Global analysis of Cdk9-dependence for VSV-induced genes in Drosophila cells

To determine the Cdk9 targets of VSV-induced genes in Drosophila cells at 4 hours post-infection Drosophila cells were treated with Bgal or Cdk9 and infected with VSV (MOI 10) for 4 hours, in two independent biological replicates. Total RNA was isolated using Trizol and microarray experiments were performed at the University of Pennsylvania Microarray Facility (U. Penn MF) following directions according to the manufacturer’s protocol (Affymetrix). In brief, 100 ng RNA were amplified with the Ovation RNA Amplification System v2 (NuGen), the Encore Biotin Module (NuGen) was used for fragmentation and labeling, Protocol FS450 002 was used for hybridization, washing, and staining. Images were scanned using the GeneChip® Scanner 3000 and image analysis was performed using the Affymetrix® GeneChip® Command Console® Software (AGCC).