Core C - Bioinformatics and Genomics Core

核心 C - 生物信息学和基因组学核心

• 批准号: 9280513
• 负责人: CHITTIBABU GUDA
• 金额: $ 12.09万
• 依托单位: WICHITA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-04-15 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9280513
• 关键词: Acute; Aging; Bioconductor; Bioinformatics; Biological; Cell physiology; Collection; Communities; Computer software; DNA; Data; Data Analyses; Data Storage and Retrieval; Databases; Environment; Gene Expression Profile; Gene Expression Profiling; Generations; Genes; Genomics; Goals; Human Resources; Imagery; In Vitro; Investigation; Kansas; Libraries; Maps; Mass Spectrum Analysis; Measures; Modeling; Nature; Oligosaccharides; Online Systems; Pathway Analysis; Pathway interactions; Pattern; Polysaccharides; Population; Preparation; Publications; RNA; Research; Research Infrastructure; Research Project Grants; Sampling; Signal Transduction; Standardization; Structure; Technical Expertise; Techniques; Technology; Text; Transcript; Universities; Wichita; age related; base; biological research; computer infrastructure; data acquisition; differential expression; experimental analysis; experimental study; glycosylation; in vivo; instrument; next generation sequencing; pituitary gonadal axis; programs; reference genome; relational database; reproductive senescence; success; tool; transcriptome; transcriptome sequencing; web app

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.

项目摘要 生物信息学和基因组学核心（核心C）将支持项目1-3的科学研究 通过协助分析聚糖质谱法（MS）和下一代测序（NGS） 数据。项目2和3都提出了使用NG作为研究转录组的工具 样品之间的水平差异。 NGS实验具有生成大量的能力 具有专门数据分析和存储要求的数据。核心将为所有的支持提供支持 通过以下特定目的进行研究项目：1：开发一个糖数据库和网络 用于存储，处理和分析质量数据的应用程序服务器 光谱实验。这将替换在Wichita State启动的糖数据库， 转移到堪萨斯大学，发现缺乏基本功能。新数据库 将提供自动数据输入，基于自由文本的MS数据表转换为可搜索的 关系数据库，以及更好的工具，用于比较糖型制剂的聚糖种群。 2： 支持对体外和体内研究产生的基因表达数据的分析 使用微阵列或RNA-seq实验。核心将从项目2和3的项目中接收RNA样品， 监督图书馆的构建和测序，并进行生物信息学数据分析以识别 差异表达的基因。 3：基因的比较和功能表征 体外和体内研究的表达模式。差异表达的基因 将进一步分析样品，以将这些基因与细胞的功能意义相关联 与卵巢衰老相关的途径和监管网络。