RNA-Seq of MRSA USA300
Total RNA was extracted using TRIzol, followed by DNase I treatment. RNA quality was assessed by NanoPhotometer and Agilent 2100 Bioanalyzer, with all samples showing A260/A280 ratios of 1.8-2.0 and RIN > 8.0. Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs, UAS) and sequenced on an Illumina NovaSeq 6000 platform (Novogene, China) to generate 150 bp paired-end reads (~20 million reads/sample). Raw data were processed using FastQC, Trimmomatic, and HISAT2 for quality control and alignment.