Kidney single cell and spatial molecular atlas project - KIDSSMAP

肾脏单细胞和空间分子图谱项目 - KIDSSMAP

• 批准号: 10705737
• 负责人: Sanjay Jain
• 金额: $ 178.58万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 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/10705737
• 关键词: 3-Dimensional; ATAC-seq; Adult; Anatomy; Atlases; Biological Assay; Biopsy; Blood Vessels; Cell Nucleus; Cells; Chromatin; Clinical; Communities; Complex; Data; Data Analyses; Data Set; Detection; Dimensions; Disease; Drug or chemical Tissue Distribution; Emerging Technologies; Ethics; Extracellular Matrix; Feedback; Filtration; Fluorescence Microscopy; Gene Expression; Genetic Transcription; Goals; Heterogeneity; Homeostasis; Human; Human BioMolecular Atlas Program; Immune; Immunofluorescence Immunologic; Immunologic Surveillance; In Situ; Infrastructure; Kidney; Label; Life Cycle Stages; Light; Link; Lipids; Lobe; Lobule; Longevity; Maps; Methods; Microscopy; Modality; Molecular; Neighborhoods; Nephrons; Nerve; Organ; Output; Patients; Phase; Physiological; Process; Proteins; Protocols documentation; Quality Control; RNA; Race; Raman Spectrum Analysis; Resolution; Resources; Role; Sampling; Site; Small Nuclear RNA; Source; Specimen; Technology; Tissues; Transcript; Water; Work; absorption; blood pressure regulation; cell type; genome-wide; genomic data; improved; interest; interoperability; multimodality; neurovascular; new technology; preservation; sex; solute; tissue processing; tool; transcriptomics; usability; 3-Dimensional; ATAC-seq; Adult; Anatomy; Atlases; Biological Assay; Biopsy; Blood Vessels; Cell Nucleus; Cells; Chromatin; Clinical; Communities; Complex; Data; Data Analyses; Data Set; Detection; Dimensions; Disease; Drug or chemical Tissue Distribution; Emerging Technologies; Ethics; Extracellular Matrix; Feedback; Filtration; Fluorescence Microscopy; Gene Expression; Genetic Transcription; Goals; Heterogeneity; Homeostasis; Human; Human BioMolecular Atlas Program; Immune; Immunofluorescence Immunologic; Immunologic Surveillance; In Situ; Infrastructure; Kidney; Label; Life Cycle Stages; Light; Link; Lipids; Lobe; Lobule; Longevity; Maps; Methods; Microscopy; Modality; Molecular; Neighborhoods; Nephrons; Nerve; Organ; Output; Patients; Phase; Physiological; Process; Proteins; Protocols documentation; Quality Control; RNA; Race; Raman Spectrum Analysis; Resolution; Resources; Role; Sampling; Site; Small Nuclear RNA; Source; Specimen; Technology; Tissues; Transcript; Water; Work; absorption; blood pressure regulation; cell type; genome-wide; genomic data; improved; interest; interoperability; multimodality; neurovascular; new technology; preservation; sex; solute; tissue processing; tool; transcriptomics; usability

6XPPDU\$EVWUDFW 3URMHFW The goal of the KIDney Organ Specific Project (KIDOSP) is to generate comprehensive multimodal and multiscalar single cell and spatial data of the adult human kidney spanning micro, meso and macro scales with a focus on resident functional tissue units (FTU). These maps spanning 11 different data outputs from 9 technologies will be used for integrated analysis by the KIDney Data Analysis Core (KIDDAC) to generate a high resolution and comprehensive integrated atlas for the KIDney Single cell and Spatial Molecular Atlas Project (KIDSSMAP). Implementation of KIDOSP requires robust, highly quality-controlled protocols applied to different regions of the kidney that economizes tissue usage and enables interrogation by multiple orthogonal methods at different scales. The KidOSP team is uniquely poised to meet these challenges and generate a multimodal and multiscalar atlas through an established infrastructure. This includes enrolment of patients from multiple sources that permit broad sharing of genomic data, controlled preanalytical parameters and careful processing and preservation of samples in a manner compatible with all the assays to be performed. To ensure that the information is captured at the cell, FTU, region, organ and whole-body level, registration in spatial coordinates is necessary during the life cycle of the specimen. Diversity in regions sampled across lifespan, sex and race are needed for the atlas to be broadly usable. 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 micro-FTUs), 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). Our team's work in multiple national consortia and in the setup phase of HuBMAP have established the key tissue processing methods and quality control pipelines needed to generate multimodal, multiscalar data at a single-cell resolution and in spatial contexts. These will be processed through an analytical pipeline in the data analysis core (DAC) to build a comprehensive high-resolution spatial atlas of the kidney. The protocols established are applicable to human clinical disease biopsies, extensible to new technologies, and adaptable by other sites, and will become a great resource, through HuBMAP, for the community.

6xppdu \ $ evwudfw 3urmhfw 肾脏器官特定项目（KIDOSP）的目标是生成全面的多模式和 成年人类肾脏的多叶片单细胞和空间数据，跨越微型，中eso和宏尺度 关注居民功能组织单元（FTU）。这些地图跨越了9个不同的数据输出 技术将用于肾脏数据分析核心（KIDDAC）的综合分析以生成一个 肾单细胞和空间分子地图集的高分辨率和全面的集成图集 项目（儿童图）。 Kidosp的实施需要适用于高质量控制的协议 肾脏的不同区域，可以节省组织使用并通过多个正交审讯 不同尺度的方法。 Kidosp团队有独特的准备应对这些挑战并产生 通过已建立的基础架构多模式和多幕图集。这包括从 多种来源允许广泛共享基因组数据，受控的预分析参数和仔细的 以与要执行的所有测定法兼容的方式处理和保存样品。到 确保信息在单元，FTU，区域，器官和全身水平，注册中捕获 在样品的生命周期中，需要空间坐标。在各个地区进行采样的多样性 为了广泛使用，地图集需要寿命，性和种族。生成数据的技术包括 配对的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（有针对性的高分辨率空间询问30-1000个转录本）， 空间转录组学（分离技术的无靶基因组广泛的空间映射），法典 （用RNA技术桥接的多路复用空间蛋白质询问，如果技术（技术）），3D 多路复用免疫荧光（3D IF-细胞分辨率以定义微型FTUS中的邻居）， 灯表荧光显微镜（LSFM-摩托图的钥匙和3D地图的3D图 与FTU的神经血管相关）和散射拉曼光谱（SRS-2D，3D标签游离体积 亚细胞尺度映射）。我们团队在多个国家财团中的工作以及 Hubmap已经建立了生成所需的关键组织加工方法和质量控制管道 在单细胞分辨率和空间上下文中，多模式的多幕数据。这些将通过 数据分析核心（DAC）中的分析管道，以建立一个全面的高分辨率空间地图集 肾脏。建立的方案适用于人类临床疾病活检，可扩展为新的 技术，并由其他网站适应，并将通过Hubmap成为一个很好的资源 社区。