinical chemistry analysis, alanine aminotransferase (ALT, U/L), aspartate aminotransferase (AST, U/L), creatinine kinase (CK, U/L), blood urea nitrogen (BUN, mmol/L), creatinine (umol/L) and lactate dehydrogenase (LDH, U/L) were measured from the blood of each mouse. Two sections of liver, two sections of kidney, one or two sections of skeletal muscle, and one section of heart were prepared from each mouse, stained with hematoxylin and eosin (H&E), and examined by a veterinary pathologist. RNA was extracted and processed as per the established protocol from heart, skeletal muscle, liver and kidney tissue samples of all the 9 mice for profiling with Affymetrix Mouse Genome 430 2.0 Array and in total 36 chips were prepared. Using various quality control measures, the data was analysed for its quality. As it was found to be good in quality, the data from all the 36 chips were used for further analysis. The results from histopathology and clinical chemistry analysis were compared with the gene expression to determine if the dosages selected for the study were associated with findings in target organs. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Mudaliar Crowther Mudaliar Haggart Miele Person First Name Manikhandan Daniel Manikhandan Ross Gino Person Mid Initials A V J A D Person Email bioinfo786@gmail.com Person Affiliation University of Glasgow Person Address College of Medical, Veterinary and Life Sciences, University of Glasgow, B3-08, Joseph Black Building, University Place, Glasgow, Scotland, United Kingdom Person Roles submitter Protocol Name P-GSE31561-1 P-GSE31561-5 P-GSE31561-4 P-GSE31561-2 P-GSE31561-3 P-GSE31561-6 Protocol Description ID_REF = VALUE = RMA normalised log2 transformed expression values generated using Partek GS 6.5 software Microarrays were scanned using Genechip Scanner 3000 7G. Probe quality and fragmentation were confirmed using Bioanalyser 2100 prior to microarray hybridisation. Fragmented and labelled probes were hybridised for 18 hours onto Affymetrix GeneChipM-. Mouse Genome 430 2.0 Array (cat. 900496, Affymetrix) using GeneChip Hybridization, Wash, and Stain Kit (cat. 900720-900722, Affymetrix). RNA extraction was performed in random batches by polytron homogenisation of tissue in Trizol (cat. 15596-026, Invitrogen) followed by phenol chloroform extraction. RNAs were quantitated and qualified using Nanodrop ND8000 (Thermo Scientific) and 2100 Bioanalyser (Agilent). Prior to cDNA probe generation RNAs were subjected to sample clean up and DNAse I treatment using RNEasy Micro (Qiagen) before repeat quantitation and qualification. 50ng RNA from each sample were used to generate complementary DNA strands using Ovation RNA Amplification System V2 (cat. 3100-12, Nugen) and 3.75ug of each cDNA were fragmented and biotin labelled using EncoreM-bM-^DM-" Biotin Module (cat. 4200-12, Nugen). The data in the matrix table were generated from raw CEL files using RMA normalisation method in Partek GS 6.5 software. Protocol Type bioassay_data_transformation image_aquisition hybridization nucleic_acid_extraction labeling feature_extraction Experimental Factor Name RNA INTEGRITY NUMBER RIN DOSAGE L TREATMENT MOUSE NUMBER ORGANISM PART Experimental Factor Type rna integrity number rin dosage l treatment mouse number organism part Publication Title Simultaneous non-negative matrix factorization for multiple large scale gene expression datasets in toxicology. Publication Author List Lee CM, Mudaliar MA, Haggart DR, Wolf CR, Miele G, Vass JK, Higham DJ, Crowther D PubMed ID 23272042 Publication DOI 10.1371/journal.pone.0048238 Comment[SecondaryAccession] GSE31561 Comment[GEOReleaseDate] 2013-02-19 Comment[ArrayExpressSubmissionDate] 2011-08-22 Comment[GEOLastUpdateDate] 2013-02-19 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-31561.sdrf.txt