Bacillary growth and global transcriptome analysis of rabbit lungs during Mtb CDC1551 infection. Bacterial CFU in the lungs were enumerated up to 24 weeks and microarray analysis of gene expression profile was performed in the lungs of Mtb-infected rabbits at 2, 4, 8 and 12 weeks post-infection and compared to the uninfected animals. A: Total lung bacillary load determined by plating organ homogenates from each infected rabbit on agar plates. For each animal, about 30% of the entire lung, comprising all 5 lung lobes, was used to prepare the homogenates. B: PCA mapping of data points obtained from pooled samples from uninfected (n = 3) or one experiment from each of the three biological replicates from Mtb-infected rabbit lungs at each time point (n = 3 per time point). Eclipse drawn around the triplicate data points for each time point represents area spanning two-fold standard deviation from the median expression levels. C: Venn diagram showing the number of statistically significantly differentially expressed genes (SDEG) by Mtb infection of rabbit lungs at 2, 4, 8 and 12 weeks post-infection. The genes were selected based on a False Discovery Rate (FDR) of 5% (equivalent to p ≤0.05).