For cloning, reporter protein assays and maintaining strains: cultures were grown in LB or LB-agar media at 37°C and, when required, supplemented with ampicillin (100 µg/ml; Sigma-Aldrich), kanamycin (30 µg/ml; Sigma-Aldrich), erythromycin (1.5 µg/ml; Sigma-Aldrich) and/or bicyclomycin (BCM; Astellas Corporation) (8-10 µg/ml – low concentration used for extended treatments, minimally affects bacterial growth). When grown in liquid media, cells were cultivated with constant aeration (shaking at 200 rpm). The RNA library from SELEX cycle 7 was first reverse transcribed to cDNA and amplified by 16 cycles of PCR with Phusion High-Fidelity DNA polymerase (New England Biolabs) using primers with fixed part and added barcode for multiplexing according to (Parameswaran et al., 2007), (Windbichler et al., 2008)  (fixFW: TATAGGGGAATTCGGAGCGGG, fixRV_multi: TAGCCCGGGATCCTCGGGGCTG (Sigma)). Library preparation (adapter ligation step) and deep sequencing were performed at the CSF NGS unit http://csf.ac.at/. The SELEX library was multiplexed and sequenced with the Solexa technology on a GAIIx with paired-end 76 base-pair reads.
GEO Accession
GSM2608038