RNA-seq of Staphylococcus aureus: WT and  ko-rsp-3
Total RNA was extracted from the tissue using TRIzol Reagent according the manufacturers instructions (Invitrogen) and genomic DNA was removed using DNase I (D2215, TaKaRa). RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (RS-122-2001, Illumina) using 2 g of total RNA. The ribosomal RNA (rRNA) depletion instead of poly (A) purification is performed by Ribo-Zero Magnetic kit (MRZB12424, Epicenter).The data generated from Illumina platform were used for bioinformatics analysis. All of the analyses were performed using the free online platform of Majorbio Cloud Platform (www.majorbio.com) from Shanghai Majorbio Bio-pharm Technology Co.,Ltd. High-quality reads in each sample were mapped to the reference genome by Bowtie2 (NarG60, http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ). Quantify gene and isoform abundances from single-end or paired-end RNA-Seq data using RSEMhttp://deweylab.github.io/RSEM/.  Identify differentially expressed genes using edgeR (http://www.bioconductor.org/packages/2.12/bioc/html/edgeR.html), DESeq2(http://bioconductor.org/packages/release/bioc/html/DESeq4.html), or the DESeq (http://www.bioconductor.org/packages/release/bioc/html/DESeq.html)  package.