|FLEMING, DAMARIUS - Oak Ridge Institute For Science And Education (ORISE)|
Submitted to: Genomics Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/29/2016
Publication Date: 9/30/2016
Citation: Fleming, D.S., Miller, L.C. 2016. Leading edge analysis of transcriptomic changes during pseudorabies virus infection. Genomics Data. 10:104-106.
Interpretive Summary: Pseudorabies virus (PRV) can cause severe disease in swine and is an economically important disease, or disease threat in most swine producing countries. This "data-in-brief" paper describes the experimental procedures and publicly available gene expression datasets from a study that evaluated the pig' response to an experimental PRV infection. As the pig responds to a PRV infection changes in metabolism reflect changes in the expression of specific genes. Gene expression describes the regulation of the pig's metabolic processes which involves the expression of a partial copy of the gene's DNA sequence—called messenger RNA or mRNA. The mRNA is used as a template to direct the synthesis of a protein which in turn regulates cellular function. Gene expression profiling is the process of determining which genes are active in a specific cell or group of cells. It is accomplished by measuring mRNA, the intermediary between genes and proteins. Variation in gene expression profiles can act as an important indicator of disease or predisposition to disease. By comparing gene expression patterns between cells from different environments, such as normal tissue vs. diseased tissue, one can determine which genes are active or inactive in various disease states. Characterizing core gene changes gives insight to how the virus affects the host, and how the host is trying to combat the infection which can lead to a greater understanding of how to build better vaccines which may help in the control of pseudorabies.
Technical Abstract: Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days’ post infection (dpi) that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA) to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO) (GSE74473) database.