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To establish a better understanding of specific epithelial cells found across different regions of the small intestine in pigs, we utilized single-cell RNA sequencing (scRNA-seq) to recover and analyze epithelial cells from duodenum, jejunum, and ileum. Cells identified included crypt cells, enterocytes, BEST4 enterocytes, goblet cells, and enteroendocrine (EE) cells. EE cells were divided into two subsets based on the level of expression of the EE lineage commitment gene, NEUROD1. NEUROD1hi EE cells had minimal expression of hormone-encoding genes and were dissimilar to EE cells in humans and mice, indicating a subset of EE cells unique to pigs. Recently discovered BEST4 enterocytes were detected in both crypts and villi throughout the small intestine via in situ staining, unlike in humans, where BEST4 enterocytes are found only in small intestinal villi. Proximal-to-distal gradients of expression were noted for hormone-encoding genes in EE cells and nutrient transport genes in enterocytes via scRNA-seq, demonstrating regional specialization. Regional gene expression in EE cells and enterocytes was validated via quantitative PCR (qPCR) analysis of RNA isolated from epithelial cells of different small intestinal locations. Though many genes had similar patterns of regional expression when assessed by qPCR of total epithelial cells, some regional expression was only detected via scRNA-seq, highlighting advantages of scRNA-seq to deconvolute cell type-specific regional gene expression when compared to analysis of bulk samples. Overall, results provide new information on regional localization and transcriptional profiles of epithelial cells in the pig small intestine.<\/jats:p>","DOI":"10.1093\/jas\/skac318","type":"journal-article","created":{"date-parts":[[2022,10,2]],"date-time":"2022-10-02T11:08:20Z","timestamp":1664708900000},"source":"Crossref","is-referenced-by-count":36,"title":["Regional epithelial cell diversity in the small intestine of pigs"],"prefix":"10.1093","volume":"101","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9538-2720","authenticated-orcid":false,"given":"Jayne E","family":"Wiarda","sequence":"first","affiliation":[{"name":"Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture , Ames, IA , USA"},{"name":"Immunobiology Graduate Program, Iowa State University , Ames, IA , USA"},{"name":"Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University , Ames, IA , USA"},{"name":"Oak Ridge Institute for Science and Education, Agricultural Research Service Participation Program , Oak Ridge, TN , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sage R","family":"Becker","sequence":"additional","affiliation":[{"name":"Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture , Ames, IA , USA"},{"name":"Immunobiology Graduate Program, Iowa State University , Ames, IA , USA"},{"name":"Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University , Ames, IA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sathesh K","family":"Sivasankaran","sequence":"additional","affiliation":[{"name":"Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture , Ames, IA , USA"},{"name":"Genome Informatics Facility, Iowa State University , Ames, IA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Crystal L","family":"Loving","sequence":"additional","affiliation":[{"name":"Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture , Ames, IA , USA"},{"name":"Immunobiology Graduate Program, Iowa State University , Ames, IA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,2]]},"reference":[{"key":"2023112010543166000_CIT0001","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat. 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