LBAK13
Total RNA was obtained from mid-exponentially grown AK13 strain cells (6 hr) from pH 7 and pH 10 Luria-Bertani medium using a RNeasy kit (Qiagen, Hilden, Germany) following the manufacturers instructions. The extracted total RNA was then sent to Chunlab (Seoul, South Korea) for RNA sequencing and alignment. RiboZero rRNA removal kit (Epicentre, Medison, WI, USA) was used for ribosomal RNA depletion according to the manufacturers instructions. Libraries for Illumina sequencing were made with the Universal library (Tecan, USA) following the manufacturers protocol. RNA performed on the Illumina HiSeq 2500 platform using paired-end 100bp sequencing. Sequence data for the reference genome (Bacillus miscanthi AK13) were retrieved from the NCBI database. Quality-filtered reads were aligned to the reference genome sequence using Bowtie2. The abundance of relative transcript was shown by reads per kilobase of the exon sequence per million mapped sequence reads (RPKM) defined as total exon reads / (mapped reads in millions exon length in kilobases). Metabolic pathways were analyzed based on KEGG pathway analysis and BLAST alignment with proteins using CLRNASeq program provided by Chunlab.