Heatmap depiction of differentially expressed genes as determined via RNA-seq and microarrays under multiple experimental conditions: (A) unstimulated AECs cultured in monolayer vs. ALI; (B) unstimulated vs. flagellin-exposed AECs cultured in monolayer; (C) unstimulated vs. flagellin-exposed AECs cultured in ALI.

<p>Note the very large number of differentially expressed genes between ALI vs. monolayer AEC cultures at baseline. When stimulated with flagellin, AECs grown in ALI displayed a blunted transcriptional response when compared to the robust response of epithelial cells cultured in monolayer. In each condition, RNA-seq identified many more differentially expressed genes compared to microarrays while capturing the majority of genes deemed significant by microarrays. Heatmaps are based on adjusted <i>P</i>-values of differentially expressed genes, and for purposes of clarity, are not drawn to the same scale in height across conditions.