Pregnant Female Reproductive Tissue Mapping Center Data Analysis Core

总结 HuBMAP妊娠女性生殖组织定位中心（PFR）的数据分析核心（DAC） TMC）将对器官特异性项目（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，旨在建立开发和 足月妊娠胎盘、足月子宫肌内膜和输卵管;探索细胞外RNA- 胎盘和母体组织之间介导的信号传导;以及追踪细胞分化和 在整个妊娠期胎盘发育中的迁移。这些综合分析将由两个人来促进 策略：1）收集桥接数据集（连接两种数据类型的数据集，例如10 ×多组分析， 其收集索引到相同核的snRNAseq/snATACseq，或GeoMX DSP WTA，其中操作者 使用组织形态学和免疫组织化学来选择用于空间转录组学分析的特征， 将形态学和/或蛋白质表达与转录物丰度相关联）;以及2）将以下广泛调查相结合： 少量样品用于许多样品，并对所选样品的多个连续切片进行深度空间分析 样本组织块以建立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），以在上下文中构建3D组织地图集 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密切互动并协调互动 与其他HuBMAP TMC、HIVE和NIH计划工作人员一起。发援会确保数据、元数据、软件 和工具将是开放的、可查找的、可访问的、可互操作的、可重用的（FAIR），并保持适应的灵活性 处理和分析能力，以新兴技术在HuBMAP联盟。DAC具有 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，以优化二次分析管道并实施 配准用户界面，用于将组织切片配准到参考器官和通用坐标框架 来完全整合个体之间的空间和分子数据。自PFR TMC成立以来， 几个月前，DAC参与了联盟范围元数据标准、数据质量的开发 指标、分析技术和数据结构，特别是涉及特定数据的领域， PFR TMC使用的组织类型。

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.