A Single-Cell Transcriptome Atlas for Zebrafish Development

斑马鱼发育的单细胞转录组图谱

基本信息

批准号：
9922372
负责人：
CHARLES B KIMMEL
金额：
$ 69.32万
依托单位：
UNIVERSITY OF OREGON
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-05-01 至 2023-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9922372
关键词：
Address Adolescent Adult Affect Amacrine Cells Animal Model Animals Atlases Back Bioinformatics Categories Cell Extracts Cell Therapy Cell physiology Cells Chromium Communities Computer software Coupled Data Databases Development Dimensions Disease Ear Embryo Equipment and supply inventories Estrogens Etiology Expression Profiling Eye Female Gene Combinations Gene Expression Gene Expression Profile Genes Genetic Transcription Genomics Goals Hair Cells Health Histologic Human Immunity Improve Access In Situ Hybridization Individual Information Networks Institutes Internet Investigation Islet Cell Islets of Langerhans Kidney Knowledge Larva Location Medical Melatonin Microfluidics Modeling Molecular Monoclonal Antibody R24 Names Nephrons Nucleic acid sequencing Ontology Organ Outcome Ovarian Follicle Phenotype Pituitary Gland Research Resources Skin Somatotropin System T-Lymphocyte Time Tissues United States National Institutes of Health Vertebral column Zebrafish bioinformatics pipeline body system cell type differential expression effective therapy exhaustion experimental study gene function gene interaction genome resource genome-wide human disease human model improved in vivo innovation interest male melanocyte model organisms databases molecular drug target novel side effect single-cell RNA sequencing software development targeted treatment transcriptome transcriptomics zebrafish development

项目摘要

Safe, effective therapies generally target specific disease-related molecules that appear only in disease-related cell types. The problem: Gaps in our knowledge include a comprehensive definition of cell types in any vertebrate species over developmental time and knowledge of which genes each cell type expresses at what levels. Genes currently known only by sequence might provide unique targets for cell therapies if we knew which cell types express them. A way forward: It has recently become possible to identify the transcriptional profile of individual, single cells with unprecedented molecular precision using single-cell RNA sequencing (scRNA-seq) coupled with powerful highly dimensional-reducing software that groups cells into bioinformatically identified clusters containing cell types with closely related gene expression profiles. The goals of this project are first, the comprehensive identification of transcriptionally unique cell types over developmental time in zebrafish, a major medical model, and second, the release of these data as a resource to the research community in a convenient searchable format through the Zebrafish Information Network (ZFIN). Approach: Aim 1 is to define single cell transcriptome phenotypes for various stages of wild-type zebrafish embryos, larvae, and juveniles and to locate these annotated cell types by in situ hybridization experiments displaying the expression of cell type-specific marker genes on whole mounts and histological sections. Aim 2 is to define the single cell transcriptome phenotype for all major organs in wild-type zebrafish adult males and females and to identify prominent cell types in vivo by in situ hybridization for cell type-specific marker genes on histological sections. Aim 3 is to develop an automated bioinformatic pipeline to identify cell types in scRNA-seq clusters by comparing gene expression profiles to existing resources, including ZFIN, other model organism databases (AGR, Alliance of Genome Resources), and human gene expression data. Aim 4 is to develop an interface in ZFIN to enable the research community to easily query zebrafish scRNA- seq data. Innovation: No animal species currently has a comprehensive compendium of cell types organized by gene expression patterns on a genome-wide scale during development. Significance: This R24 application will develop resources and related materials that will 1) enhance, further characterize, and improve a critical animal model for the investigation of human disease mechanisms; 2) facilitate access to data generated from the use of animal models of human disease; and 3) address the research interests of many categorical NIH Institutes and Centers that focus on various organ systems and disease types. This resource will identify previously unknown cell types, thus facilitating the precision targeting of cell types for potential therapies; will associate previously unknown genes with specific cell types, thus increasing potential molecular targets for drug therapies; and will suggest hypotheses for gene expression networks, thus improving our knowledge of cellular mechanisms in health and deepening our understanding of gene interaction webs in disease etiology.

安全，有效的疗法通常靶向仅出现在疾病有关的特定疾病相关分子细胞类型。问题：我们知识中的差距包括对任何细胞类型的全面定义在发育时间和知识中，脊椎动物物种每种细胞类型的知识都以什么为表示水平。如果我们知道，目前仅按序列知道的基因可能会为细胞疗法提供独特的靶标。哪种细胞类型表达它们。前进的道路：最近有可能识别转录使用单细胞RNA测序的单个单个细胞具有前所未有的分子精度（SCRNA-SEQ）与强大的高度还原软件结合，将细胞分组为生物信息性鉴定的簇包含具有紧密相关的基因表达谱的细胞类型。这该项目的目标首先是对转录独特单元类型的全面识别斑马鱼是一种主要的医学模型，其次是将这些数据作为资源发布通过斑马鱼信息网络以方便的可搜索格式到研究社区（Zfin）。方法：目标1是为野生型的各个阶段定义单细胞转录组表型斑马鱼胚胎，幼虫和少年，并通过原位杂交定位这些带注释的细胞类型在整个安装和组织学上显示细胞类型特异性标记基因表达的实验部分。 AIM 2是定义野生型斑马鱼中所有主要器官的单细胞转录组表型成年男性和女性，并通过原位杂交特异在组织学部分上的标记基因。 AIM 3是开发自动生物信息学管道以识别细胞通过将基因表达曲线与包括Zfin在内的现有资源进行比较，在SCRNA-SEQ簇中的类型其他模型生物数据库（AGR，基因组资源联盟）和人类基因表达数据。目标4是在Zfin中开发一个接口，以使研究界可以轻松查询斑马鱼scrna- SEQ数据。创新：目前尚无动物物种对细胞类型的全面汇编在发育过程中，通过基因组范围的基因表达模式。意义：此R24应用将开发资源和相关材料，以1）增强，进一步表征并改善关键用于研究人类疾病机制的动物模型； 2）促进访问从使用人类疾病动物模型； 3）解决许多分类NIH的研究兴趣专注于各种器官系统和疾病类型的机构和中心。此资源将确定以前未知的细胞类型，从而促进了潜在疗法的细胞类型的精确靶向。将要将先前未知基因与特定细胞类型相关联，从而增加了潜在的分子靶标的药物疗法；并将提出有关基因表达网络的假设，从而提高我们对健康中的细胞机制，加深了我们对疾病病因中基因相互作用网的理解。