A major goal in diabetes research is to understand how alterafions in the epigenome and subsequent responses in gene expression impact disease phenotype and treatment regimens. The Epigenefic and Genomics Core (EGC) will provide access to microarray platforms, massively parallel sequencing instrumentafion and computafional infrastructure to advance the diabetes and metabolism research goals of DRC investigators. The EGC will provide the following services: 1. Expression microarray technology;Affymetrix, Agilent, Codelink, NimbleGen, and lllumina platforms will be provided for microarray-based mRNA expression profiling. Affymetrix, Life Technologies and Exiqon platforms will be provide for miRNA profiling. 2. Technical support will be provided for high-throughput sequencing assays on lllumina HiSeq 2000 platforms, including RNA sequencing (RNAseq), microRNA sequencing (mlRNAseq), global run-on sequencing (GRO-Seq), ribosome profiling and deep sequencing (Ribo-Seq), chromafin immunoprecipitafion linked to massively parallel sequencing (ChlP-Seq) and MethylC-sequencing. 3. Bioinformatics support will be provided for assistance with experimental design, choice of technological platform, data analysis and data quality control. Implementafion of new data management and analysis pipelines will facilitate effective data mining. 4. Training of students, postdoctoral fellows, invesfigators and technical staff in the application of highthroughput sequencing methodologies and data analysis 5. High-performance computing resources, systems administrators, and data storage/backup systems will enable users to efficiently access and analyze their data. A major emphasis in the configurafion of the ECG will be implementafion of new Core services to reduce barriers to entry to new investigators. This will be achieved by providing direct Core support at three of the crifical steps required to take advantage of sequencing-based technologies;1) Preparafion of sequencing libraries, 2) provision of computafional resources, and 3) assistance with data analysis through both training and provision of informatics services.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Center Core Grants (P30)
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Special Emphasis Panel (ZDK1-GRB-S)
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University of California San Diego
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Sen, Supriya; Langiewicz, Magda; Jumaa, Hassan et al. (2015) Deletion of serine/arginine-rich splicing factor 3 in hepatocytes predisposes to hepatocellular carcinoma in mice. Hepatology 61:171-83
Chung, H; Lee, Y S; Mayoral, R et al. (2015) Omega-3 fatty acids reduce obesity-induced tumor progression independent of GPR120 in a mouse model of postmenopausal breast cancer. Oncogene 34:3504-13
Adar, Sara D; Kaufman, Joel D; Diez-Roux, Ana V et al. (2015) Air pollution and percent emphysema identified by computed tomography in the Multi-Ethnic study of Atherosclerosis. Environ Health Perspect 123:144-51
Weizman, Adam; Huang, Brian; Berel, Dror et al. (2014) Clinical, serologic, and genetic factors associated with pyoderma gangrenosum and erythema nodosum in inflammatory bowel disease patients. Inflamm Bowel Dis 20:525-33
Baker, Michael E; Hardiman, Gary (2014) Transcriptional analysis of endocrine disruption using zebrafish and massively parallel sequencing. J Mol Endocrinol 52:R241-56
Huang, Jie; Huffman, Jennifer E; Yamakuchi, Munekazu et al. (2014) Genome-wide association study for circulating tissue plasminogen activator levels and functional follow-up implicates endothelial STXBP5 and STX2. Arterioscler Thromb Vasc Biol 34:1093-101
Bis, Joshua C; White, Charles C; Franceschini, Nora et al. (2014) Sequencing of 2 subclinical atherosclerosis candidate regions in 3669 individuals: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study. Circ Cardiovasc Genet 7:359-64
Tang, Wenbo; Kowgier, Matthew; Loth, Daan W et al. (2014) Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function. PLoS One 9:e100776
Lubitz, Steven A; Lunetta, Kathryn L; Lin, Honghuang et al. (2014) Novel genetic markers associate with atrial fibrillation risk in Europeans and Japanese. J Am Coll Cardiol 63:1200-10
Nalls, Mike A; Pankratz, Nathan; Lill, Christina M et al. (2014) Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease. Nat Genet 46:989-93

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