Single-cell and spatial transcriptomics profile of porcine jejunum and ileum containing Peyer's patches

To establish better understanding of cells found in jejunal and ileal Peyer's patches of pigs, we utilized single-cell RNA sequencing scRNA-seq and spatial transcriptomics to recover and analyze cells and spatial regions from sections of jejunum and ileum containing Peyer's patches. Cells identified via single-cell RNA sequencing included B, T/innate lymphoid cell, myeloid, epithelial, and stromal lineage cells. Spatial dots recovered via spatial transcriptomics belonged to regions including villi, crypts, interfollicular/parafollicular zones, follicles, and muscularis. Overall, results provide new information on regional localization and transcriptional profiles of cells in the pig small intestine. Tissues were collected from 7.5 week old pigs from distal ileum containing Peyer's patches and jejunum where the distal-most discrete Peyer's patch was located. Tissues for spatial transcriptomics were frozen and cryosectioned onto 10X Visium spatial transcriptomics slides. Cells were isolated with a collagenase incubation and mechanical dissociation and processed for single-cell RNA sequencing with the 10X Chromium protocol. Libraries were prepared using Illumina library prep and sequenced using Illumina HiSeq 3000 and NovaSeq 6000 for single-cell RNA sequencing data and a NovaSeq 6000 for spatial transcriptomics data.