Penn Center for Multi-scale Molecular Mapping of the Female Reproductive System

女性的生殖系统，包括子宫、输卵管和卵巢，是一个复杂的相互关联的集合 生理上动态的器官，不仅对生育很重要，而且与 一般健康。人类女性生殖系统和相关组织的单细胞研究 以前已经研究过，但是，到目前为止，一个全面的计划，与目标一致， HuBMAP，定义整个系统的分子图谱，整合多模式测定，空间分析， 多样性和个体差异尚未建立。宾夕法尼亚大学产科和 妇科每年进行约3 500例外科手术，其中许多手术 允许在正常条件下对同一受试者的多个器官和部位进行采样。在这里， 我们建议利用宾州妇产科小组提供的抽样机会， 宾夕法尼亚大学研究人员的细胞生物学专业知识，建立了宾夕法尼亚大学多尺度分子图谱中心， 女性生殖系统我们将获得一个全面的分子表征的 使用6种不同的分子检测方法对至少约700份组织样本进行雌性生殖系统检测， 这是一个具有解剖学索引的样本，为基础科学和妇女健康创造了一个关键资源。的 分子测定包括单细胞RNAseq、clampFISH空间转录组学、同时单细胞RNAseq、同时 细胞开放染色质和RNA测定，以及空间开放染色质测定等。我们还将 生成3D解剖模型，为我们的分子表征提供空间坐标。所有 分析数据将配准到我们的3D解剖图，该图将与HIVE通用 协调框架。来自受试者记录、临床程序、分子程序的所有元数据， 和信息学管道将被收集、管理和存储为结构化数据。所有数据，包括 一套广泛的元数据将作为公共资源提供。完成这一 资源将影响妇女健康的生殖医学，并为人类的基本生物学提供信息。 细胞群落

The female reproductive system, the uterus, fallopian tubes and the ovaries, is a complex interrelated set of organs that is physiologically dynamic and not only important for fertility but critically interrelated with general health. Single cell studies of the human female reproductive system and related tissues have been previously studied, but, as of yet, a comprehensive program, aligned with the goals of the HuBMAP, to define a molecular map of the entire system, integrating multi-modal assays, spatial diversity, and individual variations has not been established. The Penn Department of Obstetrics and Gynecology performs approximately 3,500 surgical procedures annually, of which many procedures allow sampling of multiple organs and locations from the same subject under normal conditions. Here, we propose to leverage the sampling opportunities afforded by the Penn ObGyn group and the single cell biology expertise of Penn investigators to establish a Penn Center for Multi-scale Molecular Map of the Female Reproductive System. We will obtain a comprehensive molecular characterization of the female reproductive system using six different molecular assays for at least ~700 tissue samples in anatomically indexed samples, creating a key resource for both basic science and women’s health. The molecular assays include single cell RNAseq, clampFISH spatial transcriptomics, simultaneous single cell open chromatin and RNA assays, and spatial open chromatin assay, among others. We will also generate a 3D anatomical model to provide spatial coordinate for our molecular characterization. All assay data will be registered to our 3D anatomical map that will be integrated with the HIVE Common Coordinate Framework. All metadata from subject records, clinical procedures, molecular procedures, and informatics pipelines will be collected, curated, and deposited as structured data. All data, including an extensive set of metadata, will be made available as a public resource. The completion of this resource will impact reproductive medicine for women’s health and also inform basic biology of human cell communities.