GSE130301
Identification of genes regulated by the antitermination factor NasT during denitrification in Bradyrhizobium diazoefficiens.
Purpose: Identification of genes regulated by NasT during denitrifying growth in B. diazoefficiens.  Methods: Two biological replications were processed for each strain (wild-type USDA 110 and ?nasT mutant). Sequencing was performed in an Illumina HiSeq 2000 Sequencing System in paired-end mode running 100x2 cycles (performed by Hokkaido System Science Co., Ltd.). Mapping of reads to the reference genome, read counting, normalization to RPKM (reads per kilobase per million mapped reads), and calculations of expression values were performed with default values with the CLC Genomic Workbench software 9.5.3. From the total reads that were generated, ~85% were trimmed, and from those, ~42% could be mapped onto the B. diazoefficiens genome. Genes with fewer than 10 reads per 1 million mRNA reads were omitted from the following analysis. A gene with a fold change =2 or =?2 and a q value (estimate of false discovery rate) =0.05 was considered up- or down- regulated, respectively. The results were validated by qRT–PCR. Conclusion: A total of 77 genes were differentially expressed in the ?nasT mutant compared to those of the wild-type strain, with 38 genes decreased and 37 genes increased in the ?nasT mutant. Most of these genes were related to nitrogen metabolism. Overall design: RNA-seq transcription profiling of two replicates of B. diazoefficiens wild type and ?nasT mutant grown anaerobically in the presence of nitrate at 10 mM.