Illumina HiSeq 2000 sequencing; The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori
The core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori
H. pylori strains were grown in liquid cultures as described in: Bubendorfer, S., Krebes, J., Yang, I., Hage, E., Schulz, T.F., Bahlawane, C., Didelot, X. and Suerbaum, S. (2016) Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori. Nat. Commun., 7, 11995.  For RNA extraction, 5 ml of bacterial cells grown in liquid medium were pelleted (4°C, 6000 x g, 3 110 min), snap-frozen in liquid nitrogen and stored at -80 °C. Afterwards, bacterial pellets were disrupted with a FastPrep® FP120 Cell Disrupter (Thermo Savant) using Lysing Matrix B 2 ml tubes containing 0.1 mm silica beads (MP Biomedicals, Eschwege, Germany). Isolation of RNA was performed using the RNeasy kit (Qiagen, Hilden, Germany) and on-column DNase digestion with DNase I. A second DNase treatment was carried out using the TURBO DNA-free™ Kit (Ambion, Kaufungen, Germany).  Total rRNA depletion was performed prior to cDNA synthesis using a RiboZero Kit (Illumina, Germany). cDNA library was performed with random primers.
Experimental Factor: strain
BCM-300
Experimental Factor: phenotype
wild type