Omics, Bioinformatics, and Data Management Core

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CORE D PROJECT SUMMARY The `Omics, Bioinformatics, and Data Management Core (Core D) serves this Program by providing high resolution functional genomics and bioinformatics computation analyses with statistical integration. The main objective of the Core is to define the gene expression signatures and their functional output that program the immune response for 68-1 RhCMV/SIV vaccine mediated SIV replication arrest in pre-clinical rhesus macaque (RM) vaccine studies. The Core will interrogate single CD8+ T cells in blood and tissues, their linkage of specific T cell receptor usage (to identify SIV-specific clonotypes), single non-CD8+ T cells in blood and tissues, and whole immune tissues including whole blood, lymph node (LN), spleen, bone marrow (BM) and gut-associated lymphoid tissues (GALT), and will link data sets with spatial transcriptomic data sets, to define gene expression signatures and networks, and will apply cutting edge bioinformatics approaches to model their functional output and inform the mechanisms of action by which RhCMV/SIV vaccination programs the immune response for replication arrest-type protection against SIV infection. To meet these goals, Core D will address the following Specific Aims: 1) provide specialized CITE-seq and/or TCR sequence identification using the 10X Genomics platform, 2) conduct Nanostring and bulk RNAseq analysis of whole blood and tissues, 3) provide bioinformatic and biostatistical analyses, and computational modeling, to define immune response gene expression signatures linked with vaccine actions and virus control, and 4) develop and manage a comprehensive database for all Program data to facilitate integrated data analysis. Core D is directed by Dr. Michael Gale, Jr., working closely with Drs. Ben Bimber and Paul Edlefsen, to provide consistent, high-quality functional genomics data generation, integrated data analysis, biostatistical analyses and computational modeling, with big data management, for all aspects of the scientific program.