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：
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
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/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

项目摘要

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人肾脏的多标量单细胞和空间数据，涵盖微观、中观和宏观尺度重点关注常驻功能组织单位（FTU）。这些地图涵盖 9 个国家/地区的 11 个不同数据输出 KIDney 数据分析核心 (KIDDAC) 将使用技术进行集成分析，以生成用于肾脏单细胞和空间分子图谱的高分辨率和全面的集成图谱项目（KIDSSMAP）。 KIDOSP 的实施需要稳健、高度质量控制的协议肾脏的不同区域，节省组织使用并能够通过多个正交进行询问不同尺度的方法。 KidOSP 团队以独特的方式应对这些挑战并创造通过已建立的基础设施提供多模式和多标量地图集。这包括来自以下地区的患者入组多个来源，允许广泛共享基因组数据、受控的分析前参数和谨慎的以与所有要进行的测定兼容的方式处理和保存样品。到确保在细胞、FTU、区域、器官和全身层面捕获信息，并在空间坐标在样本的生命周期中是必要的。各地抽样地区的多样性寿命、性别和种族是地图集的广泛使用所必需的。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 个转录本的定向高分辨率空间询问）、空间转录组学（解离技术的非靶向全基因组空间映射），CODEX （多重空间蛋白质询问，以连接 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微型 FTU 中的邻域），光片荧光显微镜（关键的中尺度LSFM解剖图和3D图）神经血管与 FTU 的关联）和散射拉曼光谱（SRS-2D、3D 无标记体积亚细胞尺度作图）。我们的团队在多个国家财团以及在建立阶段的工作 HuBMAP 已经建立了生成所需的关键组织处理方法和质量控制流程单细胞分辨率和空间背景下的多模态、多标量数据。这些将通过处理数据分析核心 (DAC) 中的分析管道，用于构建全面的高分辨率空间图集肾脏。建立的协议适用于人类临床疾病活检，可扩展到新的技术，并可被其他网站采用，并将通过 HuBMAP 成为一个重要的资源社区。