GSM6705687: in vitro cultured Bb enriched with aBb, rep 1; Borreliella burgdorferi; RNA-Seq
Total RNA was extracted from immunomagnetically separated samples using the Zymo Direct-zol RNA Microprep Kit with on-column DNase treatment. RNA-seq libraries were constructed from 50 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Borrelia rRNAs were depleted from the libraries using Depletion of Abundant Sequences by Hybridization (DASH)(Gu et al. 2016). Libraries were mixed with Cas9 and custom dgRNAs (Ring et al. 2022) for a total of 2 hours at 37°C to deplete rRNAs, purified 0.9X sparQ PureMag Beads (QuantaBio) then reamplified with the Kapa HiFi Real-Time Amplification Kit before sequencing.