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).

项目总结/摘要 在上一个资助期，生物标本和生物信息学核心（核心C）在其 开发新的方法，并提供必要的核心资源，用于处理、储存和 从临床研究中收集的生物标本的分布和“2型”的高级生物信息学支持 炎症表型分析”和基因组分析。在此资助期间，生物标本和生物信息学 核心将继续提供必要的处理，储存和分发从生物标本收集， 该基金资助的临床研究，将完善质谱细胞术（CyTOF协议），并提供新的服务 质谱仪（mass cytometry，CyTOF）这些CyTOF服务包括CyTOF的开发和验证 实验样品的图和CyTOF染色。核心的生物信息学资源也得到了优化 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 研究者整合了批量RNA-seq、单细胞测序、ATAC-seq和DNA甲基化分析 项目中提出的研究。核心C将利用所有3个项目的科学投入整合这些分析 并在实验和实验组之间进行迭代分析。最后，这一核心将共享银行 来自IRB批准的现有UCSF气道组织库的样本，用于本P01的项目。的 生物信息学核心将在国家犹太健康中心进行扩展，由Max A. Seibold，也是一个Co-I 项目3。它还将有来自Matthew Spitzer博士（核心的Co-I）和专家的CyTOF专家意见。 来自大卫尔勒博士（顾问/合作者）的单细胞RNA-seq分析输入。