Diurnal changes in bacterial settlement on the Peyer’s patch and surrounding mucosa in the rat ileum and its effect against the intestinal immune system

To investigate how stimulation from indigenous bacteria for a day affects the local transcriptome of both Peyer's patch and surrounding ordinary mucosa in the rat ileum, we treated rats with a nonabsorbable antibiotics cocktail (vancomycin, polymyxin B and sucrose) for antibiotics-treatment group or sucrose solution for control group in drinking water 1 day before euthanasia. We then performed gene expression profiling analysis using data obtained from RNA-seq of ileal Peyer's patch and surrounding ordinary tissue from rats with or without antibiotics treatment. Comparative gene expression profiling analysis of RNA-seq data from Peyer's patch and ordinary ileal tissue between control group and antibiotics treated group.