title: Lifestyle of lactobacilli in the murine gut_Illumina-3
design: Total RNA was reverse-transcribed using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) with modifications as described before (Berry et al. 2011). cDNA libraries generated from total RNA derived from the forestomach were sequenced by a PGM IonTorrent (LifeSciences) using 200 bp sequencing chemistry and 316er chips according to instructions supplied by the manufacturer. Double stranded cDNA libraries from the lumen were paired-end sequenced using an Illumina HiSeq (CSF Vienna). Read pairs were overlapped using FLASH yielding reads of approx. 170 bp (9).