Identification of differentially expressed genes in MDV-transformed cells lines treated with sodium butyrate

In order to characterize alterations in cellular regulatory mechanisms associated with MDV reactivation, we employed microarray analysis to identify changes in gene expression in chemically-reactivated MDV transformed cell lines, specifically MSB1, RP2 and CU115. Differentially expressed genes identified in the MDV-transformed cell lines were then compared against differentially expressed genes in the REV-transformed CU91 cell line. This step was done to reduce the number of false positives (i.e. genes likely responding solely to sodium butyrate rather than MDV reactivation). Multiple cellular pathways are also affected by MDV reactivation, including those associated with apoptosis, the cell cycle, DNA repair, and immune response. A loop design (one replicate per loop) and a dye swap design scheme was used. RNA was amplified using an Amino Allyl MessageAmpII aRNA Amplification kit (Ambion), aliquoted into two pools per sample, and each pool was separately labeled with either Cy3 or Cy5 reactive dyes (GE Healthcare). RNA samples from the same cell line and from a different time-point (either 0 or 12 or 24 hr post-treatment (hpt)) were co-hybridized. The chicken (20.7 K) oligoarray (GPL6049) was purchased from Steele Children’s Research Centre, Tucson, Arizona. Two replicates of each cell line and each time-point were used, for a total of 24 slides.