Pure populations of nonsmoker and smoker small airway                     samples were obtained by bronchoscopy. Smoking status was confirmed by tobacco                     urine metabolites. Active smokers had consistently high cotinine levels (=104                     ng/ml) and nonsmokers had undetectable urine cotinine and urine nicotine levels.                     Total RNA was extracted with TRIzol with subsequent RNA clean-up using the                     RNeasy MinElute RNA purification kit to remove residual DNA The TruSeq RNA                     Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to                     generate cDNA that was then purified with QIA-quick PCR purification kit                     (Qiagen, Valencia, CA) Samples were loaded onto an Illumina flowcell for                     paired-end 125 x 2 sequencing reactions using the Illumina HiSeq 2500. HiSeq                     Control Software (Illumina) was used to perform image analysis, base calling and                     sequence analysis on HiSeq generated sequence                     images.