Salt concentration was set to 0.1 M. QGramMatch was used to analyse uniqueness of the oligos. Experimental design The experiment designs of FZB42 in response to various conditions are summarized in Additional file 3: Table S6. Independent experiments were used as biological replicates. In all comparisons dye-swap were carried out to minimize the effect of dye biases. 1 C medium (0.7% w/v pancreatic digest of casein, 0.3% w/v papain digest of soya flour, 0.5% w/v NaCl) containing 0.1% glucose was used in all experiments. Except the controls of the experiment “Response to SE” (Additional

file 3: Table S6), 10% soil extract was also supplemented in the media. Soil extract was prepared by extracting 500 g dried, fertile garden soil Foretinib chemical structure with one litre distilled water for 2 hrs and autoclaving. After cooling down, selleck kinase inhibitor the supernatant was filtered with 0.22 μm Nuclepore unit and then stored at 4°C until use. Total RNA preparation One overnight colony of FZB42 was inoculated into 1 C medium plus 0.1% glucose and then shaken at 210 rpm at 24°C. After 14 hours the obtained preculture was used to inoculate a new 1 C medium (containing 0.1% glucose)

plus the corresponding solution to be studied (maize root exudates, soil extract, or interaction exudates. See Additional file 3: Table S6). The main cultures were grown at 24°C until they reached late exponential growth phase (OD 1.0) and/or the transition to stationary phase (OD3.0, see Additional file 4: Figure S1). The FZB42 cells of OD1.0 or OD3.0 were harvested for preparation of total RNA. A volume of 15 ml of the culture was mixed with 7.5 ml “killing buffer” (20 mM Tris–HCl, 5 mM MgCl2, 20 mM NaN3, pH 7.5) and then centrifuged at 5,000 rpm for 3 minutes at room temperature. The pellet was washed once more with 1 ml “killing buffer” and then second immediately frozen in liquid nitrogen. The frozen cell pellets were stored at −80°C until RNA isolation. Isolation of RNA was performed using the Nucleo Spin® RNA L (Macherey Nagel) according to the manufacturer’s instructions. The isolated RNA was additionally digested with DNaseI to avoid possible

trace DNA contamination. After ethanol precipitation RNA pellets were resuspended in 300 μl RNase-free water. The concentration of total RNA was spectrophotometrically determined, whereas its quality was checked on a 1.5% RNA agarose gel in 1 × MEN buffer (20 mM MOPS; 1 mM EDTA, 5 mM NaAc; pH7.0) with 16% formaldehyde. Synthesis of labeled cDNA, hybridization and image see more acquisition Synthesis of first-strand cDNA, microarray hybridization and image acquisition were performed in CeBiTec, the Center for Biotechnology at Bielefeld University. Briefly, aminoallyl-modified first-strand cDNAs were synthesized by reverse transcription according to DeRisi et al [73]. and then coupled with Cy3- and Cy5-N-hydroxysuccinimidyl ester dyes (GE Healthcare, Little Chalfont, UK).