CORE C: EPIGENETICS AND GENOMICS CORE

核心 C：表观遗传学和基因组学核心

基本信息

批准号：
9066637
负责人：
Christopher K Glass
金额：
$ 26.58万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2003
资助国家：
美国
起止时间：
2003-05-01 至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/9066637
关键词：
Administrator Base Sequence Binding Sites Bioinformatics Biological Assay Cells Complex Computational Biology Consultations Data Data Analyses Data Quality Data Storage and Retrieval Development Diabetes Mellitus Disease Electrocardiogram Endocrinology Engineering Enhancers Epigenetic Process Experimental Designs Gene Expression Gene Expression Microarray Analysis Gene Targeting Genes Genetic Genomic Segment Genomics Goals High Performance Computing High-Throughput Nucleotide Sequencing Informatics Knock-out Libraries Life Link Massive Parallel Sequencing Metabolism Methodology MicroRNAs Microarray Analysis Mining Mission Molecular Biology Molecular Genetics Molecular Profiling Mus Mutation Pathogenesis Physiology Postdoctoral Fellow Preparation Quality Control Recruitment Activity Research Research Infrastructure Research Personnel Resources Ribosomes Services Signal Transduction Signal Transduction Pathway Structure System Technology Tissues Training Transgenic Organisms Treatment Protocols base chromatin immunoprecipitation computer infrastructure computing resources data management data mining deep sequencing disease phenotype epigenome epigenomics genome-wide analysis global run on sequencing instrumentation mRNA Expression programs response ribosome profiling student training targeted sequencing transcription factor transcriptome sequencing treatment strategy type I and type II diabetes

项目摘要

A major goal in diabetes research is to understand how alterations in the epigenome and subsequent responses in gene expression impact disease phenotype and treatment regimens. The Epigenetic and Genomics Core (EGC) will provide access to microarray platforms, massively parallel sequencing instrumentation and computational infrastructure to advance the diabetes and metabolism research goals of DRC investigators. The EGC will provide the following services: 1. Expression microarray technology; Affymetrix, Agilent, Codelink, NimbleGen, and lllumina platforms will be provided for microarray-based mRNA expression profiling. Affymetrix, Life Technologies and Exiqon platforms will be provide for miRNA profiling. 2. Technical support will be provided for high-throughput sequencing assays on lllumina HiSeq 2000 platforms, including RNA sequencing (RNAseq), microRNA sequencing (mlRNAseq), global run-on sequencing (GRO-Seq), ribosome profiling and deep sequencing (Ribo-Seq), chromatin immunoprecipitation linked to massively parallel sequencing (ChlP-Seq) and MethylC-sequencing. 3. Bioinformatics support will be provided for assistance with experimental design, choice of technological platform, data analysis and data quality control. Implementation of new data management and analysis pipelines will facilitate effective data mining. 4. Training of students, postdoctoral fellows, investigators and technical staff in the application of highthroughput sequencing methodologies and data analysis 5. High-performance computing resources, systems administrators, and data storage/backup systems will enable users to efficiently access and analyze their data. A major emphasis in the configuration of the ECG will be implementation of new Core services to reduce barriers to entry to new investigators. This will be achieved by providing direct Core support at three of the critical steps required to take advantage of sequencing-based technologies; 1) Preparation of sequencing libraries, 2) provision of computational resources, and 3) assistance with data analysis through both training and provision of informatics services.

糖尿病研究的主要目标是了解表观基因组的变化以及基因表达的随后反应如何影响疾病表型和治疗方案。表观遗传学和基因组学核心（EGC）将提供对微阵列平台的访问权限，大规模平行的测序仪器和计算基础设施，以促进刚果民主共和国研究者的糖尿病和代谢研究目标。 EGC将提供以下服务： 1。表达微阵列技术； Affymetrix，Agilent，Codelink，Nimblegen和Lllumina平台将用于基于微阵列的mRNA表达分析。 Affymetrix，Life Technologies和Exiqon平台将提供miRNA分析。 2。将在Lllumina HISEQ 2000平台上进行高通量测序测定法，包括RNA测序（RNASEQ）（RNASEQ），MicroRNA测序（MLRNASEQ）（MLRNASEQ），全球跑步测序（GRO-SEQ）（GRO-SEQ），核糖组分析和深度测序（核糖表测序），质量 - SEEQ），质量seq链接（ribo-seq）（CHLP-SEQ）和甲基序列。 3。将提供生物信息学支持，以帮助实验设计，技术平台的选择，数据分析和数据质量控制。新的数据管理和分析管道的实施将有助于有效的数据挖掘。 4。在应用高通量测序方法和数据分析的学生中培训学生，博士后研究员，调查人员和技术人员5。高性能计算资源，系统管理员以及数据存储/备份系统将使用户能够有效地访问和分析其数据。 ECG配置的主要重点将是实施新的核心服务，以减少进入新调查人员的障碍。这将通过在利用基于测序的技术所需的三个关键步骤中提供直接核心支持来实现。 1）编制库的准备，2）提供计算资源，3）通过培训和提供信息学服务来协助数据分析。