Spatial and temporal mapping of cell fate within lymphoid tissue

淋巴组织内细胞命运的空间和时间图谱

基本信息

批准号：
10468207
负责人：
ELLEN A ROBEY
金额：
$ 64.77万
依托单位：
UNIVERSITY OF CALIFORNIA BERKELEY
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：
2020-09-11 至 2025-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10468207
关键词：
3-Dimensional Anatomy Antibodies Area Bar Codes CD4 Positive T Lymphocytes CD8-Positive T-Lymphocytes Cell Surface Proteins Cell physiology Cells Cellular Indexing of Transcriptomes and Epitopes by Sequencing Communities Computational Biology Computer Analysis Computer software Computing Methodologies Data Development Engineering Environment Flow Cytometry Four-dimensional Gene Expression Profile Gene Proteins Genes Genetically Engineered Mouse Genomics Immune Immune response Immune system Immunology Individual Infection Internet Lasers Location Lymphoid Tissue Maps Mature Thymocyte Measurement Membrane Proteins Messenger RNA Metadata Methods Microdissection Microscopy Molecular Names Pathway interactions Pattern Preparation Proteins RNA RNA analysis Raman Spectrum Analysis Regulatory T-Lymphocyte Research Research Personnel Resolution Resources Services Signal Transduction Slice Structure of thymic medulla Suspensions System T-Cell Development T-Lymphocyte Thymic Tissue Thymus Gland Time Tissues Wild Type Mouse base cell type cohort computational pipelines imaging modality interdisciplinary approach interest laser capture microdissection mRNA Expression multiphoton imaging multiphoton microscopy new technology novel strategies optical imaging protein expression single cell analysis single-cell RNA sequencing temporal measurement thymocyte tool transcriptome user-friendly web portal

项目摘要

Summary: Spectacular recent advances in single cell genomics have provided high-resolution information about cell identity, however relating molecular information to the spatial and temporal context remains a major challenge. This is particularly relevant for the immune system, since immune responses occur in highly organized tissue environments, and involve tightly-controlled changes in cell state over time. Here we propose to develop new approaches to increase the spatial and temporal resolution of single cell analyses, and to use these methods to generate and then disseminate a 4-dimensional (time and 3D spatial coordinates) map of T cell development and the associated microenvironment in the thymus. In Aim 1, we will use simultaneous measurement of mRNA and surface proteins on single cells, together with computation and experimental approaches to develop a temporal map of cell state transitions during T cell development in the thymus. In Aim 2, we will use coherent Raman and multiphoton microscopy of living thymic tissue slices, together with laser microdissection, to isolate functionally relevant regions of tissues. We will then perform single cell analyses of individual cells within these defined regions and use computational analyses to define cell types and resolve cellular cross-talk. In Aim 3, we will increase the value of this resource to the scientific community, we will make the data readily accessible to researchers via a user-friendly interface. !

摘要：单细胞基因组学的最新进展提供了高分辨率信息关于细胞身份，然而，将分子信息与空间和时间背景联系起来仍然是一个问题重大挑战。这与免疫系统尤其相关，因为免疫反应发生在高度组织化的组织环境，并且涉及细胞状态随时间的严格控制的变化。这里我们建议开发新方法来提高单细胞的空间和时间分辨率分析，并使用这些方法生成并传播 4 维（时间和 3D 空间坐标）T 细胞发育图和胸腺中相关的微环境。在目标 1，我们将同时测量单细胞上的 mRNA 和表面蛋白，以及开发 T 细胞期间细胞状态转换时间图的计算和实验方法胸腺的发育。在目标 2 中，我们将使用相干拉曼和多光子显微镜来观察活体胸腺组织切片与激光显微切割一起分离功能相关的组织区域。然后，我们将对这些定义区域内的单个细胞进行单细胞分析，并使用计算分析来定义细胞类型并解决细胞串扰。在目标 3 中，我们将增加该资源对科学界的价值，我们将使研究人员可以轻松访问数据通过用户友好的界面。！