title: RNAseq data from Bacteroides thetaiotaomicron genetically modified to silence a prophage gene (RepCHP)
design: RNAseq data from Bacteroides thetaiotaomicron genetically modified to silence a prophage gene (RepCHP)
library_construction_protocol: Overnight cultures were mixed with RNAprotect (Qiagen) in the anaerobic chamber to prevent RNA degradation and bacteria were lysed using QIAGEN Proteinase K and TE buffer containing lysozyme. Bacteroides strains were grown in brain-heart infusion medium supplemented (BHIS) with cysteine 0.1%, hemin 5 μg/mL and sodium bicarbonate 0.2% (NaCOH3). Cultures were incubated statically at 37°C in a C400M Ruskinn anaerobic chamber (95% N2, 5%CO2) or in anaerobic bags (GenBag anaero, Biomerieux). E. coli strains were grown in Luria-Bertani (LB) broth (Corning) supplemented with or without ampicilin 100 μg/mL and incubated at 37°C aerobically with 180 rpm shaking. Total RNA was extracted using the Direct Zol kit (Zymo Cat. R2050) according to the manufacturer's instructions and treated with Dnase I from the same kit. RNA concentration, quality, and integrity from 3 independent replicates were checked using the 4195 Tapestation system (Agilent). Ribosomal RNA depletion was performed using the Bacteria RiboZero Plus kit (Illumina). From rRNA-depleted RNA, directional libraries were prepared using the TruSeq Stranded Total RNA Sample preparation kit following the manufacturer's instructions (Illumina). Libraries were checked for quality on Bioanalyzer DNA 1000 chips (Agilent). Quantification was performed with the fluorescent-based quantitation Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific)