Gene expression, Epigenetics and Bioinformatics Core
基因表达、表观遗传学和生物信息学核心
基本信息
- 批准号:10024586
- 负责人:
- 金额:$ 23.93万
- 依托单位:
- 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:2020-08-01 至 2021-07-31
- 项目状态:已结题
- 来源:
- 关键词:AddressAlgorithmsAwardB-LymphocytesBase PairingBindingBinding SitesBioinformaticsBiological AssayCD8-Positive T-LymphocytesCell CountCell physiologyCellsCellular ImmunityChIP-seqChromatinChromatin StructureCloningClustered Regularly Interspaced Short Palindromic RepeatsComputer AnalysisCore FacilityDNADNA Polymerase IIDNA-Protein InteractionData AnalysesDoctor of PhilosophyEpigenetic ProcessEventEvolutionFacultyGene ExpressionGene Expression ProfilingGenesGenetic TranscriptionGenomicsGoalsGuide RNAHuman ResourcesImmune responseIndividualInfectionLaboratoriesLibrariesLymphocyteMapsMeasuresMemoryMessenger RNAMethodsMolecularNucleic Acid Regulatory SequencesNucleosomesRNARNA InterferenceRNA interference screenRNA libraryRecording of previous eventsRegulationRegulator GenesResearch InstituteResolutionSamplingServicesStandardizationSystemT cell differentiationT cell regulationT-Lymphocyte SubsetsTransposaseWorkbasebioinformatics pipelinechromatin immunoprecipitationchromatin remodelingdata managementeffector T cellexperienceexperimental studygenome-widegenomic datahistone modificationin vivoinnovationinstrumentlarge datasetsloss of functionmRNA Expressionnext generation sequencingprogramssingle-cell RNA sequencingtooltranscription factortranscriptome sequencingtumor
项目摘要
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
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Matthew Eugene Pipkin其他文献
Matthew Eugene Pipkin的其他文献
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{{ truncateString('Matthew Eugene Pipkin', 18)}}的其他基金
Nuclear Receptor Networks in Mucosal Immune Regulation
粘膜免疫调节中的核受体网络
- 批准号:
10822885 - 财政年份:2023
- 资助金额:
$ 23.93万 - 项目类别:
Nuclear Receptor Networks in Mucosal Immune Regulation
粘膜免疫调节中的核受体网络
- 批准号:
10591752 - 财政年份:2021
- 资助金额:
$ 23.93万 - 项目类别:
Nuclear Receptor Networks in Mucosal Immune Regulation
粘膜免疫调节中的核受体网络
- 批准号:
10459564 - 财政年份:2021
- 资助金额:
$ 23.93万 - 项目类别:
Nuclear Receptor Networks in Mucosal Immune Regulation
粘膜免疫调节中的核受体网络
- 批准号:
10283045 - 财政年份:2021
- 资助金额:
$ 23.93万 - 项目类别:
Transcription factor regulation of CD4 and CD8 T cell effector and memory differentiation and function
CD4 和 CD8 T 细胞效应及记忆分化和功能的转录因子调节
- 批准号:
10488579 - 财政年份:2020
- 资助金额:
$ 23.93万 - 项目类别:
shRNAmir and CRISPR sgRNA Library Construction Core
shRNAmir 和 CRISPR sgRNA 文库构建核心
- 批准号:
10591867 - 财政年份:2020
- 资助金额:
$ 23.93万 - 项目类别:
shRNAmir and CRISPR sgRNA Library Construction Core
shRNAmir 和 CRISPR sgRNA 文库构建核心
- 批准号:
10024585 - 财政年份:2020
- 资助金额:
$ 23.93万 - 项目类别:
shRNAmir and CRISPR sgRNA Library Construction Core
shRNAmir 和 CRISPR sgRNA 文库构建核心
- 批准号:
10224890 - 财政年份:2020
- 资助金额:
$ 23.93万 - 项目类别:
Transcription factor regulation of CD4 and CD8 T cell effector and memory differentiation and function
CD4 和 CD8 T 细胞效应及记忆分化和功能的转录因子调节
- 批准号:
10683256 - 财政年份:2020
- 资助金额:
$ 23.93万 - 项目类别:
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:
10591868 - 财政年份:2020
- 资助金额:
$ 23.93万 - 项目类别:
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