PRODIGE: A high-throughput tool for joint profiling of protein-DNA interactions and gene expression in single cells
PRODIGE:一种高通量工具,用于联合分析单细胞中蛋白质-DNA 相互作用和基因表达
基本信息
- 批准号:10303542
- 负责人:
- 金额:$ 27.45万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2021
- 资助国家:美国
- 起止时间:2021-09-30 至 2023-08-31
- 项目状态:已结题
- 来源:
- 关键词:AddressAntibodiesBar CodesBenchmarkingBindingBiological AssayCell Differentiation processCell LineCellsChromatinClinicalComplexDNADNA-Binding ProteinsDNA-Protein InteractionDataData SetDevelopmentDiseaseDropsEpigenetic ProcessGene ExpressionGenesGenetic TranscriptionGenomeGenomicsHeterogeneityHistonesHydrogelsIndividualJointsLibrariesMaintenanceMapsMeasurementMeasuresMediatingMessenger RNAMethodsMicrofluidic MicrochipsMicrofluidicsModalityModelingMolecularOutputPatternPerformancePhenotypePlayPoly APopulationPost-Translational Protein ProcessingProcessProtein AnalysisProteinsProtocols documentationRNARegulator GenesReportingReproducibilityResearch PersonnelResolutionRoleSamplingSystemTechniquesTechnologyTestingTissuescancer cellcell fixationcell typecomputational pipelinesdata analysis pipelinedroplet sequencingepigenomicsgenetic manipulationgenome-widehistone modificationinsightinterestmethylomemultiple omicsnext generationnext generation sequencingnovelprogramsprotein profilingsingle-cell RNA sequencingtooltranscription factortranscriptome
项目摘要
PROJECT SUMMARY/ABSTRACT
Protein-DNA interactions control access to genes in chromatins and regulate the spatial- and temporal-specific
gene expression. These interactions are crucial for cell differentiation and the maintenance of cellular diversity.
Dysregulated patterns of protein-DNA interactions are often associated with disease states. Applications of next-
generation epigenomic sequencing techniques have enabled deconvolution of protein-DNA interactions at
single-cell level. However, it remains challenging to define how cell-to-cell heterogeneity in protein-DNA
interactions impacts gene expression variability. Currently available methods for joint profiling protein-DNA
interactions and gene expression from single cells require laborious genetic manipulation, suffer relatively low
throughput, and are impossible to specifically map proteins with post-translational modifications, such as histone
marks. To address these unmet needs, we propose to develop PRODIGE – a high-throughput tool for joint
profiling of protein-DNA interactions and gene expression in the same single cells without the need of genetic
manipulations. It is enabled by a strategic integration of reversible cell fixation, antibody-guided chromatin
tagmentation, novel deformable and degradable barcoded hydrogel beads, droplet microfluidics, and next-
generation sequencing technology. In Aim 1, we will develop technical components and analytical pipelines of
PRODIGE. We will prepare protein A-Tn5 transposome for antibody-guided Tn5 tagmentation, fabricate
microfluidic devices for single-cell PRODIGE assay, and synthesize a barcoded library of deformable and
degradable barcoded hydrogel beads for single-cell barcoding. In Aim 2, we will optimize the method in bulk and
single-cell levels, and assess the performance of PRODIGE (joint analysis) in comparison to other stand-alone
counterparts. In Aim 3, we will benchmark PRODIGE to established tools for joint single-cell profiling of protein-
DNA interactions and transcriptome. Successful implementation of the proposed program will deliver a high-
throughput tool to quantify how cell-to-cell heterogeneity in protein-DNA binding influences gene expression
variability, decipher cell-type-specific patterns of upstream protein-DNA interactions and their transcriptional
outputs, and identify protein-mediated mechanisms that regulate cell-type-associated transcriptional programs
in heterogeneous cell populations and under different developmental and/or disease conditions.
