Gene expression in the ileum of Cftr null mice

Transcriptome sequencing was performed on ileum of Cftr null mice and wildtype littermates Overall design: Tissue from the distal small intestine (<6 cm proximal to the ileocecal valve) was collected from Cftr null mice (Cftrtm1Cam; congenic FVB) and littermate controls (Cftr N/N). In some cases, animals had been treated with the antibiotics ciprofloxacin (0.3 g/L) and metronidazole (0.5 g/L). For transcriptome analysis, mRNA was isolated from tissue RNA extracts, fragmented, and, subsequently used for cDNA synthesis. The cDNA libraries were sequenced using an HiSeq 2000 sequencer (TruSeq SBS KIT-HS V3; Illumina) and the Ion Proton System (4476610). Data analysis was performed using CLC genomic workbench 7.5 (CLC Bio), and the sequence reads were mapped to the Genome Reference Consortium (GRC) genome data set GRCm38.76, using default parameters.