# The roles of regional specialization, mechanical forces and epigenetic memory after perturbation and injury of the intestinal stem cell microenvironment

> **NIH NIH U01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2023 · $320,000

## Abstract

Project Summary
The increased complexity of methods to analyze high-throughput genomic data, particularly single cell
datasets, mandates the tight interaction between experimental and computational scientists. Analysis of how
different compartments of the intestine interact with each other and react to insults is greatly advanced by
studies at the single cell level. This project will accelerate progress of genomic analysis of the intestinal stem
cell niche by ISCC members through the following two aims, (1) collaborations on projects from individual
centers, and (2) collaboration on a consortium-wide project to determine the minimum set of genetic factors
that support the intestinal stem cell niche in human and mouse using a comparative approach. In the previous
years of this project, we have established collaborations with six ISCC teams to help with their project; some of
these collaborations have been completed and resulted in publications, others are ongoing, and we continue
establishing new collaborations. The consortium-wide project has the goal of annotating a set of gene modules
and communication modules in the intestinal stem cell niche in mouse and human. We are analyzing single-
cell gene expression datasets generated by ISCC labs; mouse data are provided by the Shivdasani lab, and
human data by the Helmrath lab; we are also integrating publicly available datasets into our analysis. This
project will deliver a set of conserved and derived factors that participate in the maintenance of the intestinal
stem cell niche and a consortium-endorsed nomenclature of all mesenchymal, epithelial, and other cell
subtypes in human and mouse intestine.

## Key facts

- **NIH application ID:** 10888547
- **Project number:** 3U01DK103147-10S1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Ophir D Klein
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $320,000
- **Award type:** 3
- **Project period:** 2014-09-05 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10888547

## Citation

> US National Institutes of Health, RePORTER application 10888547, The roles of regional specialization, mechanical forces and epigenetic memory after perturbation and injury of the intestinal stem cell microenvironment (3U01DK103147-10S1). Retrieved via AI Analytics 2026-06-02 from https://api.ai-analytics.org/grant/nih/10888547. Licensed CC0.

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