intestinal epithelial cells (IEC) from 3 mice per group were pooled, stained and FACS-purified based on a CD45-EpCAM+ gate from small intestine cellular preparations at day 9 post-infection. Sorted cells were placed in 350 μl RLT (Qiagen) + beta-mercaptoethanol (10 μl/ml, Life Technologies) and stored at -80 C. The following day, RNA was extracted with RNAeasy Micro Kit (Qiagen) by following the manufacturer's protocol and re-suspended in molecular grade distilled H2O and stored at -80 C until library preparation. mRNA stranded libraries were constructed by using TruSeq RNA Library Prep Kit v2 (Illumina) followed by single-end sequencing of 75 base-pair fragments with a HiSeq 4000 (Illumina). Raw sequencing files were processed with CASAVA 1.8.2 (Illumina) to generate .fastq files.
GEO Accession
GSM4695823