Submitted to: International Plant and Animal Genome IX Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/4/2005
Publication Date: 1/14/2006
Citation: Tuggle, C.K., Qu, L., Wang, Y., Couture, O., Nettleton, D., Dekkers, J., Zhao, S., Uthe, J.J., Bearson, S.M. 2006. Using a first-generation Porcine Affymetrix GeneChip® to investigate the functional genomics of immune response and reproductive biology [abstract]. International Plant and Animal Genome IX Conference. p.W407 Interpretive Summary:
Technical Abstract: Functional genomics in pigs is in a preliminary stage. In 2005, an Affymetrix Porcine GeneChip was created, and we have initiated its use to profile gene expression in two projects; the immune response to bacterial infection and maternal-fetal communication at implantation. Technical reproducibility testing by repeated hybridizations using the same liver RNA target indicated the GeneChip had sufficient precision to accurately measure expression differences across treatments. We then used this tool to profile expression in triplicate mesenteric lymph node RNA from uninfected or pigs infected with Salmonella enterica serovar Choleraesuis (SC) or Typhimurium (ST). We also profiled expression in quadruplicate endometrial RNA from cycling or pregnant Yorkshire gilts at several stages of the cycle/pregnancy, as well as comparable samples from Meishan gilts. We evaluated data quality and preprocessed data from these two projects in R, including pair-wise MA plots, 5'/3' ratio, present call%, and boxplots of mas5 expression measures. Then ANOVA models were fitted to mas5 expression measures with default scaling to detect differential expression. We will present these analyses for over 50 hybridizations, as well as our further annotation and bioinformatic integration of the probe sets with other commercial profiling tool elements. Preliminary analysis of the infection data indicates significantly different pathways respond to ST compared to SC. For the reproduction project, large numbers of genes were found differentially expressed across stages, between pregnant and cycling animals, and between breeds. For these tissues, the GeneChip appears to be highly sensitive and useful in detecting differentially expressed genes.