title: Klebsiella pneumoniae SGSB107 Transcriptome or Gene expression
design: "Transcriptome analysis was performed for the 15 h point in batch culture, respectively. Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA). The samples were enriched for mRNA using the Ribo-Zero rRNA removal kit for gram-negative bacteria (Epicentre, Madison, WI), following the manufacturer’s protocol. RNA concentration was determined with the NanoDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. But we excluded the step of purification using oligo-dT attached magnetic beads.  Libraries were sequenced on an Illumina HiSeq2000 sequencer. RNA-seq reads were mapped to the K. pneumoniae KCTC2242 genome (NCBI NC_017540) using Bowtie2 to report the paired-end reads, unique alignments. Gene expression was measured as RPKM (sum of nucleotides in gene per million mapped nucleotides per gene kb) using in-house script, excluding CDS region from RPKM calculations. Data with zeroed RPKM values more than one for total samples were excluded."
identifiers.namespace: Sogang University
identifiers.id: Klebsiella pneumoniae SGSB107