GSM1846880: P.putida (mt-2) C-runout (succinate-96h); Pseudomonas putida; RNA-Seq
Total RNAs from m-xylene-treated cells or reference condition were prepared. rRNA was depleted using the RiboZero rRNA removal kit (Epicenter Biotechnologies) for Gram-negative bacteria with a total RNA input of 4 μg. To confirm rRNA removal, we analyzed the samples with the Bioanalyzer system. RNA libraries were prepared using the TruSeq RNA sample prep kit (Illumina) following the protocol described in the Wiley-Blackwell and Society for Applied Microbiology of TruSeq RNA Sample Preparation Guide, starting at the fragmentation step. The library was validated by running a High Sensitivity DNA chip (Agilent Technologies) on the Bioanalyzer system and quantified by qPCR according to the Illumina Sequencing Library qPCR Quantification Guide, using KAPA SYBR FAST qPCR kit for LC480 (KAPA Biosystems). The libraries were denatured and adjusted to 14 pM prior to generating the clusters as indicated in the Illumina Cluster Generation Guide for a Cluster Station instrument.