The overall objective of the proposed center CCHI is to investigate the adaptive immune response in influenza vaccination and immunity. The genomics core will serve two research projects (Projects 2 and 3), and the purpose of the core is to provide leading edge genomic techniques, tools, and equipment to aid in the completion of the research objectives. We will 1) provide research projects with convenient and rapid access to highly multiplexed qRT-PCR as well as next-generation sequencing (NGS) including immune repertoire sequencing; 2) provide a novel platform and methodology to enable studies of immune cell responses to infection and vaccination at single-cell resolution; 3) optimize the single-cell approaches for each research project; 4) bridge the gap between research projects and the bioinformatics core by turning raw samples into pre-processed data ready for in-depth statistical and analytical analysis; and 5) serve as a source of information to research projects with respect to genomic technology and tools.
The specific aims of the genomics core are:
Specific Aim 1 - Provide access to genomics technologies. The Genomics Core will carry out NGS sequencing on the samples generated by the research projects, as well as provide access to the single-cell analysis platform. The core also has a variety of peripheral equipment for sequencing library preparation and quality control, which will also be available to the projects. The core can also process raw sequence data ready to be interfaced with the bioinformatics core's analytical tools, if needed.
Specific Aim 2 - Optimize single-cell approaches for whole transcriptome analysis of immune cells. The methodology and pipeline for single-cell whole transcriptome profiling allows elucidation of the transcriptional profile for all genes from each single cell in an automated fashion without complex hands-on workflows. This platform can be coupled with either NGS for whole transcriptome analysis, or with highly multiplexed qRT-PCR for targeted gene expression analysis. The core will optimize this methodology to work with immune cells, which are smaller in size and lower in RNA content than the epithelial cells that were used to initially validate the technology.
The influenza virus negatively impacts public health and well being every year, and contributes a significant financial burden to the health system. The proposed CCHI center aims to understand the immune response to influenza at multiple levels, including at the genomic and transcriptomic level. The genomics core plays an essential role in this objective by providing research projects access to cutting edge genomic tools, thereby helping to address questions of immunological health in the context of influenza.
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