High-throughput Single Cell Co-assay of Histone Modifications andTranscriptome

组蛋白修饰和转录组的高通量单细胞联合分析

• 批准号: 10698374
• 负责人: Christopher Hartl
• 金额: $ 113.31万
• 依托单位: EPIGENOME TECHNOLOGIES, INC.
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-03 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10698374
• 关键词: Address; Adoption; Antibodies; Architecture; Automation; Bar Codes; Binding; Bioinformatics; Biological; Biological Assay; Biopsy; Cancerous; Cell Nucleus; Cells; Chemicals; Chromium; Chromosomes; Collection; Computer software; Contract Services; Custom; DNA; DNA Crosslinking; DNA Methylation; DNA-Binding Proteins; Data; Data Analyses; Data Set; Disease; Ensure; Epigenetic Process; Equipment; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genes; Genetic Fingerprintings; Genetic Materials; Genetic Transcription; Goals; Heritability; Heterogeneity; Hour; Image; Individual; Informatics; Infrastructure; Intestines; Investments; Joints; Laboratories; Laboratory Research; Libraries; Management Information Systems; Manuals; Memory; Methodology; Methods; Microfluidics; Molecular; Monitor; Neurons; Nuclear; Organism; Performance; Permeability; Persons; Phase; Population; Preparation; Protocols documentation; Publishing; Reagent; Regulator Genes; Regulatory Element; Renal Tissue; Reproducibility; Research; Research Institute; Running; Sampling; Scanning; Services; Signal Transduction; Small Business Innovation Research Grant; System; Technology; Testing; Tissue Sample; Tissues; Tn5 transposase; Tube; Work; analysis pipeline; cell type; chromatin immunoprecipitation; combinatorial; computerized data processing; cost; crosslink; data complexity; design; developmental disease; epigenetic profiling; epigenome; experimental study; histone modification; human error; improved; insight; multiple omics; new technology; next generation; preservation; programs; protein expression; relational database; segregation; single cell technology; tool; transcription factor; transcriptome sequencing; tumor; tumorigenesis; virtual; web site

Summary Disruption of gene regulation is a major causal factor in heritable disease, developmental disorders, and oncogenesis. While chromatin immunoprecipitation followed by sequencing (ChIP-seq) and Tn5- transposase based tagging (Cut&Tag) enable analysis of transcription factor binding and epigenetic state profiling in bulk tissue samples and tumor biopsies, they produce only population average signals. Yet regulatory networks and perturbations are heterogeneous between cell classes and types. Single-cell technologies can overcome the challenge of cellular heterogeneity and provide deeper insight into cell type-specific gene regulatory programs in healthy, diseased, and cancerous tissues. In prior work, we developed a single-cell joint assay of histone modification and RNA expression (Paired-Tag), enabling cell-type-stratified epigenetic profiling from bulk samples. This technology has attracted customers in both academic and nonprofit research. In the proposed study, we will develop automated protocols and effect laboratory informatics systems to establish a Paired-Tag services laboratory, we will refine our protocol to improve experimental throughput and reduce cost, and we will develop a Paired-Tag “TF” protocol for profiling transcription factor binding profiles. If successful, the research would enable next- generation multi-omic analysis of tumor or disease samples at comparable cost to single-omic technologies.

总结 基因调控的破坏是遗传性疾病、发育障碍、 和肿瘤发生。而染色质免疫沉淀随后测序（ChIP-seq）和Tn 5- 基于转座酶的标签（Cut&Tag）使得能够分析转录因子结合和表观遗传状态 在大量组织样品和肿瘤活组织检查中，它们仅产生群体平均信号。然而 调节网络和扰动在细胞类别和类型之间是异质的。单细胞 技术可以克服细胞异质性的挑战， 在健康、患病和癌组织中的类型特异性基因调控程序。在之前的工作中，我们 开发了一种组蛋白修饰和RNA表达的单细胞联合测定法（Paired-Tag）， 来自大量样品的细胞类型分层表观遗传分析。这项技术吸引了客户， 学术和非营利研究。在拟议的研究中，我们将开发自动化协议， 为建立配对标签服务实验室，我们会改善 协议，以提高实验吞吐量和降低成本，我们将开发一个配对标签“TF” 用于分析转录因子结合谱的方案。如果成功，这项研究将使下一个- 以与单组学相当的成本生成肿瘤或疾病样本的多组学分析 技术.