Collaborative support of investigators and research and development of analytical methods, computational tools and scientific databases: 1) Additional implementation of a high-performance computing mixed model approach to test significance of nuclear and mitochondrial SNPs interactions with kinship relationships in various strains of mice. 2) Analysis pipeline for whole genome, whole exome, and targeted gene sequencing data for development of a validated genomic reference for assessing performance of human cancer panels or for cancer mutation signature identification in rats. 3) Comparison of gene expression platforms using liver mode of action samples from rats exposed to chemicals and studies with the same experimental design. 4) Analysis of dilution reference standards on the TempO-Seq platform for evaluation of sensitivity and other performance metrics. 5) Launched the Rat Atlas of Tissue-specific and Enriched miRNAs (RATEmiRs) web application database. 6) Compiled, quality controlled, preprocessed and deposited the NCI/NIEHS cancer therapeutics combination exposure microarray gene expression data set for public availability.

Project Start
Project End
Budget Start
Budget End
Support Year
13
Fiscal Year
2019
Total Cost
Indirect Cost
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Lozoya, Oswaldo A; Martinez-Reyes, Inmaculada; Wang, Tianyuan et al. (2018) Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation. PLoS Biol 16:e2005707
Duncan, Christopher G; Kondilis-Mangum, Hrisavgi D; Grimm, Sara A et al. (2018) Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells. G3 (Bethesda) 8:805-813
Duncan, Christopher G; Grimm, Sara A; Morgan, Daniel L et al. (2018) Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver. Sci Rep 8:10138
Nguyen, Thuy-Ai T; Grimm, Sara A; Bushel, Pierre R et al. (2018) Revealing a human p53 universe. Nucleic Acids Res :
Mav, Deepak; Shah, Ruchir R; Howard, Brian E et al. (2018) A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. PLoS One 13:e0191105
Muñoz, M D; Della Vedova, M C; Bushel, P R et al. (2018) The nitrone spin trap 5,5-dimethyl-1-pyrroline N-oxide dampens lipopolysaccharide-induced transcriptomic changes in macrophages. Inflamm Res 67:515-530
Osgood, Ross S; Upham, Brad L; Bushel, Pierre R et al. (2017) Secondhand Smoke-Prevalent Polycyclic Aromatic Hydrocarbon Binary Mixture-Induced Specific Mitogenic and Pro-inflammatory Cell Signaling Events in Lung Epithelial Cells. Toxicol Sci 157:156-171
Funderburk, Karen M; Auerbach, Scott S; Bushel, Pierre R (2017) Crosstalk between Receptor and Non-receptor Mediated Chemical Modes of Action in Rat Livers Converges through a Dysregulated Gene Expression Network at Tumor Suppressor Tp53. Front Genet 8:157
Bennett, Brian D; Bushel, Pierre R (2017) goSTAG: gene ontology subtrees to tag and annotate genes within a set. Source Code Biol Med 12:6
Bushel, P R; Fannin, R D; Gerrish, K et al. (2017) Blood gene expression profiling of an early acetaminophen response. Pharmacogenomics J 17:230-236

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