title: Transcriptome K. stuttgartiensis mbr1: ammonium limiting conditions
design: Kuenenia stuttgartiensis uses nitrite and ammonium for its central energy metabolism. Bioreactor with mixed culture (95% K. stuttgartiensis mbr1) ran with ammonium (NH4) as the limiting factor. RNA extracted using TRIzol Reagent and the RiboPure bacteria kit and treated with DNAse. RNA and cDNA were quantified using the Qubit RNA HS Assay Kit and dsDNA HS Assay Kit. The quality of the RNA and cDNA was determined using the Agilent 2100 Bioanalyser with the Agilent RNA 6000 Nano Kit and the high sensitivity DNA kit. cDNA libraries were made using TruSeq stranded mRNA Library Prep Kit v2. Transcriptome sequencing, using the 150 bp sequence chemistry and the Miseq Reagent Kit v3, was performed with the Illumina MiSeq sequencer. CLC Genomics Workbench 11.0.1 (Qiagen bioinformatics, Denmark) was used to trim reads using the following settings: quality limit was set to 0.01, with a maximum of 2 ambiguous nucleotides, no adapter trimming, and removal of 10 nucleotides at the 5 and 5 nucleotides at the 3 end. Reads smaller than 50 bp were discarded. Non-mRNA sequences were removed by mapping the reads to all non-coding RNAs obtained from the K. stuttgartiensis MBR1 genome  (GCA_900232105.1).