Kidney single cell and spatial molecular atlas project - KIDSSMAP

6XPPDU\$EVWUDFW 3URMHFW 肾脏器官特异性项目(KIDOSP)的目标是产生全面的多模式和 成人肾脏的多标度单细胞和空间数据跨越微、中、宏观尺度 关注常驻功能组织单元(FTU)。这些地图涵盖了来自9个不同数据输出的11个不同数据 肾脏数据分析核心(KIDDAC)将使用这些技术进行综合分析，以生成 肾脏单细胞和空间分子图谱的高分辨率综合集成图谱 项目(KIDSSMAP)。KIDOSP的实施需要强大的、高度质量控制的协议应用于 肾脏的不同区域，节省组织使用并允许通过多正交法进行询问 方法采用不同尺度的研究方法。KidOSP团队以独特的姿态迎接这些挑战，并产生 通过已建立的基础设施编制多式联运和多标量地图集。这包括招收来自 允许广泛共享基因组数据的多个来源，受控的分析前参数和仔细的 以与所有要进行的分析相兼容的方式处理和保存样品。至 确保在细胞、FTU、区域、器官和全身级别捕获信息，登记在 在标本的生命周期中，空间坐标是必需的。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(30-1000个记录的定向高分辨率空间询问)， 空间转录学(解离技术的非定向基因组全空间图谱)，食典 (多路复用空间蛋白质询问与RNA技术和3D IF技术相结合)、3D 多路免疫荧光(3DIF-亚细胞分辨率以定义微型FTU中的邻域)， 光片荧光显微镜(LSFM)-关键中尺度解剖图和3D图 神经血管与FTUS的相关性)和散射拉曼光谱(SRS-2D、3D无标记体积 亚细胞尺度的测绘)。我们团队在多个国家财团的工作以及在 HuBMAP已经建立了生成所需的关键组织处理方法和质量控制管道 在单个单元格分辨率和空间上下文中的多模式、多标量数据。这些将通过以下方式处理 数据分析核心(DAC)中的分析管道，以建立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，并可被其他站点改编，并将通过HuBMAP成为用于 社区。

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.