Gene expression, Epigenetics and Bioinformatics Core

基因表达、表观遗传学和生物信息学核心

• 批准号: 10683264
• 负责人: Matthew Eugene Pipkin
• 金额: $ 15.07万
• 依托单位: UNIVERSITY OF FLORIDA
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-08-01 至 2025-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10683264
• 关键词: ATAC-seq; Address; Algorithms; Award; B-Lymphocytes; Base Pairing; Binding; Binding Sites; Bioinformatics; Biological Assay; CD8-Positive T-Lymphocytes; Cell Count; Cell physiology; Cells; Cellular Immunity; ChIP-seq; Chromatin; Chromatin Structure; Cloning; Clustered Regularly Interspaced Short Palindromic Repeats; Computer Analysis; Core Facility; Creativeness; DNA; DNA Polymerase II; DNA-Protein Interaction; Data; Data Analyses; Dedications; Doctor of Philosophy; Epigenetic Process; Event; Evolution; Faculty; Gene Expression; Gene Expression Profiling; Genes; Genetic Transcription; Genomics; Goals; Guide RNA; Human Resources; Immune response; Individual; Infection; Laboratories; Libraries; Lymphocyte; Maps; Measures; Memory; Messenger RNA; Methods; Molecular; Nucleic Acid Regulatory Sequences; Nucleosomes; RNA; RNA Interference; RNA Sequences; RNA interference screen; RNA library; Recording of previous events; Regulation; Research Institute; Resolution; Sampling; Services; Standardization; System; T cell differentiation; T cell regulation; T-Lymphocyte Subsets; Transposase; bioinformatics pipeline; chromatin immunoprecipitation; chromatin remodeling; data management; effector T cell; experience; experimental study; gene regulatory network; genome-wide; genomic data; histone modification; in vivo; innovation; instrument; large datasets; loss of function; mRNA Expression; next generation sequencing; programs; tool; transcription factor; transcriptome sequencing; tumor

PROJECT SUMMARY / ABSTRACT Core C (Pipkin) The overarching goal of Core C is to provide standardized, uniform and innovative next generation sequencing (NGS) and computational approaches to address the genome-scale experiments proposed in Projects 1-3. The individual Projects goals are to analyze pooled in vivo screens, gene expression, transcription and chromatin structure and to discern the basic molecular regulation of T and B cell mediated immunity. Core C will facilitate these objectives by using NGS approaches to analyze (1) pooled in vivo gene loss-of-function screens by sequencing, (2) expression of chromatin-associated RNA (nascent RNA), and mature mRNA from limiting ex vivo cell numbers, and single cells (scRNA-seq) using RNA-seq; (3) chromatin accessibility via the assay for transposase-accessible chromatin followed by sequencing (ATAC-seq), and nucleosome organization (MNase- seq and BEM-seq); and (4) CRF and TF binding to near base-pair resolution after chromatin immunoprecipitation from small numbers of primary lymphocytes using ChIP-exo (Aims 1 and 2). Core C has demonstrated experience in developing and applying all of these approaches. In addition, Core C has established a centralized, interlinked and documented framework for the storage, analysis and sharing of these large datasets between Projects 1-3 (Aim 3), and will apply available algorithms in creative arrangements that comprise computational approaches to identify and define operational cis-regulatory regions based on chromatin accessibility, nucleosome organization and histone modifications, and to infer utilized TF binding site motifs within these regions and predict their cognate TFs. Furthermore, these observations will be correlated with transcriptional activity (nascent RNA expression) and RNA Pol II activity (ChIP-seq) and TF and CRF binding events (ChIP- exo), and overall gene expression (mRNA) in the context of gene-perturbations to clarify functionally how gene regulatory networks drive T cell differentiation and function during immune responses in vivo.

项目摘要/摘要