Transcriptomes of AH- and VH-grown <i>S. aureus</i> SA564.

a<p> ORFs were identified by BLAST analysis of Affymetrix array target sequences, as described in the materials and methods. If a corresponding ORF was identified in <i>S. aureus</i> COL, that strain's ORF identifiers were used as default. SACOL####, <i>S. aureus</i> COL (GenBank accession number CP000046.1); SAV####, <i>S. aureus</i> Mu50 (BA000017.4); SA####, <i>S. aureus</i> N315 (BA000018.3); SAOUHSC_####, <i>S. aureus</i> NCTC 8325 (CP000253.1). Vertical lines indicate genes computationally predicted to be in the same transcriptional unit. Gene names in brackets were assigned in this study using data shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110872#pone.0110872.s001" target="_blank">Table S1</a>.</p>b<p> Fold change in expression of genes during <i>S. aureus</i> SA564 growth in AH as compared to growth in glucose-supplemented CDM; a positive number indicates an up-regulation of the gene during growth in AH. Standard deviation is shown in parentheses. Fold changes ≥3 and <10 are shown and italicized.</p>c<p> Fold change in expression of genes during <i>S. aureus</i> SA564 growth in VH as compared to growth in glucose-supplemented CDM; a positive number indicates an up-regulation of the gene during growth in VH. Standard deviation is shown in parentheses. Fold changes ≥3 and <10 are shown and italicized.</p>d<p> Fold change in expression of genes during <i>S. aureus</i> SA564 growth in VH as compared to growth in AH; a positive number indicates an up-regulation of the gene during growth in VH. Standard deviation is shown in parentheses. Fold changes ≥3 and <10 are shown and italicized.</p>e<p> At least two differentially expressed probe sets were assigned to these ORFs. Data for all probe sets are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110872#pone.0110872.s001" target="_blank">Table S1</a>.</p>f<p> On genomic island <i>v</i>SA4 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110872#pone.0110872-Gill1" target="_blank">[48]</a>.</p>g<p> On φCOL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110872#pone.0110872-Gill1" target="_blank">[48]</a>.</p>h<p> On φSa1 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110872#pone.0110872-Gill1" target="_blank">[48]</a>.</p>i<p> On φSa3 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110872#pone.0110872-Gill1" target="_blank">[48]</a>.</p><p>Transcriptomes of AH- and VH-grown <i>S. aureus</i> SA564.