Each of the projects within this PPG proposes aims that will determine the transcriptional and epigenetic programs of plasma cell development and maintenance. To provide expertise, ensure standardized protocols, integration of results and their subsequent analyses, and the sharing of data, the creation of an Epigenomics, Sequencing and Bioinformatics Core (Core B) within this PPG is proposed. Core B will provide state-of-the-art technologies, molecular biology expertise, and bioinformatic services that assess DNA methylation, chromatin state and accessibility, and transcript expression through deep sequencing. Core B will be an independent division within the Emory Integrated Genomics Core (EIGC), which is a full service genomics and computational facility. This relationship will allow Core B to take advantage of the EIGC's computational expertise, equipment, negotiated sequencing costs, and data storage. To serve the projects, four tasks are proposed. Task 1: Provide uniform and quality sequence library sample preparation. Core B will create high-quality sequencing libraries based on four technologies to derive an epigenetic program. RNA-seq will be used to determine the transcriptome. Reduced Representation Bisulfite Sequencing (RRBS) will be used to assess DNA methylation. The Assay for Transposase Accessible Chromatin (ATAC-seq) will determine chromatin accessibility. Chromatin Immunoprecipitation-sequencing (ChIP-seq) will be used to determine histone posttranslational modifications or transcription factor binding. Task 2: Determine library quality and complexity and coordinate sequence runs. This task will identify library quality, determine the final sequencing depth for each sample, and provide significant cost savings to the PPG by coordinating DNA sequencing across projects. Task 3: Provide initial DNA sequence mapping, quality analysis, and data storage and sharing. Core B will use an established pipeline for mapping of sequences to the respective reference genome, provide long-term data storage, and facilitate sharing of processed datasets. Task 4: Provide iterative bioinformatic computational analysis of datasets. A question driven, iterative bioinformatics analysis will be used to derive epigenetic maps, features, metabolic processes, and transcriptional circuitry associated with plasma differentiation and maintenance in each of the experimental systems of the PPG. The iterative process will allow similar datasets (e.g., RRBS vs. RRBS) to be compared and then integrated across technologies (e.g., RNA-seq and ATAC-seq). By combining all four technologies, we will develop a multi-dimensional view of the epigenetic programming of plasma cells. Accordingly, Core B will allow seamless integration of data across projects, allow systems comparisons between species, as well as determine differences between healthy vs disease states to take place. Thus, Core B will provide a common resource and analytical platform that will serve to facilitate the success of each of the projects.
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