Effects of Pseudorabies Virus Infection on the Tracheobronchial Lymph Node Transcriptome

• Main Authors: Laura C. Miller, Darrell O. Bayles, Eraldo L. Zanella, Kelly M. Lager
• Format: Article
• Language: English
• Published: SAGE Publishing 2015-01-01
• Series: Bioinformatics and Biology Insights
• Online Access: https://doi.org/10.4137/BBI.S30522

This study represents the first swine transcriptome hive plots created from gene set enrichment analysis (GSEA) data and provides a novel insight into the global transcriptome changes occurring in tracheobronchial lymph nodes (TBLN) and spanning the swine genome. RNA isolated from draining TBLN from 5-week-old pigs, either clinically infected with a feral isolate of Pseudorabies virus or uninfected, was interrogated using Illumina Digital Gene Expression Tag Profiling. More than 100 million tag sequences were observed, representing 4,064,189 unique 21-base sequences collected from TBLN at time points 1, 3, 6, and 14 days post-inoculation (dpi). Multidimensional statistical tests were applied to determine the significant changes in tag abundance, and then the tags were annotated. Hive plots were created to visualize the differential expression within the swine transcriptome defined by the Broad Institute's GSEA reference datasets between infected and uninfected animals, allowing us to directly compare different conditions.