This document presents the results of a study examining the transcriptional profiling of Pseudomonas aeruginosa lineages that evolved during infection of cystic fibrosis patients. The study aimed to identify potential adaptive expression traits in P. aeruginosa through isolating bacteria from patients, performing genetic and expression analyses, and microarray experiments. Key results included hierarchical clustering of microarray data identifying differentially expressed genes between and within clonal groups over time. Future work could involve altering current therapeutics based on expression profiles and better understanding genes of unknown function that were differentially expressed.