Core C - Biospecimans and Bioinformatics Core

核心 C - 生物样本和生物信息学核心

• 批准号: 10681270
• 负责人: PRESCOTT G WOODRUFF
• 金额: $ 37万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-08-15 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10681270
• 关键词: ATAC-seq; Achievement; Aliquot; Asthma; Bioinformatics; Biological; Biology; Biometry; Cells; Clinical; Clinical Research; Cytometry; DNA Methylation; Data Analyses; Data Analytics; Development; Enrollment; Funding; Gene Expression Profiling; Genomics; Grant; Health; Human; Hypersensitivity; Inflammation; Inflammatory; Institutional Review Boards; Investments; Medical; Methods; Methylation; Peer Review; Phenotype; Process; Productivity; Protocols documentation; Public Health; Publications; Research; Research Personnel; Resources; Sampling; Secure; Services; Sputum; Stains; Standardization; Tissue Banks; Validation; Work; airway epithelium; bioinformatics resource; cost; effective therapy; experimental group; experimental study; follower of religion Jewish; insight; novel strategies; single cell sequencing; single-cell RNA sequencing; transcriptome sequencing

Project Summary/Abstract In the prior funding period, the Biospecimen and Bioinformatics Core (Core C) was extremely productive in its development of new methods and provision of an essential core resource for the processing, storage, and distribution of biospecimens collected from the clinical studies and advanced Bioinformatics support for “Type 2 inflammatory phenotyping” and genomic analyses. In this funding period, the Biospecimen and Bioinformatics Core will continue to provide essential processing, storage, and distribution of biospecimens collected from the clinical studies funded by this grant and will refine mass cytometry (CyTOF protocols) and perform new services related to mass cytometry (CyTOF). These CyTOF services include development and validation of CyTOF panels and CyTOF staining of the experimental samples. The Core’s Bioinformatics resource also has optimized pipelines for handling the new data analysis challenges related to CyTOF and will provide specialized cross- investigator integrated analyses of bulk RNA-seq, single cell sequencing, ATAC-seq and DNA methylation studies proposed in the projects. Core C will integrate these analyses using scientific input from all 3 projects and perform iterative analyses across experiments and experimental groups. Finally, this core will share banked samples from the IRB-approved existing UCSF Airway Tissue Bank to the Projects of this P01. The Bioinformatics Core will have an extension at National Jewish Health led by Max A. Seibold, who is also a Co-I for Project 3. It will also have expert input on CyTOF from Dr. Matthew Spitzer (a Co-I on the Core) and expert input on single cell RNA-seq analyses from Dr. David Erle (a consultant/collaborator).

项目摘要/摘要 在以前的资金期间，生物测量和生物信息学核心（核心C）的生产力极高 开发新方法，并为处理，存储和 从临床研究和高级生物信息学支持“ 2型”中收集的生物测量的分布 炎症表型”和基因组分析。在此资助期间 核心将继续提供从从 该赠款资助的临床研究将完善质量细胞仪（CYTOF方案）并执行新服务 与质量细胞仪（CYTOF）有关。这些服务包括开发和验证Cytof 实验样品的面板和细胞染色。核心的生物信息学资源也已优化 处理与Cytof相关的新数据分析挑战的管道，并将提供专业的跨 研究者的整体RNA-SEQ，单细胞测序，ATAC-SEQ和DNA甲基化的综合分析 项目提出的研究。核心C将使用所有3个项目的科学意见来整合这些分析 并在实验和实验组之间进行迭代分析。最后，这个核心将分享银行 来自IRB批准的现有UCSF气道纸巾的样品到该P01的项目。这 生物信息学核心将在由Max A. Seibold领导的国家犹太人卫生中延长，他也是Co-I 对于项目3。它还将对Matthew Spitzer博士（核心的一家Co-I）和专家提供有关Cytof的专家投入 David Erle博士（顾问/合作者）对单细胞RNA-Seq分析的输入。