RNA-Seq for Methylobacterium sp. 22A grown on methanol in the presence of calcium, lanthanum, holmium, and lutetium.. Methylobacterium sp. MA-22A

Methylobacterium sp. 22A was grown in 100-ml methanol medium (composition described below) prepared in 500-ml shaking flask. The media contain 0.5% methanol or 0.5% succinate. For methanol, 30 micromolar Ca (Calcium chloride), La (Lanthanum chloride), or Ca plus La, Ca plus Ho (Holmium chloride), or Ca plus Lu (Lutetium chloride) was added. Cultivation was done at 28 C for 38-84 hours. In log phase of the growth (OD600=0.3-0.4), the cells were harvested by centrifugation (9,000 rpm, 4 C, 5 min), and frozen by liquid nitrogen. The cells were subjected to total RNA extraction with hot phenol extraction procedure (Babst et al., 1996, Mol Microbiol 19:827-839). Then ribosomal RNA was depleted by using Ribo-Zero rRNA removal kits (Gram-negative bacteria) (Epicentre) according to the manufacturer's protocol.