Pregnant Female Reproductive Tissue Mapping Center Data Analysis Core

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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.