Core C - Bioinformatics and Genomics Core

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Project Abstract The Bioinformatics and Genomics Core (Core C) will support the scientific investigations of Projects 1-3 by assisting with the analysis of glycan mass spectrometry (MS) and next-generation sequencing (NGS) data. Projects 2 and 3 have both proposed the use of NGS as a tool for investigating the transcriptome- level differences between samples. NGS experiments have the capacity to generate large volumes of data with specialized data analysis and storage requirements. Core C will provide support to all the research projects via the following specific aims: 1: Develop a glycomics database and a web application server for storing, processing and analyzing oligosaccharide data from Mass Spectrometry experiments. This will replace the Glycomics Database initiated at Wichita State, transferred to the University of Kansas, and found to be lacking essential functions. The new database will provide automated data entry, conversion of free-text based MS data tables into a searchable relational database, and better tools for comparing glycan populations of glycoform preparations. 2: Support the analysis of gene expression data generated from both in vitro and in vivo studies using microarray or RNA-seq experiments. The Core will receive RNA samples from Projects 2 and 3, oversee library construction and sequencing and carry out bioinformatics data analyses to identify differentially expressed genes. 3: Comparison and functional characterization of the gene expression patterns from the in vitro and in vivo studies. Differentially expressed genes between samples will be further analyzed to relate the functional significance of these genes with cellular pathways and regulatory networks associated with ovarian senescence.