# characteristics.INSDC center name[].text
Universite Lyon 1 -CNRS - UMR5240 Microbiologie Adaptation Pathogenie

# characteristics.Submitter Id[].tag
Namespace:Universite Lyon 1 -CNRS - UMR5240 Microbiologie Adaptation Pathogenie

# characteristics.description[].text
Protocols: Bacteria were grown with shaking (150 rpm) at 28 degrees C in YPG media (5 g/L yeast extract; 5 g/L peptone; 10 g/L glucose; pH 7.2), in AT minimal media (80 mM KH2PO4; 0.65 mM MgSO4, 7H2O; 18 uM FeSO4, 7H2O; 70 uM CaCl2, 2H2O; MnCl2, 10 uM 4H2O; pH 7.2) supplemented with 10 mM succinate as carbon source and 10 mM ammonium sulfate as nitrogen source (Petit, Tempe et al. 1978). Total RNAs were extracted as previously described (Hommais, Oger-Desfeux et al. 2008) and DNA contamination was eliminated with a DNase I treatment (Roche). 100 ug of total RNAs were separated on a 15 % denaturing polyacrylamide gel (7M urea, 1X TBE) and RNAs with size ranging from 25 to 500 nt were extracted. Rapidly, piece of gel containing RNAs was broken mechanically and incubated 4 h in 500 ul of 10 mM Tris-HCl, 1 mM EDTA, 300 mM NaCl buffer with soft shaking at 15 degrees C. Size-selected RNAs were twice filtrated and ethanol precipitated. 5S RNA and tRNAs depletions were performed from 2.5 ug of size-selected RNAs by reverse transcription treatment using First strand cDNA synthesis kit (Life biosciences) with 100 ng of primer 5S and 50 ng of each other primer representing tRNAs (Table S2). A RNAse H treatment was then performed and newly synthesized DNAs were eliminated with a DNAse I treatment (DNA-free kit, Ambion). The library preparation was an adaptation of the Illumina directional mRNA-Seq protocol, using the DGE-Small RNA sample preparation kit. 200 ng of selected small RNAs were treated by Antarctic Phosphatase (NEB, cat.#M0289S) and T4 PolyNucleotide Kinase (NEB, cat.#M0201S) and purified on RNeasy MinElute spin column (Qiagen, cat.#74204). Ligations with Illumina v1.5 sRNA 3' adapter and sRNA 5' adapter, reverse transcription, PCR amplification and purification with Agencourt AMPure beads (Beckman, A63880) were performed as described in the Illumina directional mRNA-Seq protocol from Illumina.