Transcriptome & Networks Analysis Core

转录组

• 批准号: 10593070
• 负责人: Jose Luis Gonzalez Hernandez
• 金额: $ 38.92万
• 依托单位: SOUTH DAKOTA STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-03-20 至 2027-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10593070
• 关键词: Access to Information; Acute-Phase Reaction; Adoption; Algorithms; Antibodies; Bar Codes; Binding; Biochemical; Bioinformatics; Biomedical Research; Cell Death; Cells; Cilia; Clustered Regularly Interspaced Short Palindromic Repeats; Cryoultramicrotomy; Data; Data Analyses; Data Set; Experimental Designs; Face; Frequencies; Funding; Future; Gene Expression; Gene Expression Profile; Genes; Genetic; Genetic Transcription; Genomics; Goals; Individual; Inflammation; Inflammation Process; Inflammatory; Libraries; Lymphangiogenesis; Lymphatic; Macrophage; Measurement; Mediating; Meta-Analysis; Methods; Microscopy; Molecular; Pathway Analysis; Pathway interactions; Pattern; Phenotype; Preparation; Printing; Proteomics; Public Domains; Research Personnel; Research Project Grants; Resolution; Series; Site; Small RNA; Surveys; TNF gene; Techniques; Technology; Testing; Time; Tissue-Specific Gene Expression; Tissues; Translating; Translational Research; United States National Institutes of Health; Validation; Work; bioinformatics resource; bioinformatics tool; cell type; data integration; deep sequencing; differential expression; experience; experimental analysis; gene function; gene network; gene regulatory network; genome-wide; genome-wide analysis; innovation; insight; interactive tool; interdisciplinary collaboration; large datasets; new technology; next generation sequencing; novel; optical imaging; programs; response; screening; single-cell RNA sequencing; skills; tissue repair; tool; transcription factor; transcriptome; transcriptome sequencing; transcriptomics; whole genome; wound

Project Summary – Core B: TRANSCRIPTOME AND NETWORK ANALYSIS CORE The advent of high-throughput omics technologies enables powerful analyses of cellular transcriptional programs, gene-function relationships and genome-wide surveys at unprecedented detail. Individual investigators face many hurdles in implementing these new technologies and effectively translating these large datasets into mechanistic understanding of molecular pathways. The goal of the Transcriptome and Network Analysis Core (TNAC) is to facilitate the effective use of omics technologists and the downstream bioinformatics analyses. This core leverages the expertise of Dr. Gonzalez Hernandez, Director of the SDSU Genomics Sequencing Facility, with expertise in genetics and genomics analysis, and Dr. Xijin Ge, experienced bioinformatician and biomedical researcher. Specifically, this core will enable the project leads to use the following technology to study inflammation: RNA sequencing (RNA-seq), CRISPR whole genome screening, spatially resolved RNA-seq, and proteomics. The TNAC has 3 specific aims: 1) Transcriptomic analyses by conventional RNA-Seq and deep sequencing for analysis of CRISPR insertions; 2) The use of spatially resolved and single cell RNA-seq technology and associated bioinformatics workflows; and 3) Data integration and extensive pathway analysis using and adapting bioinformatics tools and resources, including those developed by Dr. Xijin Ge, to construct gene regulatory networks underlying inflammation, integrate proteomics data, and conduct meta-analysis of data generated by the three projects alongside data in the public domain. This core is innovative in that it brings together cutting-edge experimental technology with the latest bioinformatics tools and approaches. Working closely with the four project leads, this core will exemplify interdisciplinary collaboration, and significantly promote the adoption of cutting-edge technologies among biomedical researchers in the region.

项目摘要 - 核心B：转录组和网络分析核心 高通量奥米奇技术的冒险实现了细胞转录的强大分析 程序，基因功能关系和全基因组范围的调查以前所未有的细节。个人 调查人员在实施这些新技术时面临许多障碍，并有效地翻译了这些大型 数据集进入分子途径的机械理解。转录组和网络的目标 分析核心（TNAC）是为了促进OMICS技术人员和下游的有效使用 生物信息学分析。该核心利用了SDSU主任Gonzalez Hernandez博士的专业知识 基因组学测序设施，具有遗传学和基因组分析方面的专业知识，Xijin GE博士， 经验丰富的生物信息学家和生物医学研究人员。具体来说，该核心将使项目导致 使用以下技术研究炎症：RNA测序（RNA-SEQ），CRISPR全基因组 筛选，空间分辨的RNA-seq和蛋白质组学。 TNAC具有3个特定目的：1）转录组 通过常规RNA-Seq和深层测序分析CRISPR插入； 2）使用 空间解决和单细胞RNA-seq技术以及相关的生物信息学工作流； 3）数据 使用和调整生物信息学工具和资源的集成和广泛的途径分析，包括 由Xijin Ge博士开发的，以构建炎症的基因调节网络，整合 蛋白质组学数据，并对这三个项目生成的数据进行荟萃分析以及数据 公共领域。该核心具有创新性，因为它将尖端的实验技术汇集在一起 最新的生物信息学工具和方法。该核心将与四个项目的潜在客户紧密合作，例如 跨学科的合作，并大大促进了在 该地区的生物医学研究人员。