Blood biomarkers of the late phase asthmatic response using RNA-Seq

Methods 35 individuals (17 ERs and 18 DRs) participated in the allergen inhalation challenge. Blood samples were obtained prior to and 2 hours post allergen inhalation challenge. HiSeq-Illumina paired-ends 100bp sequencing was performed. A UCSC transcriptome using both the UCSC gene and gene-isoform transcripts was created using the RSEM (RNA-Seq by Expectation Maximization) package. RSEM uses Bowtie to align read files to the reference transcripts and estimates the expected number of counts per transcript. The biomarker pipeline consisted of 20x5-fold deep cross-validation using limma voom (linear models for microarrays and RNA-Seq using variance modeling at the observational level) for differential expression and elastic net for classification. Gene set enrichment analysis was performed using GeneGo.