ARS | Publication request: Comparative transcriptome response in swine tracheobronchial lymph nodes to viral infection

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 7, 2012
Publication Date: January 12, 2013
Citation: Miller, L.C., Harhay, G.P., Kehrli, Jr., M.E., Lager, K.M. 2013. Comparative transcriptome response in swine tracheobronchial lymph nodes to viral infection [abstract]. International Plant & Animal Genome XXI, January 12-16, 2013, San Diego, California. Paper No. W756.

Technical Abstract: The tracheobronchial lymph node (TBLN) transcriptome response was evaluated following viral infection using Digital Gene Expression Tag Profiling (DGETP). Pigs were sham-treated or infected intranasally with porcine reproductive and respiratory syndrome virus, porcine circovirus type 2, pseudorabies virus, or swine influenza virus. Five pigs from each group were euthanized and necropsied on 1, 3, 6, and 14 days post-inoculation (dpi). Total RNA from the TBLN was pooled for each group and timepoint to make 24 libraries for analysis by DGETP. Multidimensional statistical tests and clustering analysis identified significant changes in tag abundance. Tags were annotated with available transcript information from swine RefSeq sequences and HarvardGI Accessions. Hiveplots were created to visualize the differential expression (DE) within the swine transcriptome defined by the Broad Institute’s Gene Set Enrichment Analysis reference datasets (GSEA) for each treatment vs control, allowing us to directly compare different conditions such as dpi and treatment. Hiveplots identified regions of the swine genome that encompassed all chromosomes (1-18, X,Y) and the mitochondrial genome, that are negatively or positively correlated, on each horizontal axis, associated with the GSEA gene set, on the vertical axis, indicated by colored lines, where the color is proportional to the fold change with respect to uninfected controls. This study represents the first swine transcriptome hiveplots created from GSEA data and provides a novel insight into the global transcriptome changes spanning the swine genome.