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 孕妇生殖组织图谱中心 (PFR) 的数据分析核心 (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，旨在构建发育中和发育中的 3D 多尺度组织图 足月妊娠胎盘、足月子宫内膜和输卵管；细胞外RNA的探索 胎盘和母体组织之间介导的信号传导；和跟踪细胞分化和 妊娠期发育中胎盘的迁移。这些综合分析将由两个方面来促进 策略：1）收集桥接数据集（链接两种数据类型的数据集，例如 10x Multi-ome 检测， 它收集索引到相同核的 snRNAseq/snATACseq 或 GeoMX DSP WTA，其中操作员 使用组织形态学和免疫组织化学来选择空间转录组分析的特征，从而 将形态和/或蛋白质表达与转录本丰度联系起来）； 2）结合广泛的调查 许多样本的少量样本，并对选定的多个连续部分进行深度空间分析 样本组织块来构建组织结构的详细模型。 DAC 将与 HuBMAP 合作 集成、可视化和参与协作实验室 (HIVE)，用于在上下文中构建 3D 组织图谱 整个人体。 DAC 负责数据处理、注释、元数据管理、分析、 以及 PFR TMC 内的地图构建。 DAC 与 OSP 密切交互并协调交互 与其他 HuBMAP TMC、HIVE 和 NIH 项目工作人员一起。 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、可重用的（公平），并保持适应的灵活性 HuBMAP 联盟内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，该团队由所包含的每种数据模式的专家组成， 直接与 HIVE 接口，以确保数据质量控制、元数据标准并促进数据传输。 DAC 与 HIVE 密切合作，优化二级分析流程并实施 注册用户界面，用于将组织切片注册到参考器官和通用坐标框架 充分整合个体之间的空间和分子数据。自 PFR TMC 成立以来 15 几个月前，DAC 一直参与制定联盟范围内的元数据标准、数据质量 指标、分析技术和数据结构，特别是涉及特定数据和数据的领域 PFR TMC 使用的组织类型。