The Single Cell and Integrative Genomics Core will provide support for individual Projects by performing assays requiring specialized technology and offering unique bioinformatics methodology. More specifically, Core B will be responsible for the following work: (i) conducting bulk and single-cell RNA-Seq profiling; (ii) running bulk and single-cell ATAC-Seq assays to assess chromatin accessibility, and (iii) providing computational expertise and bioinformatics for the analysis of Core B generated data that is beyond the capabilities of individual Projects. Core B is led by Dr. Steven Bosinger at Emory University, with Dr. Will Greenleaf at Stanford as a key Co-Investigator. Core B will be physically located at both Emory and Stanford. The Emory site of Core B (Bosinger) will conduct bulk and single-cell RNA-Seq library preparation and sequencing for the experiments described in each project. The Stanford site of Core B (Greenleaf) will be responsible for ATAC-Seq library preparation on bulk and single-cell samples. Both sites will take advantage of novel liquid handling platform work-flows to enable single-cell RNA-Seq and sc-ATAC-Seq library generation to be performed in a high-throughput, cost-effective manner. Hence, Core B will be able to obtain information on the epigenetic landscape of individual immune cells longitudinally after vaccination at a resolution and scale that has previously not been feasible. Core B will also provide unique expertise in analyzing sc-ATAC-Seq data that will take advantage of the availability of the sc-RNA-Seq data from matching samples. By integrating single-cell RNA-Seq and ATAC-Seq data, these analytical approaches allow for epigenetic states that predict transcriptional states to be identified with accuracy. Additionally, Core B, has developed methodology to construct lymphocyte differentiation ?trajectories? to order epigenetic and transcriptional changes at different stages of development in single cells. This analytical approach will be applied to assess lymphocyte differentiation following vaccination and in aging. In summary, the technological expertise offered by Core B will allow for high-quality single-cell genomic data to be generated in a highly efficient and cost-effective manner. More importantly, the integrated analytical pipelines developed and offered by Core B will be central to attaining the research aims of each Project, specifically in building high resolution models of genetic states that are imparted on lymphocytes during the acquisition of memory or senescence and identifying factors that dictate these long-term fates.
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