Pregnant Female Reproductive Tissue Mapping Center Data Analysis Core

孕妇生殖组织图谱中心数据分析核心

• 批准号: 10531090
• 负责人: Kathleen Marie Fisch
• 金额: $ 22.18万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-08-01 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10531090
• 关键词: 3-Dimensional; Adopted; Anatomy; Architecture; Area; Atlases; Biological Assay; Cell Communication; Cell Nucleus; Cells; Cellular Structures; Clinical; Collaborations; Collection; Data; Data Analyses; Data Set; Development; Emerging Technologies; Ensure; Extracellular Matrix; FAIR principles; Female; Funding; Human BioMolecular Atlas Program; Human body; Image; Immunohistochemistry; Individual; Link; Mammalian Oviducts; Maps; Mediating; Metadata; Modality; Molecular; Morphology; Organ; Pathologic; Placenta; Placentation; Policies; Pregnancy; Procedures; Quality Control; RNA; Sampling; Signal Transduction; Software Tools; Structure; Surveys; Techniques; Tissue Model; Tissues; Touch sensation; Transcript; United States National Institutes of Health; Uterus; Visualization; analysis pipeline; cell type; collaboratory; computerized data processing; data analysis pipeline; data exchange; data format; data integration; data quality; data standards; extracellular; flexibility; imaging modality; in vivo imaging; indexing; interoperability; metadata standards; migration; multiple data types; multiscale data; organ growth; pregnant; programs; protein expression; reproductive; secondary analysis; spatiotemporal; tissue mapping; tool; transcriptomics

SUMMARY The Data Analysis Core (DAC) of the HuBMAP Pregnant Female Reproductive Tissue Mapping Center (PFR TMC) will perform analysis of each data type generated by the Organ Specific Project (OSP), as well as integrative analysis of multiple data types aimed at building 3D multiscale tissue maps of the developing and term pregnant placenta, and term uterine endomyometrium and fallopian tubes; exploration of extracellular RNA- mediated signaling between the placental and maternal tissues; and tracking of cellular differentiation and migration in the developing placenta across gestation. These integrative analyses will be facilitated by two strategies: 1) collection of bridging datasets (datasets that link two data types, such as the 10x Multi-ome assay, which collects snRNAseq/snATACseq indexed to the same nuclei, or GeoMX DSP WTA, in which the operator uses tissue morphology and immunohistochemistry to select features for spatial transcriptomic profiling, thus linking morphology and/or protein expression with transcript abundance); and 2) combining broad surveys of small numbers of samples for many samples with deep spatial profiling of multiple serial sections from selected exemplar tissue blocks to build detailed models of tissue architecture. The DAC will collaborate with the HuBMAP Integration, Visualization & Engagement Collaboratory (HIVE) to build an atlas of 3D tissue maps in the context of the whole human body. The DAC is responsible for data processing, annotation, metadata curation, analysis, and map construction within the PFR TMC. The DAC interacts closely with the OSP and coordinates interactions with the other HuBMAP TMCs, HIVE and NIH Program staff. The DAC ensures that data, metadata, software and tools will be open, findable, accessible, interoperable, reusable (FAIR) and maintains flexibility to adapt processing and analysis capabilities to emerging technologies within the HuBMAP Consortium. The DAC has assembled a PFR TMC Data Release Team comprised of experts in each of the included data modalities that interfaces directly with the HIVE to ensure data quality control, metadata standards and facilitate data transfer. The DAC collaborates closely with the HIVE to optimize secondary analysis pipelines and to implement the Registration User Interface to register tissue sections to reference organs and a Common Coordinate Framework to fully integrate spatial and molecular data across individuals. Since the establishment of the PFR TMC 15 months ago, the DAC has been involved in development of Consortium-wide metadata standards, data quality metrics, analysis techniques and data structures, particular in the areas touching upon the specific data and tissue types utilized by the PFR TMC.

摘要 HuBMAP孕期女性生殖组织测绘中心数据分析核心(DAC) TMC)将对器官特定项目(OSP)生成的每种数据类型进行分析，以及 多种数据类型的综合分析，旨在建立正在发育的和 足月妊娠胎盘、足月子宫肌层和输卵管；细胞外RNA的探索 胎盘和母体组织之间的中介信号；细胞分化和细胞分化的跟踪 妊娠期间发育中的胎盘的迁移。这些综合分析将由两个 策略：1)桥接数据集(链接两种数据类型的数据集，例如10倍多基因组分析， 它收集索引到相同核或GeoMX DSP WTA的SnRNAseq/SnATACseq，其中操作员 使用组织形态和免疫组织化学来选择空间转录图谱的特征，因此 将形态和/或蛋白质表达与转录本丰度联系起来)；以及2)结合对 从精选的多个序列剖面进行深空间剖面图的小样本多样本 样本组织块，以建立详细的组织结构模型。DAC将与HuBMAP合作 集成、可视化和参与性合作实验室(HIVE)，以构建上下文中的3D组织图图集 整个人类的身体。DAC负责数据处理、注释、元数据整理、分析、 以及PFR TMC内的地图构建。DAC与OSP密切互动并协调互动 与其他HuBMAP TMC、HIVE和NIH计划工作人员一起。DAC确保数据、元数据、软件 工具将是开放的、可查找的、可访问的、可互操作的、可重复使用的(公平的)，并保持适应的灵活性 对HuBMAP联盟内的新兴技术的处理和分析能力。DAC有 组建了一个PFR TMC数据发布团队，该团队由以下每种数据模式的专家组成 直接与蜂巢接口，以确保数据质量控制、元数据标准和促进数据传输。 DAC与HIVE密切合作，以优化二次分析管道并实施 用于将组织切片与参考器官配准的配准用户界面和公共坐标框架 完全集成各个个体的空间和分子数据。自PFR TMC 15成立以来 几个月前，发改委参与了联盟范围内元数据标准、数据质量的开发 指标、分析技术和数据结构，特别是在涉及特定数据和 PFR TMC使用的组织类型。