Liver and Ileum Transcriptome Profiling by RNA-Seq

Hepatic and ileal transcriptome analysis was performed by RNA sequencing on RNA extracts from terminal liver samples, as described[19 (link)]. RNA sequence libraries were prepared with NeoPrep (Illumina, San Diego, CA, United States) using Illumina TruSeq stranded mRNA Library kit for NeoPrep (Illumina, San Diego, CA, United States) and sequenced on the NextSeq 500 (Illumina, San Diego, CA) with NSQ 500 hi-Output KT v2 (75 CYS, Illumina, San Diego, CA, United States). Reads were aligned to the GRCm38 v84 Ensembl Mus musculus genome using STAR v.2.5.2a with default parameters[23 (link)]. Differential gene expression analysis was performed with DEseq215[24 (link)].