Metadata for Integrative RNA-Seq and Co-expression Analyses Uncover Confident sRNA Networks in Staphylococcus aureus Strains of the Brazilian ST239 and USA Lineages

Supplementary Tables S1–S5. Categorization of sRNA genomic localization across strains. Each table presents the classification of sRNAs according to their genomic annotation (antisense, intragenic, intergenic, 5′ UTR, and 3′ UTR). One table is provided per strain, except for USA500, whose annotation was propagated from USA300, according to the original study (Tomlinson, Malof and Shaw, 2021). Supplementary Tables S6–S11. Differential gene expression (DEG) between biofilm and planktonic conditions. Tables list log2 fold changes (log2FC) for each strain, with positive values indicating higher expression in biofilm relative to planktonic growth. Supplementary Table S12. Cross-lineage module assignment of genes from co-expression analysis. For each row, the table lists the locus IDs for Bmb9393 (ST239), N315 (USA100), MRSA252 (USA200), LAC (USA300/USA500), and MW2 (USA400); the final column reports the WGCNA module (color name) assigned to that locus. Entries include both CDSs and sRNAs; blank cells indicate that no ortholog was identified in the corresponding strain. Supplementary Table S13. Hub genes identified within co-expression modules. For each strain, hub genes are listed along with their unique IDs, module membership, correlations of modules with biofilm/planktonic states, and, when available, gene product, protein ID, GO ID, and associated GO terms. Supplementary Table S14. Gene Ontology (GO) enrichment of co-expression modules. GO terms associated with individual modules, highlighting biological functions enriched among the genes within each module. Supplementary Table S15. High-confidence mRNA–sRNA interaction pairs. List of candidate regulatory pairs retained after all filtering steps (see Methods). Because of these filters—including cross-tool thresholds, WGCNA co-assignment, and cross-strain expression-consistency—not all antisense (cis) sRNA–CDS pairs were retained; antisense pairs that failed any criterion were excluded and therefore do not appear here.