Kidney single cell and spatial molecular atlas project - KIDSSMAP

肾脏单细胞和空间分子图谱项目 - KIDSSMAP

基本信息

批准号：
10531099
负责人：
Sanjay Jain
金额：
$ 200万
依托单位：
WASHINGTON UNIVERSITY
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：
2022-09-15 至 2026-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10531099
关键词：
3-Dimensional APRIN gene ATAC-seq Address Adult Affect Age Aging Agreement Anatomy Antibodies Antigens Area Atlases Award Biological Biological Assay Biology Biopsy Blood Budgets Calibration Cell Communication Cell Nucleus Cells Cellular Structures Chromatin Classification Collaborations Communities Complex Data Data Analyses Data Collection Data Set Detection Dimensions Disease Dissection Drops Duct (organ) structure Engineering Ensure Epithelium Experimental Designs Extracellular Domain Extracellular Matrix Feedback Fibroblasts Fishes Fluorescence Fluorescence Microscopy Foundations Funding Future Gene Expression Gene Expression Regulation Generations Genetic Transcription Goals Graph Health Histology Human Human BioMolecular Atlas Program Image Imaging technology Immune Immunofluorescence Immunologic In Situ Individual Industry Standard Joints Kidney Label Lasers Light Link Lipids Machine Learning Manuals Maps Metadata Methods Microscopy Minor Modality Molecular Molecular Profiling Morphology Neighborhoods Nephrons Nerve Normalcy Organ Output Paper Participant Pathologist Pathway interactions Patient Recruitments Patients Phase Population Population Heterogeneity Process Production Proteins Proteome Proteomics Protocols documentation Published Comment Publishing RNA Race Raman Spectrum Analysis Readability Regulation Renal function Research Personnel Resolution Resources Rest Route Sample Size Sampling Scheme Selection Criteria Site Slice Slide Small Nuclear RNA Spottings Stains Standardization Structure Students Supervision Technology Testing Three-Dimensional Image Time Tissue Banks Tissue imaging Tissues Training Transcript United States National Institutes of Health Update Validation Variant Visualization software Work base cell type confocal imaging cost cost effective data integration density epigenomics extracellular genome-wide high dimensionality innovation insight instrument interest interoperability kidney biopsy kidney cell lipidomics machine learning algorithm metabolomics movie multimodality multiple omics neurovascular next generation novel preservation protein biomarkers protein metabolite response sex single cell analysis spatial integration spectroscopic imaging summer program synergism timeline tool tool development transcriptome sequencing transcriptomics user-friendly

项目摘要

Abstract (Overall) The goal of the KIDney Single cell and Spatial Molecular Atlas Project (KIDSSMAP) is to create an anatomical and molecular “metaverse” of the human kidney. KIDSSMAP will accomplish this by generating multiscalar, multidimensional and multimodal maps of the adult non-diseased human kidney at a single cell resolution. This work will build on and extend the existing efforts of the investigative team through the first phase of HuBMAP. We will specifically focus on micro functional tissue units (FTUs) and structures that are along the cortico- medullary axis of the kidney. The technologies generating data include paired single nucleus chromatin accessibility and RNA expression (snRNA/ATAC-seq -cell type and state diversity), smFISH and DART-FISH (targeted high resolution spatial interrogation of 30-1000 transcripts), spatial transcriptomics (untargeted genome wide spatial mapping of dissociative technologies), CODEX (multiplexed spatial protein interrogation to bridge with RNA technologies and 3D IF technologies), 3D multiplexed immunofluorescence (3D IF- subcellular resolution to define neighborhoods in microFTUs), lightsheet fluorescence microscopy (LSFM- anatomical maps at mesoscale of key and 3D maps of neurovascular associations with FTUs) and Scattering Raman Spectroscopy (SRS-2D, 3D label free volumetric mapping at subcellular scale). The maps generated will define quantitative metrics of cell diversity, spatial defined neighborhoods across wide scales for different types of analytes interrogated by a diverse set of single call based and spatial technologies encompassing chromatin states, gene expression, protein, extracellular matrix, metabolites and lipids ranging from subcellular to volumetric meso and anatomic scale. These will be further augmented by characterizing biologically diverse (sex, age, race) samples. These tasks will be accomplished through a KIDney Organ Specific Project (KIDOSP) and a KIDney Data Analysis Center (KIDDAC), with their outputs, milestones and delivery to the HIVE centrally managed. KIDSSMAP is formed by the alliance of investigators who have extensive expertise in kidney tissue interrogation, spatial mapping and data integration. The investigators have a track record of contributing to large consortia such as HuBMAP and KPMP through fruitful and collaborative interactions. By mapping the human kidney with its diverse functional units at high resolution and large scale, KDSSMAP will generate a valuable resource for the community to understand kidney health and disease.

摘要（总体）肾脏单细胞和空间分子图谱项目 (KIDSSMAP) 的目标是创建一个解剖学模型人类肾脏的分子“metaverse”将通过生成多标量来实现这一目标。成人非患病人类肾脏的单细胞分辨率的多维和多模态图。工作将建立在 HuBMAP 第一阶段调查团队现有努力的基础上并加以扩展。我们将特别关注沿着皮质的微功能组织单位（FTU）和结构生成数据的技术包括配对单核染色质。可及性和 RNA 表达（snRNA/ATAC-seq - 细胞类型和状态多样性）、smFISH 和 DART-FISH （对 30-1000 个转录本进行定向高分辨率空间询问）、空间转录组学（非靶向解离技术的全基因组空间图谱），CODEX（多重空间蛋白质询问）连接 RNA 技术和 3D IF 技术）、3D 多重免疫荧光（3D IF- 亚细胞分辨率来定义 microFTU 中的邻域）、光片荧光显微镜（LSFM- 关键中尺度解剖图和神经血管与 FTU 关联的 3D 图）和散射拉曼光谱（SRS-2D、亚细胞尺度的 3D 无标记体积映射）。将定义细胞多样性的定量指标，以及不同尺度的空间定义邻域通过多种基于单一调用的空间技术询问分析物类型，包括染色质状态、基因表达、蛋白质、细胞外基质、代谢物和脂质（范围从亚细胞）通过表征生物多样性，这些将进一步增强到体积细观和解剖尺度。（性别、年龄、种族）样本这些任务将通过肾脏器官特定项目来完成。 (KIDOSP) 和肾脏数据分析中心 (KIDDAC)，及其输出、里程碑和交付给 HIVE 集中管理，KIDSSMAP 由具有丰富专业知识的调查人员联盟组成。研究人员对肾脏组织询问、空间绘图和数据整合有跟踪记录。通过富有成效的协作互动，为 HuBMAP 和 KPMP 等大型联盟做出贡献。 KDSSMAP 将以高分辨率和大比例尺绘制人类肾脏及其不同功能单位的图谱为社区了解肾脏健康和疾病提供宝贵的资源。