Construction and validation of a first-generation Bordetella bronchiseptica long-oligonucleotide microarray by transcriptional profiling the Bvg regulon

Additional file 1:

Table S1. Missing array elements due to gene duplications, prophage duplications, and ORF assignments missing from the completed genome annotation. In the Gene Duplication category, the ORF number representing the array element for both genes is given. Table S2. Oligonucleotide sequence for each ORF/represented array element. Table S3. Fold-Change expression values from a direct comparison between the transcriptional profile of B. bronchiseptica RB50 and RB54. DNA microarray analysis was used to measure mRNA levels present in B. bronchiseptica RB50 compared to mRNA levels present in B. bronchiseptica RB54. Differences in mRNA levels are listed as mean fold-changes + standard error. Fold-changes were calculated by averaging the data from three biological sample sets. The fluorescent labels were exchanged in dye-swap experiments performed on all three biological replicates. ORF, Name, Product, Function, and General Category headings were parsed from both Sanger annotation files [17] and Cummings et al. [14]. Data presented in the SAM, Score(d), q-value, and localdr(%) columns were assessed by using the significant analysis of microarrays (SAM) program [31]. A one-class unpaired SAM analysis using a false discovery rate of 0.063% (<0.1%) was preformed. Table S4. Quantitative real-time PCR primers.

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