# Comparing transcriptional and protein-based approaches in 3D tissue altasing

> **NIH NIH U54** · STANFORD UNIVERSITY · 2024 · $449,850

## Abstract

PROJECT SUMMARY ABSTRACT: Overall
The small bowel and colon are organs critical for maintaining homeostasis of the human body by
mediating nutritional absorption upon the ingestion of food. Though both organs are extensive in
length, there are known differences in function and cellular heterogeneity within different portions
of each. Also, a cross section anywhere in the bowel reveals a complex layering of components
involved in absorption and secretion, motility of gut contents, circulation, and immunity. In this
submission, we propose to continue our efforts in the Stanford Tissue Mapping Center (TMC) to
produce multi-modal, three-dimensional single-cell resolution maps of the small bowel and colonic
wall structure. This will serve as a community resource to further study intestinal function and
disease. We will collect tissues from deceased organ donors with explicit consent for distribution
among the HuBMAP consortium and broad access genome data sharing (GDS). Three sets of
technologies will then be employed. Tissue samples will be subjected to single-nuclei ATAC-seq
and RNA-seq. These open chromatin and transcriptomic profiles will be spatially mapped to tissue
sections using the CODEX (CO-Detection by indEXing) multiplexed spatial immunoassay. We will
also employ the Molecular Cartography multiplexed fluorescence in situ hybridization (FISH)
assay to enable more accurate integration of CODEX and single-nuclei data. The resultant three-
dimensional maps will span all layers of the bowel wall and include the epithelial, enteroendocrine,
vascular, lymphatic, nervous, immune, and muscular cell populations that contribute to normal
bowel function.

## Key facts

- **NIH application ID:** 11089006
- **Project number:** 3U54HG012723-03S1
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** GARRY P NOLAN
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $449,850
- **Award type:** 3
- **Project period:** 2022-09-23 → 2026-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11089006

## Citation

> US National Institutes of Health, RePORTER application 11089006, Comparing transcriptional and protein-based approaches in 3D tissue altasing (3U54HG012723-03S1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/11089006. Licensed CC0.

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