Peyer's patches are gut-associated lymphoid tissue located throughout the 
intestinal wall. Peyer's patches consist of highly organized ovoid-shaped 
follicles, classified as non-encapsulated lymphatic tissues, populated with B 
cells, T cells, macrophages, and dendritic cells and function as an organism's 
intestinal surveillance. Limited work compares the gene profiles of Peyer's 
patches derived from different intestinal regions. In the current study, we 
first performed whole transcriptome analysis using RNAseq to compare duodenal 
and ileal Peyer's patches obtained from the small intestine of Long Evans rats. 
Of the 12,300 genes that were highly expressed, 18.5% were significantly 
different between the duodenum and ileum. Using samples obtained from additional 
subjects (n = 10), we validated the novel gene expression patterns in Peyer's 
patches obtained from the three regions of the small intestine. Rats had a 
significantly reduced number of Peyer's patches in the duodenum in comparison to 
either the jejunum or ileum. Regional differences in structural, metabolic, and 
immune-related genes were validated. Genes such as alcohol dehydrogenase 1, gap 
junction protein beta 2, and serine peptidase inhibitor clade b, member 1a were 
significantly reduced in the ileum in comparison to other regions. On the other 
hand, genes such as complement C3d receptor type, lymphocyte cytosolic protein 
1, and lysozyme C2 precursor were significantly lower in the duodenum. In 
summary, the gene expression pattern of Peyer's patches is influenced by 
intestinal location and may contribute to its role in that segment.