The main objective of the Genomics Core will be to provide access to researchers on the collaborator to genomics technologies and the bioinformatic analysis needed to analyze the complex data derived from such technologies. Genomics technologies have become essential laboratory tools and will generate data that will guide the research in the collaboratory towards an HIV-1 cure. The Genomics Core will interact with every project in every objective and with the other cores proposed in the collaboratory. Specifically, with respect to virus genomics, the Genomics Core will provide access to sequencing, which will be used to identify the defects in proviral DNA that result in non-competent virus (Project 4.1) and will also be used to identify additional virus reservoirs by revealing viruses in the plasma whose sequence does not correlate with virus derived from the well-characterized CD4+ T cell reservoir (Project 4.2). Additionally, each project will benefit from the assays at the Genomics Core to monitor HIV replication in order to evaluate latency and the effects of HlV-inducing compounds. In respect to host genomics, the Genomics Core will primarily provide gene expression assays (whole genome microarray and qRT-PCR) in order to define the molecular mechanisms underlying viral persistence (Projects 1.1, 1.2,1.4 and 1.5) and determine biomarkers indicative of effective HlV-inducing compounds (Project 2.1). In addition, chromatin immunoprecipitation (ChIP) coupled with high throughput sequencing (ChlP-Seq) will be used to investigate gene regulation by the BAF chromatin remodeling complex (Project 1.2). When these studies are complete the genomics assays provided by the Genomics Core will have provided a better understanding of HIV latency, identified new pathways and avenues for therapeutic intervention, delineated the mode of action of HlV-inducing compounds, and characterized new viral reservoir in HIV-infected individuals.
The experiments performed at the Genomics Core will use the latest technologies for analyzing virus and host genomes. The results of these experiments will accelerate research towards a cure for HIV-1.
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