项目总结/摘要
蛋白质-DNA相互作用控制染色质中基因的进入,并调节空间和时间特异性
基因表达。这些相互作用对于细胞分化和维持细胞多样性至关重要。
蛋白质-DNA相互作用的失调模式通常与疾病状态相关。下一个应用-
第二代表观基因组测序技术使得蛋白质-DNA相互作用的解卷积成为可能,
单细胞水平。然而,它仍然具有挑战性,以确定如何细胞间异质性蛋白质-DNA
相互作用影响基因表达变异性。目前可用的联合分析蛋白质-DNA的方法
来自单细胞的相互作用和基因表达需要费力的遗传操作,
并且不可能特异性地映射具有翻译后修饰的蛋白质,例如组蛋白,
标记.为了解决这些未满足的需求,我们建议开发PRODIGE -一种高通量的联合检测工具,
蛋白质-DNA相互作用和基因表达谱在同一个单细胞中,而不需要遗传分析。
操纵它是通过可逆的细胞固定,抗体引导的染色质
标签片段化、新型可变形和可降解的条形码化水凝胶珠、液滴微流体,以及接下来的
代测序技术。在目标1中,我们将开发技术组件和分析管道,
PRODIGE.我们将制备蛋白A-Tn 5转座体用于抗体引导的Tn 5标签片段化,
用于单细胞PRODIGE测定的微流控装置,并合成可变形和可降解的条形码文库。
用于单细胞条形码化的可降解条形码化水凝胶珠。在目标2中,我们将批量优化该方法,
单细胞水平,并评估PRODIGE(联合分析)的性能与其他独立
同行在目标3中,我们将对PRODIGE进行基准测试,以建立用于蛋白质的联合单细胞分析的工具,
DNA相互作用和转录组。该计划的成功实施将带来巨大的...
一种通量工具,用于量化蛋白质-DNA结合中细胞间异质性如何影响基因表达
可变性,破译上游蛋白质-DNA相互作用的细胞类型特异性模式及其转录
输出,并确定蛋白质介导的机制,调节细胞类型相关的转录程序
在异质细胞群体中以及在不同的发育和/或疾病条件下。
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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Wei Wei其他文献
Random sampling in shift invariant spaces
平移不变空间中的随机采样
- DOI:
10.1016/j.jmaa.2012.08.030 - 发表时间:
2013-02 - 期刊:
- 影响因子:1.3
- 作者:
Yang Jianbin;Wei Wei - 通讯作者:
Wei Wei
Differential Protection for an Outgoing Transformer of Large-Scale Doubly Fed Induction Generator-Based Wind Farms
大型双馈感应发电机出线变压器差动保护
- DOI:
10.3390/en7095566 - 发表时间:
2014-08 - 期刊:
- 影响因子:3.2
- 作者:
Bingtuan Gao;Wei Wei;Luoma Zhang;Ning Chen;Yingjun Wu;Yi Tang - 通讯作者:
Yi Tang
Wei Wei的其他文献
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{{ truncateString('Wei Wei', 18)}}的其他基金
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10512982 - 财政年份:2022
- 资助金额:
$ 27.45万 - 项目类别:
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- 批准号:
10684704 - 财政年份:2021
- 资助金额:
$ 27.45万 - 项目类别:
PRODIGE: A high-throughput tool for joint profiling of protein-DNA interactions and gene expression in single cells
PRODIGE:一种高通量工具,用于联合分析单细胞中蛋白质-DNA 相互作用和基因表达
- 批准号:
10492769 - 财政年份:2021
- 资助金额:
$ 27.45万 - 项目类别:
Liquid biopsy-based toolkits for neoantigen and cognate TCR discovery for cancer immunotherapy
基于液体活检的工具包,用于癌症免疫治疗的新抗原和同源 TCR 发现
- 批准号:
10272350 - 财政年份:2021
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Profiling fatty acid uptake and activity in single tumor cells
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9904572 - 财政年份:2019
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Circuit mechanisms for encoding naturalistic motion in the mammalian retina
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Circuit mechanisms for encoding naturalistic motion in the mammalian retina
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9788123 - 财政年份:2018
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8614797 - 财政年份:2014
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Synaptic basis of motion detection in the retina
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8788406 - 财政年份:2014
- 资助金额:
$ 27.45万 - 项目类别:
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