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: 10670433
• 负责人: Kathleen Marie Fisch
• 金额: $ 22.14万
• 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/10670433
• 关键词: 3-Dimensional; Adopted; Agreement; Anatomy; Architecture; Area; Atlases; Biological Assay; Cell Communication; Cell Nucleus; Cells; Cellular Structures; Clinical; Collaborations; Collection; Computer software; 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; 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; data submission; extracellular; feature selection; 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; spatial integration; spatiotemporal; tissue mapping; tool; transcriptomic profiling

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.

概括 Hubmap怀孕的女性生殖组织映射中心的数据分析核心（DAC）（PFR 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 旨在构建开发和发展的3D多尺度组织图的多种数据类型的综合分析 术语孕妇胎盘和术语子宫内膜和输卵管；探索细胞外RNA- 胎盘和母体组织之间的介导信号传导；并跟踪细胞分化和 在妊娠遍布发育中的胎盘中迁移。这些综合分析将由两个促进 策略：1）收集桥接数据集（链接两种数据类型的数据集，例如10倍多组测定， 收集snrnaseq/snatacseq索引到同一核或GEOMX DSP WTA，其中操作员 使用组织形态和免疫组织化学来选择用于空间转录组的特征，从而选择 将形态学和/或蛋白质表达与转录物丰度联系起来）； 2）结合了广泛的调查 许多样品的少量样品，从选定的多个串行部分进行深空分析 示例组织块以构建组织结构的详细模型。 DAC将与Hubmap合作 集成，可视化和参与协作（HIVE）在上下文中建立3D组织图的地图集 整个人体。 DAC负责数据处理，注释，元数据策展，分析， 和PFR TMC中的地图构造。 DAC与OSP和坐标相互作用紧密相互作用 与其他Hubmap TMC，Hive和NIH计划人员一起。 DAC确保数据，元数据，软件 和工具将是开放的，可发现的，可访问的，可互操作的，可重复使用的（公平）的，并保持灵活性以适应 Hubmap联盟内新兴技术的处理和分析功能。 DAC有 组装了一个由专家组成的PFR TMC数据发布小组 直接与Hive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紧密合作，以优化辅助分析管道并实施 注册用户界面以注册组织截面以参考器官和一个共同的坐标框架 充分整合跨个体的空间和分子数据。自建立PFR TMC 15以来 几个月前，DAC参与了整个财团的元数据标准的发展，数据质量 指标，分析技术和数据结构，尤其是在涉及特定数据和的领域 PFR TMC使用的组织类型。