title: RNA-seq of Lysinibacillus boronitolerans YS11: calcium carbonate precipitating bacteria
design: Total RNA was obtained from mid-exponentially grown YS11 cells (6 hr) from NaAc and CaAc media 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 constructed with TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA, USA) following the manufacturers protocol. RNA sequencing was conducted on Illumina HiSeq 2500 platform using singleend 50 bp sequencing. Sequence data for the reference genome (Lysinibacillus boronitolerans YS11) were retrieved from the NCBI database. Quality-filtered reads were aligned to the referencegenome 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.