U54HG012723
Cooperative Agreement
Overview
Grant Description
Stanford Tissue Mapping Center - 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.
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.
Funding Goals
NOT APPLICABLE
Grant Program (CFDA)
Awarding Agency
Place of Performance
Palo Alto,
California
94304
United States
Geographic Scope
Single Zip Code
Related Opportunity
Analysis Notes
Amendment Since initial award the total obligations have increased 289% from $1,999,996 to $7,785,758.
The Leland Stanford Junior University was awarded
Stanford Tissue Mapping Center
Cooperative Agreement U54HG012723
worth $7,785,758
from the National Institute of Allergy and Infectious Diseases in September 2022 with work to be completed primarily in Palo Alto California United States.
The grant
has a duration of 3 years 9 months and
was awarded through assistance program 93.310 Trans-NIH Research Support.
The Cooperative Agreement was awarded through grant opportunity Tissue Mapping Centers for the Human BioMolecular Atlas Program (U54 Clinical Trial Not Allowed).
Status
(Ongoing)
Last Modified 9/24/25
Period of Performance
9/23/22
Start Date
6/30/26
End Date
Funding Split
$7.8M
Federal Obligation
$0.0
Non-Federal Obligation
$7.8M
Total Obligated
Activity Timeline
Subgrant Awards
Disclosed subgrants for U54HG012723
Transaction History
Modifications to U54HG012723
Additional Detail
Award ID FAIN
U54HG012723
SAI Number
U54HG012723-463956369
Award ID URI
SAI UNAVAILABLE
Awardee Classifications
Private Institution Of Higher Education
Awarding Office
75N400 NIH National Human Genome Research Institute
Funding Office
75NA00 NIH OFFICE OF THE DIRECTOR
Awardee UEI
HJD6G4D6TJY5
Awardee CAGE
1KN27
Performance District
CA-16
Senators
Dianne Feinstein
Alejandro Padilla
Alejandro Padilla
Budget Funding
| Federal Account | Budget Subfunction | Object Class | Total | Percentage |
|---|---|---|---|---|
| Office of the Director, National Institutes of Health, Health and Human Services (075-0846) | Health research and training | Grants, subsidies, and contributions (41.0) | $4,408,194 | 100% |
Modified: 9/24/25