Next generation sequencing is now a central tool in the analysis of signaling pathways important in development and disease. The Genome Sequencing Core (GSC) is aimed at providing researchers at the University of Kansas in Lawrence with next-generation sequencing technologies as well as expertise in experimental design and analysis of sequence data. Projects in the GSC will include whole genome assembly, genome re-sequencing for identification of mutations important in development and disease, transcriptome analysis (RNA seq), and identification of transcription factor interaction sites using chromatin immunoprecipitation combined with DNA sequencing (ChIP seq). The GSC will house a state-of-the-art lllumina Hiseq 2000 sequencer with dedicated processor and storage space to run the instrument. This core facility will enhance the genomics infrastructure already at KU, in the KU Genomics Center and the KU DNA Sequencing Facility, which provides standard, first generation sequencing. Together, the three cores allow for a thorough, integrated dissection of disease pathways using novel fluorescence probes to define a cellular process, to find mutations affecting that cellular process, and to define genes involved in the cellular process. The novel approach of the MADP is to combine the enabling technologies of fluorescent probe synthetic chemistry and next generation sequencing to set up a pipeline for target discovery in disease pathways. Next generation sequencing is an enabling technology in that it has the power to allow investigators from many different disciplines to ask new questions in their research areas of interest. The GSC will enable genomics research at the University of Kansas by eliminating the barriers of cost and communication involved with using off-campus facilities. Interest in next generation sequencing at the University of Kansas in Lawrence is high, and includes investigators in the Pharmacy School, the Department of Molecular Biosciences, and the Department of Ecology and Evolutionary Biology. Use ofthe GSC will be by Projects in this Molecular Analysis of Disease Pathways COBRE, as well as by researchers across the campus and in many different disciplines.

Public Health Relevance

Next-generation sequencing technologies have revolutionized genetic and molecular analyses by allowing the generation of tens of millions of sequencing reads and billions of sequenced bases in a relatively short time and for a relatively low cost. The uses are many and profound, such as genome re-sequencing to identify new mutations or lesions important in diseases such as cancer;transcriptome analysis to understand global gene regulation in normal and pathogenic states;and global analysis of transcription factor interactions with regulatory elements across the entire genome. Next-generation sequencing is becoming a central tool in almost every aspect of genetic and molecular research, and the Genome Sequencing Core will provide a strong base for next-generation sequencing at the University of Kansas and will serve as a base for continued growth in this area at the university.

National Institute of Health (NIH)
Exploratory Grants (P20)
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Special Emphasis Panel (ZRR1)
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University of Kansas Lawrence
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Frau, Roberto; Bini, Valentina; Pillolla, Giuliano et al. (2014) Positive allosteric modulation of GABAB receptors ameliorates sensorimotor gating in rodent models. CNS Neurosci Ther 20:679-84
Sundararajan, Lakshmi; Norris, Megan L; Schöneich, Sebastian et al. (2014) The fat-like cadherin CDH-4 acts cell-non-autonomously in anterior-posterior neuroblast migration. Dev Biol 392:141-52
Hymel, David; Woydziak, Zachary R; Peterson, Blake R (2014) Detection of protein-protein interactions by proximity-driven S(N)Ar reactions of lysine-linked fluorophores. J Am Chem Soc 136:5241-4
Blumenstiel, Justin P (2014) Whole genome sequencing in Drosophila virilis identifies Polyphemus, a recently activated Tc1-like transposon with a possible role in hybrid dysgenesis. Mob DNA 5:6
Frau, Roberto; Bini, Valentina; Pes, Romina et al. (2014) Inhibition of 17*-hydroxylase/C17,20 lyase reduces gating deficits consequent to dopaminergic activation. Psychoneuroendocrinology 39:204-13
Woydziak, Zachary R; Fu, Liqiang; Peterson, Blake R (2014) Efficient and Scalable Synthesis of 4-Carboxy-Pennsylvania Green Methyl Ester: A Hydrophobic Building Block for Fluorescent Molecular Probes. Synthesis (Stuttg) 46:158-164
Sun, Meng; Kaplan, Sam V; Gehringer, Rachel C et al. (2014) Localized drug application and sub-second voltammetric dopamine release measurements in a brain slice perfusion device. Anal Chem 86:4151-6
Gunasekara, Dulan B; Siegel, Joseph M; Caruso, Giuseppe et al. (2014) Microchip electrophoresis with amperometric detection method for profiling cellular nitrosative stress markers. Analyst 139:3265-73
Blumenstiel, Justin P; Chen, Xi; He, Miaomiao et al. (2014) An age-of-allele test of neutrality for transposable element insertions. Genetics 196:523-38
Wickersheim, Michelle L; Blumenstiel, Justin P (2013) Terminator oligo blocking efficiently eliminates rRNA from Drosophila small RNA sequencing libraries. Biotechniques 55:269-72

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