RNAseq of mRNA from murine small intestinal crypts

Spontaneous inflammation in the terminal ileum of Xiap–/– mice was observed to occur in a microbiome dependent manner. Xiap–/– mice housed alone presented with signs of inflammation which were alleviated upon co-housing the mice with wild-type counterparts. To elucidate the impact of co-housing, and thus the transfer of the microbiome to affected Xiap–/– mice, crypts from the small intestine of these mice were analyzed. Small intestinal crypts from wild-type and Xiap-deficient mice either housed according to genotype or co-housed together for four weeks were isolated and subjected to RNA-seq analysis.