# Penn TMC: Organ-Specific Project

> **NIH NIH U54** · UNIVERSITY OF PENNSYLVANIA · 2022 · $924,162

## Abstract

The female reproductive system—comprised of the uterus, fallopian tubes and the ovaries—undergoes
some of the most dynamic changes in structure and function of any adult human organ system on a
monthly basis and throughout life. Tissue organization in the female reproductive system is paramount
as it is responsible for the coordinated cyclic changes necessary not only for reproduction but also for the
maintenance of multiple other organ systems. Here, we propose to couple our unique access to the
entire normal female reproductive system with our expertise in single cell biology to establish a multi-
scale molecular map of the female reproductive system. We will collect and manage subject/donor
samples to generate a multi-scale molecular map: We will leverage our subject/donor population to
comprehensively sample up to 22 tissue locations from the same subject (16 donors), as well as sample
a single tissue over a large number of donors to collect temporal information. In total, we propose to
collect ~700 tissue samples over 22 locations from four female reproductive organs using multiple assay
modalities. We will generate a spatially coordinated multi-scale molecular map: We will collect scRNAseq
(3 different schemes), multiplex FISH (clampFISH), in situ open chromatin, as well as simultaneous
RNA/open chromatin assays and protein assays in collaboration with other TMCs for a total of six
different assay methods. We will also develop a 3D digital model of the female reproductive system using
subject/donor imaging data, and develop associated spatial annotation tools to index our clinical sample
collection in SA1 with anatomical coordinates. 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. We will use well-validated protocols (e.g., 10X Chromium platform) or
validate and optimize molecular assays before moving them to production pipelines. We will work with
other TMCs as well as other HuBMAP groups to develop community standards and validation methods
for the molecular assays. For systematic data collection and production pipeline work, we will construct a
streamlined process from Clinical Sampling, to 3D Model Indexing, to Molecular Assays, to Data Analysis
and Coordination. The completion of our data collection activities will create an unprecedented public
resource that will enhance our understanding of human reproductive biology and impact women’s health.

## Key facts

- **NIH application ID:** 10461164
- **Project number:** 5U54HD104392-03
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Kurt T Barnhart
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $924,162
- **Award type:** 5
- **Project period:** 2020-09-24 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10461164

## Citation

> US National Institutes of Health, RePORTER application 10461164, Penn TMC: Organ-Specific Project (5U54HD104392-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10461164. Licensed CC0.

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