library_construction_protocol: Portions of small intestine containing individual Peyer's patches were removed and immersed in Hank's balanced salt solution (HBSS) containing 30 mM EDTA at 4oC for 15 min.  Peyer's patches domes were micro-dissected and the FAE layer then carefully teased away from the underlying tissue using fine needles under stereomicroscopy and trimmed of villi.  Sheets of conventional VE were prepared in the same manner from 5 mm portions of ileum that lacked Peyer's patches adjacent to each dissected Peyer's patch. Isolated FAE and VE sheets as well as 5 mm sections of whole ileum from each mouse were kept at -80oC until RNA extraction.  Total RNA was isolated from FAE, VE and ileum samples using a RNeasy Plus Kit (Qiagen). TruSeq stranded mRNA-seq library