RNA seq of Bradyrhizobium diazoefficiens USDA 110 spc4 WT-Cumate
Three individual colonies of WT and Pcu-shc grown with and without 25 M cumate were cultured to early exponential phase and total RNAs were extracted by Qiagen RNeasy Mini Kit . RNA quantification was achieved using a Nanodrop one (Thermo Scientific) and RNA quality was monitored with an Agilent 2100 Bioanalyzer using an RNA 6000 Pico Kit (Agilent Technologies). Ribosomal RNA (rRNA) was depleted and cDNA libraries were prepared from 100 ng total RNA by Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Illumina). The quantity and quality of the prepared library were analyzed by the Qubit dsDNA BR Assay Kit and the Agilent 2100 Bioanalyzer using a DNA 1000 Kit, respectively. A library of samples (2 ng/sample) under each condition (30Mb read/each sample) was loaded on the Illumina Nextseq 500 system with a NextSeq 500/550 High Output Reagent CartriDEG v2 (Illumina) for single-end reads at Carnegie Embryology Departments in-house sequencing facility. Two independently biological replicates were performed.