Normal human bronchial epithelial cells were grown at air-liquid interface and then colonized with microbes for 18 or 48 hours. Following colonization, total RNA was extracted 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.