Developing Antibody-Oligonucleotide Bridges to Simplify Single Cell Spatial Transcriptomics

开发抗体-寡核苷酸桥以简化单细胞空间转录组学

基本信息

批准号：
10577774
负责人：
Nathan C Boles
金额：
$ 21.75万
依托单位：
REGENERATIVE RESEARCH FOUNDATION
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-03-01 至 2024-11-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10577774
关键词：
Adoption Affect Algorithms Antibodies B-Lymphocytes Bar Codes Bioinformatics Biological Models Biological Process Cell Communication Cells Chemistry Combinatorics Computer Simulation Computer software Data Development Dissociation Drops Financial cost Gene Expression Genetic Transcription Goals Heterogeneity High-Throughput Nucleotide Sequencing Human BioMolecular Atlas Program Image In Situ Individual Length Maps Methodology Methods Modeling Oligonucleotides Organ Organism Play Program Development Protocols documentation RNA Reagent Research Personnel Retina Role Scientist Site Slide Stains Structure Structure of retinal pigment epithelium Suspensions System Systems Analysis Technology Testing Time Tissues United States National Institutes of Health Variant Visualization Work algorithm development antibody test base cell behavior cost experience experimental study high risk improved invention manufacture monolayer next generation sequencing reconstruction restriction enzyme sequencing platform single cell sequencing single molecule single-cell RNA sequencing spatial relationship three dimensional structure tool transcriptome transcriptome sequencing transcriptomics

项目摘要

Project Summary Single cell RNA-sequencing (scRNA-seq) has enabled researchers to investigate a wide array of biological processes and how tissue heterogeneity contributes to function. These technologies have led to the development of programs, such as the NIH Human Biomolecular Atlas Program, to understand how cells interact in an organism to drive its function. The development of spatial transcriptomic technologies has allowed researchers to investigate how cell-cell interactions affect cellular gene expression within a tissue. Current approaches generally rely in situ RNA based methodolgies or slide-based sequencing in combination with scRNA-seq (e.g. Slide-seq) to generate spatial maps of interacting cells. These technologies have helped demonstrate the power of combining the tissues structural data with transcriptional data to better understand cell behavior in a tissue and going forward improving the interface between these technologies will be key to uncovering how structure and cell transcription drives function. However, multiple barriers impede the widespread adoption of the current methods for performing spatial transcriptomics, including significant financial cost, time requirements, and a lack of sufficient expertise. Herein, we propose to develop a simple reagent compatible with current protocols for drop-based and pipette-based scRNA-seq technologies. This reagent will be able to generate spatial data in the normal course of scRNA-seq experiments without significantly increasing cost or time commitments. We propose to invent “antibody-oligonucleotide bridges” and build software capable of bioinformatically generating a network of cell-cell contacts across the tissue to recapitulate the spatial relationships of the cells in a tissue. In this proposal, we will carry out a proof-of- principal experiment for the AO bridge scRNA-seq approach for generating the spatial relationships between cells.

项目摘要单细胞RNA - 序列（SCRNA-SEQ）使研究人员能够研究广泛的阵列生物过程以及组织异质性如何有助于功能。这些技术导致了开发计划，例如NIH人类生物分子图集计划，以了解细胞如何在有机体中互动以驱动其功能。空间转录组技术的发展具有允许研究人员研究细胞 - 细胞相互作用如何影响组织内的细胞基因表达。当前的方法通常依赖于基于原位RNA的方法或基于幻灯片的测序用SCRNA-SEQ（例如幻灯片seq）生成相互作用细胞的空间图。这些技术有所帮助证明将组织结构数据与转录数据相结合以更好地理解的力量组织中的细胞行为并继续改善这些技术之间的接口将是揭示结构和细胞转录驱动器的功能。但是，多个障碍阻碍了宽度采用当前执行空间转录组学的方法，包括重要的财务成本，时间要求以及缺乏足够的专业知识。在此，我们建议开发一个简单的试剂与基于液滴和基于移液管的SCRNA-SEQ技术的当前方案兼容。这试剂将能够在没有SCRNA-SEQ实验的正常过程中生成空间数据大幅增加成本或时间承诺。我们建议发明“抗体 - 寡核苷酸桥”和构建能够生物信息在整个组织上生成细胞细胞接触网络的软件概括组织中细胞的空间关系。在此提案中，我们将执行 AO桥SCRNA-SEQ方法的主要实验，用于产生空间关系细胞。