RNA-seq of Human Lower Airway Epithelial Brushings
RNA-seq was performed at University of Washingtons Northwest Genomics Center (http://nwgc.gs.washington.edu/). Library generation was performed using TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) using 1 ug total RNA.  Sequencing was performed using an Illumina HiSeq 4000 instrument. Base calls were generated in real-time on the HiSeq instrument, and RTA-generated BCL files were converted to FASTQ files. Sequence read and base quality were checked using the FASTX-toolkit and FastQC, and adaptor and low-quality bases were trimmed. Sequences were aligned to GRCh37 using STAR (v2.5.3a). Transcript abundances were quantified using Kallisto (v0.43.1). Genes with a raw count of at least 10 went into further analysis leaving 26,323 unique genes. Count data underwent variance stabilization and were converted into log2-counts per million via the Bioconductor package DESeq2. Differential gene expression between EIB(-) and EIB(+) individuals was determined using DESeq2 package in R.