title: RNA-seq of treated MRSA3
design: RNA sequencing libraries for both groups, comprising three biological replicates per group, were subsequently constructed on the Illumina HiSeq 2500 platform (Novogene, China). To ensure high-quality data, raw sequencing reads were processed by removing adaptor sequences, reads containing more than 10% unknown bases (N), and reads with over 50% low-quality bases (Q-value  10). For gene expression analysis, unigene expression levels were quantified using the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) metric. Differentially expressed genes (DEGs) between the samples were identified using DESeq2 software, with significant DEGs defined by an absolute fold change of  2 and an adjusted p-value of < 0.05. Functional categorization of these DEGs was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses.