RNA from vehicle and cytokine treated cells was hybridized to the Illumina Human HT-12 v4 array at The University of Chicago Functional Genomics Facility (FGF). Probes that were indistinguishable from background intensity (P < 0.01), contained more than one HapMap single nucleotide polymorphism (SNP), or mapped to multiple locations in the genome were removed. Since in some cases multiple probes mapped to one gene, median probe intensity was used to represent the transcriptional abundance of each individual transcript. Of the 47,231 transcripts on the Illumina Human HT12v4 array, 18,279 (39%) unique transcripts were detected as expressed in cultured ASMCs. DNA from vehicle and cytokine-treated cells was assessed for genome-wide methylation patterns using the Illumina Infinium Human MethylationEPIC Beadchip, also at the FGF.
Differential expression analyses between vehicle and cytokine-exposed cells as well as between individuals with and without asthma were performed in R (Version 1.0.136) using Limma [27 (link), 28 (link)]. Because ancestry PC1 and PC2 captured the effects of global ancestry, they were included as covariates rather than self-reported race (i.e., African American vs. European American). Imputed smoking, age, and sex were included as covariates in all analyses. The final sample size for both analyses was 70 [29 ].
Differential expression analyses between vehicle and cytokine-exposed cells as well as between individuals with and without asthma were performed in R (Version 1.0.136) using Limma [27 (link), 28 (link)]. Because ancestry PC1 and PC2 captured the effects of global ancestry, they were included as covariates rather than self-reported race (i.e., African American vs. European American). Imputed smoking, age, and sex were included as covariates in all analyses. The final sample size for both analyses was 70 [29 ].
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