Transcriptome analysis of the mRNAs and lncRNAs in porcine alveolar macrophages in response to porcine reproductive and respiratory syndrome virus or IFN-a at different time points

Purpose:We performed next-generation RNA sequencing and a comprehensive bioinformatics analyses to characterize the transcriptome landscapes, including mRNAs and long noncoding RNAs (lncRNAs) in PRRSV-infected PAMs or IFN-stimulated PAMs at different time points. Conclusions: We showed that PRRSV infection displays different transcriptome profiles of PAMs, and the aberrant function of PAMs may be reflected by significant down-regulation of essential genes at the transcriptome levels. In addition, we discovered a great amount of differentially expressed lncRNAs, including lncRNA XR_297549.1, which is highly expressed and predicted to both cis- and trans-regulate its neighboring gene PTGS2.In addition, In order to expand our understanding of these IFN-induced non-coding transcripts, especially long non-coding RNAs (lncRNAs), we performed next-generation RNA sequencing and a comprehensive bioinformatics analysis of porcine alveolar macrophages (PAMs) stimulated with pig-IFN-? for 6h and 12h, respectively. A great amount of differentially expressed mRNAs and lncRNAs were identified, and several lncRNAs are of great interest for further investigation as their potential role in regulation of the well-characterized antiviral genes, such as OAS1, PML and ISG15. Overall design: Examination of the differential expression profiles of primary porcine alveolar macrophages infected with porcine reproductive and respiratory syndrome virus or stimulated with IFN-a with two biological replicates, using Illumina Higseq 2500.