Tissue Mapping Center

Stanford Tissue Mapping Center


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. The Stanford Tissue Mapping Center (TMC) strives to map the complexity of the small bowel and colon with cell-to-cell resolution in histologic sections, both along their lengths and across multiple individuals.

To accomplish this goal, this group collects tissues from brain-dead organ donors with explicit consent for distribution among the HuBMAP consortium and open access genome data sharing (GDS). Two sets of technologies are then employed. Tissue samples are subjected to single cell (sc) ATAC-seq and scRNA-seq. These ‘omic profiles are then spatially mapped back to histologic sections using a highly multiplexed system of antibody-tagged target epitopes, which are called CO-Detection by indEXing (CODEX). An integrative analysis will be performed to identify proteins important to establishing the identity of each cell population within the tissue.​

Fast Facts
Project title:Stanford Tissue Mapping Center
Organ specialty: Small bowel and colon
PIs:Michael Snyder, Garry Nolan
Co-Investigators:Yiing Lin, Washington University in St. Louis; Garry Nolan, Stanford University
Project Manager:Annika Weimer
Assay Types:snATAC-seq, snRNA-seq, CODEX, Proteomics, Lipidomics, Metabolomics
Grant number:1U54HG010426-01
Learn more: Visit this lab's website, and follow them on Twitter.


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