Genomics Core

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The objectives of the research proposals in this application are to determine at a global scale the mechanisms that underpin the αβ versus γδ lineage choice. Many of the experiments proposed in the application involve genome-wide analyses and interpretation of the data obtained from such analyses. The purpose of the Genomics Core is to provide the laboratories with the following services that will permit the proposed studies to be completed. The Genomics Core would perform HiC, ChlP-Seq and RNA-Seq analyses, followed by bioinformatics analysis. Thus the entire spectrum of genome-wide analyses that concerns this POl would be performed at the UCSD Genomics Core Facility. Why a centralized Genomics Core? There are three reasons: (1) Except for the Murre laboratory, none of the participating laboratories have expertise in ChlP-Seq and RNA-Seq. (2) The Zhuang, Wiest and Zuniga-Pflucker laboratories do not have access to the bioinformatic infrastructure and analytical tools that have been established at UCSD. (3) The genomics core would permit us to standardize the ChlP-Seq and RNA-Seq analysis. This means using the same antibodies, same lot number and the same approach thereby allowing a careful and consistent comparison of the different binding patterns that will be derived from the various studies. (4) The Genomics Core will provide training to visiting research fellows. Thus, we envision that graduate students and postdoctoral fellows from the other laboratories would visit UCSD in order to become familiar with global approaches and analyses. Accordingly, an integral part of our approach is to provide personnel from different institutions access to these global analysis tools and provide training.