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

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 KIDney器官特异性项目（KIDOSP）的目标是产生全面的多模式和 成人肾脏的多尺度单细胞和空间数据，包括微观、中观和宏观尺度， 关注常驻功能组织单位（FTU）。这些地图跨越11个不同的数据输出从9 技术将用于KIDney数据分析核心（KIDDAC）的综合分析， KIDney单细胞和空间分子图谱的高分辨率和综合集成图谱 项目（KIDSSMAP）。KIDOSP的实施需要健壮的、高度质量控制的协议， 这节省了组织使用，并且能够通过多个正交的 不同尺度的方法。KidOSP团队是唯一准备迎接这些挑战，并产生一个 多模式和多标量地图集通过既定的基础设施。这包括以下患者的入组： 允许广泛共享基因组数据的多个来源，受控的预分析参数和仔细的 以与所有待进行的测定相容的方式处理和保存样品。到 确保在细胞、FTU、区域、器官和全身水平捕获信息， 在样品的生命周期中，空间坐标是必要的。抽样区域的多样性 寿命、性别和种族是地图集广泛使用的必要条件。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（30-1000个转录物的靶向高分辨率空间询问）， 空间转录组学（非靶向全基因组解离技术空间作图），CODEX （多重空间蛋白质询问与RNA技术和3D IF技术连接），3D 多重免疫荧光（3D IF-亚细胞分辨率，用于定义微FTU中的邻域）， 光片荧光显微镜（LSFM-关键的中尺度解剖图和3D图） 与FTU的神经血管关联）和散射拉曼光谱（SRS-2D，3D无标记体积 在亚细胞尺度上的映射）。我们的团队在多个国家联盟的工作，并在设置阶段， HuBMAP已经建立了关键的组织处理方法和质量控制管道， 多模态，多标量数据在一个单一的细胞分辨率和空间环境。这些将通过 数据分析核心（DAC）中的分析管道，以构建全面的高分辨率空间地图集， 肾脏所建立的方案适用于人类临床疾病活检，可扩展到新的 技术，并适应其他网站，并将成为一个伟大的资源，通过HuBMAP，为 社区