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

> **NIH NIH U54** · UNIVERSITY OF PENNSYLVANIA · 2022 · $350,000

## Abstract

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.

## Key facts

- **NIH application ID:** 10653357
- **Project number:** 3U54HD104392-03S1
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** JUNHYONG KIM
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $350,000
- **Award type:** 3
- **Project period:** 2020-09-24 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10653357

## Citation

> US National Institutes of Health, RePORTER application 10653357, Penn Center for Multi-scale Molecular Mapping of the Female Reproductive System (3U54HD104392-03S1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10653357. Licensed CC0.

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