RNA-seq Analysis of LacA Transcriptome

RNA samples were sequenced at Vertis Biotechnologie, where cDNA libraries were made for Illumina sequencing. Single-end 75 bp sequencing was performed using an Illumina NextSeq 500, with approximately 10 million reads obtained per library. The fastq files were run through Trimmomatic to remove adaptors and low-quality reads [38 (link)]. fastqc (Babraham Bioinformatics; http://www.bioinformatics.bbsrc.ac.uk/pro- jects/fastqc/) was run to evaluate the quality of the RNA-seq. Bowtie2 [43 (link)] with default parameters was used to align raw sequence reads to the LacA genome. The alignment was converted to BAM format using SAMtools [44 (link)]. DEseq2 [45 (link)], run in the R environment [40 ], was used to identify differentially expressed genes using a Wald test, followed by a Benjamini and Hochberg procedure. All sets were defined by a false discovery rate of 10 %. Visualization of sequencing reads and calculations of reads per kilobase million (RPKM) were performed in Artemis [46 (link)].