Comparative transcriptomic experiment of Amycolatopsis japonica in order to investigate EDDS production changes

Here we report the effect of two comparative transcriptomics experiments effect on EDDS producing biosynthetic gene cluster. The goals of this study are to compare RNA sequencing derived transcriptomes of Amycolatopsis japonica at 24 hours in zinc treated and control culture conditions in combination with control and zur regulator deleted strains, in order to target other genes for the overexpression of EDDS cluster. Overall design: RNA-Sequencing has been conducted at 24th hour of Amycolatopsis Japonica using Illumina NextSeq 500 System. In the first experiment two conditions were: zinc treated cultures wild type versus zur knockout strain. In the second experiment two conditions were: zur knockout strains vs control strains in normal culture conditions. Both experiments are conducted in triplicates. Corresponding fastq files trimmed by fastp, mapped by Hisat2 and the BAM files were generated via samtools. Read count per gene is summarized by featureCounts and differentially expressed genes were generated by DESeq2 package.