Host-specific effects on bacterial modulation of respiratory epithelial gene expression and alternative splicing
Bronchial epithelial cells grown at air-liquid interface were colonized with one of three phylogenetically diverse bacteria (Staphylococcus epidermidis, Rothia aeria, and Klebsiella aerogenes) or vehicle (media) for 12, 24, and 48 hours. Following colonization, total eukaryotic RNA was extracted from the epithelial cells and sequenced. Total RNA was extracted using Rneasy 96 QIAcube HT kit. Samples were frozen at -80C until sequencing preparation. Sequencing libraries were prepared with NEBNext rRNA Depletion Kit v2 and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. Samples were sequenced using Illumina NovaSeq targeting 30 million reads. Reads were then trimmed using Trimmomatic.
NIAID-phs004345
48hr-Kaerogenes-Donor3-rep3