GSM7220543: Donor 2 NTHI Day 0; Haemophilus influenzae; RNA-Seq
Samples for RNA isolation were collected prior to infection (day0) for uninfected NHNE and bacterial pre-cultures, and on day1, 3, 7 and 14 post-infection for NTHi-infected NHNE. RNA was extracted from 3 replicate NHNE per sample (samples 6-28) or from bacterial cell material collected following growth on BHI agar ( samples 1-5) using TRIZOL (Thermo Fisher), treated with EZDnase to remove remaining gDNA and concentrated usingRNA Clean and Concentrate Kits (Zymo). 2-3 microg total RNA (RIN >8.0) were ribodepleted using the RiboMinus kit (Termo Fisher) and the ribodepleted RNA used for library preparation. For all NHNE samples ~ 70 million reads were collected per sample and mapped to human and NTHi reference genomes. for NTHi infected NHNE samples, approximately 2 milion reads could be mapped to the bacterial genome. RNA libraries were prepared using the Illumina TruSeq kit