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集项目（Kidssmap）的目标是创建一个解剖学和人类肾脏的分子“元”。 Kidssmap将通过生成多幕，来实现这一目标，成年非养生人肾脏的多维和多模式图，单细胞分辨率。这工作将在Hubmap的第一阶段基础上建立并扩大调查团队的现有工作。我们将特别关注微功能组织单元（FTU）和沿皮质的结构肾脏的髓轴。生成数据的技术包括配对的单核染色质可访问性和RNA表达（snRNA/atac-seq-cell类型和状态多样性），smfish and dart-fish （针对30-1000个转录本的有针对性的高分辨率空间询问），空间转录组学（未定位分离技术的基因组广泛的空间映射），法典（多重空间蛋白质询问用RNA技术桥接和3D如果技术），3D多重免疫荧光（3D if- 灯表荧光显微镜（LSFM- 与FTU的神经血管关联的钥匙和3D图的中尺度上的解剖图）和散射拉曼光谱法（SRS-2D，3D标签的游离体积映射在亚细胞尺度上）。生成的地图将定义细胞多样性的定量指标，在宽尺度上为不同的街区定义了不同的街区分析物的类型由一套基于呼叫的单一基于呼叫和空间技术审问染色质状态，基因表达，蛋白质，细胞外基质，代谢物和脂质的含量从亚细胞用于体积的中索和解剖量表。这些将通过使生物学的特征来进一步增强（性别，年龄，种族）样本。这些任务将通过肾脏器官特定项目完成（KIDOSP）和肾脏数据分析中心（KIDDAC），其输出，里程碑和交付给蜂巢中心管理。 Kidssmap是由具有广泛专业知识的调查人员联盟组成的肾脏组织询问，空间映射和数据整合。调查人员有一个记录通过富有成果和协作的互动来为大型财团（例如Hubmap和KPMP）做出贡献。经过 KDSSMAP将以高分辨率和大规模的潜水功能单位映射人类肾脏为社区了解肾脏健康和疾病的宝贵资源。