Transcriptional profiling of murine small intestinal epithelial cells stimulated with interleukin-28A

Organoids derived from small intestine epithelial cells of C57BL/6 wild-type mice were cultured in the presence or absence of IL-28 (1000 ng/ml) for 24 hours. The experimental setup included 8 samples in a pairwise design (4 unstimulated vs 4 stimulated). Profiling of whole-genome transcriptomic patterns was performed by RNA-Seq on an Illumina HiSeq 2500 platform using total RNA at the Next Generation Sequencing core unit of the University Hospital Erlangen, Germany. Demultiplexed reads were quality filtered against rRNAs, tRNAs, mt-rRNAs and mt-tRNAs. Alignment against the mus musculus reference genome (Ensemble V.84 for GRCm38) was performed with RNA-seq aligner STAR (V.2.5.1b) and statistical analysis of unique mappings (HTseq count) was computed in R using the DESeq2 1.10.1.