Next Generation Sequencing Facilitates Quantitative Analysis of Ern1f/f and Ern1f/fLyz2-Cre macrophage Transcriptomes. Mus musculus

Purpose: IRE1 are indicated to play important role in LPS-induced macrophage activation. The goals of this study are to investigate the effects of IRE1a abrogation in macrophages on Interleukin-4-induced alernative activation of macrophages. Methods: Total cellular RNAs of M2-polarized BMDMs by IL-4 treatment were isolated and subjected to commercial RNA-seq analysis. RNA-seq data were uniquely mapped to mm10 reference genome by TopHat v1.4.1. Expression values were assigned to gene level by Cufflinks v1.3.0. Results: Map ratios of all RNA-seq samples were above 80%. Merged expression values of all samples included 10,863 genes. Principle component analysis showed distinguished patterns between groups. Conclusions: Our study represents detailed analysis of transcriptomes of IL-4-activated macrophages, with biologic replicates, generated by RNA-seq technology. Based on the analysis of our RNA-seq data, increased expression levels of marker genes of macrophage alternative activation were found in IRE1a-abrogated macrophages copared to control cells. Our results demonstrates the loss of ER stress sensor IRE1a in macrophages enhanced IL-4-induced alternative activation. Overall design: Macrophage mRNA profiles of 8-week old Ern1f/f and Ern1f/fLyz2-Cre mice were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000