Borrelia burgdorferi B31-5A4 37 degree
Total RNA was isolated using a hot phenol protocol. Total RNA was treated with DNase I (Roche) following the manufacturer’s protocol. RNA integrity was measured using the Agilent 2100 Bioanalyzer. RNA with an RNA Integrity Number (RIN) above 9.0 was used for cDNA library construction. Directional (strand-specific) RNA-seq cDNA libraries were constructed with a ligation based protocol as previously described with an initial size-selection{Drecktrah, 2015 #88;Lybecker, 2014 #20}. Ribosome-depleted (Ribo-Zero RNA removal kit for gram negative bacteria; Epicentre) total RNA was size fractionated on an 8% TBE-UREA gel. RNA was eluted from gel slices correlating to 50 to 500 nucleotides.