GSM5808467: A4_F88_I1_glc, rep1; Pseudomonas putida KT2440; RNA-Seq
For transcriptomic analysis, cell cultures at the exponential phase (OD600 0.4-0.6) were mixed with two volumes of RNA protect Bacteria Reagent (Qiagen, Hilden, Germany) for stabilization and their total RNA was extracted by using Quick-RNA Fungal/Bacterial Miniprep Kit (Zymo Research). Residual genomic DNA was removed by incubating the samples with DNase I (RNase-free, NEB). Ribosomal RNA was removed by hybridizing with 30-bp oligonucleotides designed to bind the ribosomal RNA of KT2440 specifically and treating with Thermostable RNase H purchased from Lucigen (Middleton, WI, USA). The remaining oligonucleotides were removed by incubating the resulting samples with DNase I (NEB). The samples were purified by using an RNA Clean & Concentrator Kit (Zymo Research). The 12 samples for the “aromatic” project were prepared with several modifications. Collected cells were resuspended in TRIzolTM reagent (ThermoFisher Scientific, Waltham, MA, USA).  Total RNA was isolated using the RNeasy Mini Kit (Qiagen) by following the manufacturer's instructions. Ribosomal RNA was removed from total RNA using the Ribo-Zero rRNA removal kit (illumina). Paired-end RNA-Seq libraries were constructed using either KAPA RNA HyperPrep kit from Kapa Biosystems (Wilmington, MA, USA) or ScriptSeqTM Complete kit (illumina, CA, USA).