# The single and same cell 3D atlas of epigenome and transcriptome of the lower urinary tract

> **NIH NIH U01** · CEDARS-SINAI MEDICAL CENTER · 2021 · $460,501

## Abstract

In response to RFA-DK-20-013 “GenitoUrinary Development Molecular Anatomy Project (GUDMAP) - Atlas
Projects”, this proposal aims “to generate data to visualize the developing urinary tract, to identify new functional
and anatomical domains, and cell types”. The embryonic hindgut or cloaca progresses from a single hollow
organ to two separate entities – the urinary tract and anorectal tract. The urinary tract further differentiates into
the bladder rostrally and the genital urethra caudally. Guided by tissue-specific gene expression patterns, we
show that several selected transcription factors and signaling molecules are critical for urinary tract development
and, are responsible for some of the most complex human birth defects. However, these low-throughput and
isolated case studies offer limited information; and it is difficult integrate these findings to discern gene-gene and
gene-cell relationships in development and in disease. Resources including spatial annotation of all genes in all
cells are needed. Using innovative technologies including single cell Multi-omics and Spatial Transcriptome, this
application aims to 1) create a series of digital libraries from all cells of mouse lower urinary tract, in which every
cell is annotated based on its' own transcriptomic and epigenomic profiles; 2) generate ultrahigh-density tissue-
specific spatial transcriptomic map of the lower urinary tract; and 3) display spatial transcriptome at near single
cell resolution onto the 3D digitalized mouse and human embryos. These resources will serve the research
community to establish a comprehensive understanding of urinary tract development, including but not limited to
cloaca septation and urinary tract differentiation.

## Key facts

- **NIH application ID:** 10356656
- **Project number:** 1U01DK131377-01
- **Recipient organization:** CEDARS-SINAI MEDICAL CENTER
- **Principal Investigator:** Xue Sean Li
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $460,501
- **Award type:** 1
- **Project period:** 2021-09-30 → 2026-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10356656

## Citation

> US National Institutes of Health, RePORTER application 10356656, The single and same cell 3D atlas of epigenome and transcriptome of the lower urinary tract (1U01DK131377-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10356656. Licensed CC0.

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