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Bacterial Whole Genome Array Analysis

Figure 1. Agilent Bioanalyzer Image of E. coli mRNA Purified Using MICROBExpress. 16S and 23S rRNAs were selectively removed from five different 10 g samples of E. coli total RNA and the remaining enriched mRNA fraction (~70 ng each) were run in Lanes 2-6. A sixth 10 g sample of the same total RNA prep was subjected to a mock MICROBExpress procedure without using the kit's rRNA capture oligo mix. Approximately 0.7 g micrograms of the mock reaction was loaded in Lane 7. As seen in the gel image the rRNA bands are virtually undetectable in the mRNA obtained with the MICROBExpress procedure versus the control lane.

Figure 2. Agilent Bioanalyzer Electropherograms of mRNA from Figure 1. As seen in the (top) electropherogram, greater than 95% of the bacterial 16S and 23S rRNA bands have been removed, leading to a selective enrichment of mRNA species as compared to the (bottom) mock MICROBExpress procedure. (Relative fluorescence units have been rescaled between the two electropherograms to allow a closer examination of the MICROBExpress enriched RNA).

Figure 3. Affymetrix GeneChip E. coli Antisense Genome Array Analysis. Illustrated above are Log Plots (Signal vs. Signal) for technical replicate GeneChips (i.e. same RNA, different probe labeling used for replicates). Panel A compares replicate arrays using 10 g RiboPure-Bacteria isolated E. coli total RNA with the standard Affymetrix labeling and hybridization protocol. Panel B compares replicate arrays utilizing the mRNA (0.69 g) obtained with the MICROBExpress Kit from 10 g of RiboPure-Bacteria
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