Epithelial cell diversity in small intestine of pigs

To establish 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. Overall, results provide new information on regional localization and transcriptional profiles of epithelial cells in the pig small intestine. Tissues were collected from 7.5 week old pigs and dissected into sample types: (1) Ileum collected 2-12 inches proximal to the ileocecal valve and divided into areas with Peyer's patches (IPP), (2) Ileum collected 2-12 inches proximal to the ileocecal valve and divided into areas without Peyer's patches (NoPP), (3) Duodenum collected immediately following pylorus (DUOD) and (4) Jejunum collected ~3 feet distal to pylorus (JEJ). Cells were extracted using 10X chrommium protocol, libraries were prepared using Illumina library prep and sequencing using Illumina HiSeq 3000. Sequences used in this study were deposited to the NCBI SRA and can be fount using the identifier PRJNA802582.