Core B: Bioinformatics & Biostatistics Core

核心B：生物信息学

基本信息

批准号：
10470927
负责人：
S. Stephen Yi
金额：
$ 29.47万
依托单位：
UNIVERSITY OF TX MD ANDERSON CAN CTR
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-09-01 至 2025-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10470927
关键词：
Adolescent Adult Antigen-Presenting Cells Area Bioinformatics Biological Biology Biometry Biostatistics Core Cell Cycle Cell Differentiation process Cells Characteristics Collaborations Data Data Set Data Storage and Retrieval Development Educational process of instructing Environment Gene Expression Gene Expression Profile Gene Expression Profiling Genes Genetic Transcription Goals Grant Growth Hematopoietic Heterogeneity High Performance Computing Human Individual Informatics Joints Link Maintenance Malignant Neoplasms Masks Methods Modeling Molecular Mus Pathway interactions Perinatal Play Population Publications Research Research Project Grants Research Support Role Sample Size Secure Services Signal Transduction Standardization Statistical Methods Stromal Cells Systems Biology Technology Texas Thymic epithelial cell Thymocyte Selection Thymus Gland Universities Work austin cell type design epithelial stem cell experience experimental study fetal genomic platform human disease medical schools post-doctoral training programs service utilization single-cell RNA sequencing success synergism transcriptome sequencing

项目摘要

PROJECT SUMMARY Recent advances in single cell RNA-seq (scRNA-seq) technology have enabled quantification of underlying heterogeneity within cell populations through identifying gene expression signatures of individual cells to reveal transcriptionally distinct cellular subsets. In addition, scRNA-seq combined with appropriate bioinformatics analyses enable modeling of developmental lineage hierarchies and discovery of rare cell types that would be otherwise masked in bulk RNA-seq data. Comprehensive and systematic analysis of both scRNA-seq and bulk RNA-seq data is critical to the success of the Research Projects (RPs) in this Program. The Bioinformatics and Biostatistics Core (Core B) has been designed to meet this need. The Core B leader (Dr. Stephen Yi) has over 10 years of experience in research and teaching in bioinformatics and biostatistics, especially in gene expression analysis, resulting in more than 30 high-impact publications in the field. Core B services will be used by all three RPs for bioinformatics analysis of scRNA-seq and bulk RNA-seq data on mouse and human (with Core C) TECs, stromal cells, and HAPCs. The Core will also provide biostatistics support for all experiments in the Program. The analytical approaches provided by Core B are essential to the goals of all RPs. The core will provide services in three Tasks for the RPs as follows: Task 1. Data storage and maintenance for all Research Projects (RP) and Cores; Task 2. Perform gene expression analyses on scRNA-seq and bulk RNA-seq data; Task 3. Provide general biostatistics support for data generated from RP 1, 2, 3 and with Core C. The Core B leader will interact frequently with RP and Core C leaders to discuss experimental goals and devise strategies for effective bioinformatics and biostatistical analyses. Successful delivery of Core B services will greatly facilitate the overall program through: (i) serving as a key link of overall program synergy; (ii) mapping transcriptional changes in cells of the human and mouse thymus microenvironment over the perinatal to juvenile transition; and (iii) identifying candidate molecular mechanisms that may play a role in the differential functional potential of cells in the perinatal versus juvenile thymic microenvironment.

项目概要单细胞 RNA-seq (scRNA-seq) 技术的最新进展使得潜在的定量分析成为可能通过识别单个细胞的基因表达特征来揭示细胞群内的异质性转录上不同的细胞亚群。此外，scRNA-seq结合适当的生物信息学分析能够对发育谱系层次进行建模并发现稀有细胞类型否则在批量 RNA-seq 数据中被掩盖。 scRNA-seq 和bulk 的全面系统分析 RNA-seq 数据对于本计划中的研究项目 (RP) 的成功至关重要。生物信息学和生物统计学核心（核心 B）旨在满足这一需求。 Core B 领导者（Stephen Yi 博士）已结束 10年生物信息学和生物统计学研究和教学经验，特别是在基因表达方面分析，产生了 30 多篇该领域高影响力的出版物。核心 B 服务将由所有三个使用用于对小鼠和人类（带有核心 C）TEC 的 scRNA-seq 和批量 RNA-seq 数据进行生物信息学分析的 RP，基质细胞和 HAPC。核心还将为该计划中的所有实验提供生物统计学支持。核心 B 提供的分析方法对于所有 RP 的目标至关重要。核心将提供服务 RP 的三项任务如下：任务 1. 所有研究项目 (RP) 的数据存储和维护以及核心；任务2.对scRNA-seq和bulk RNA-seq数据进行基因表达分析；任务 3. 提供对 RP 1、2、3 和 Core C 生成的数据的一般生物统计学支持。核心 B 领导者将经常与 RP 和核心 C 领导者互动，讨论实验目标和制定有效的生物信息学和生物统计分析策略。成功交付核心B服务将通过以下方式极大地促进整个计划： (i) 作为整个计划协同作用的关键环节； (二) 绘图人类和小鼠胸腺微环境细胞从围产期到青少年的转录变化过渡; (iii) 确定可能在差异功能中发挥作用的候选分子机制围产期与幼年胸腺微环境中细胞的潜力。