Steve Byerly, Kyle Sundin, Rajiv Raja, Jim Stanchfield, Bassem A

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Presentation transcript:

Effects of Ozone Exposure during Microarray Posthybridization Washes and Scanning Steve Byerly, Kyle Sundin, Rajiv Raja, Jim Stanchfield, Bassem A. Bejjani, Lisa G. Shaffer The Journal of Molecular Diagnostics Volume 11, Issue 6, Pages 590-597 (November 2009) DOI: 10.2353/jmoldx.2009.090009 Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Array images from each wash/scan condition for the Alexa Fluor 3 and 5 dye set, block intensity charts that compare the average ratio of the red and green intensities of all features for a given block, and a plot of the genomic profile for the dye-swap experiment with an opposite gender pairing. For the plot, clones are arranged along the x axis according to physical mapping position, with the most distal p-arm probes to the left and the most distal q-arm probes to the right. A: Results for low-ozone wash/low-ozone scan. B: Results for low-ozone wash/high-ozone scan. C: Results for high-ozone wash/low-ozone scan. D: Results for high-ozone wash/high-ozone scan. The Journal of Molecular Diagnostics 2009 11, 590-597DOI: (10.2353/jmoldx.2009.090009) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Average signal/noise ratios for red and green channels for replicates of each experimental condition. Blue bars represent the low-ozone wash/low-ozone scan, magenta bars represent the low-ozone wash/high-ozone scan, yellow bars represent the high-ozone wash/low-ozone scan, and green bars represent high-ozone wash/high-ozone scan. The Journal of Molecular Diagnostics 2009 11, 590-597DOI: (10.2353/jmoldx.2009.090009) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 SDs for microarray experiments comparing the effect of prolonged ozone exposure after the posthybridization washes on different fluorescent dyes. The Journal of Molecular Diagnostics 2009 11, 590-597DOI: (10.2353/jmoldx.2009.090009) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Total intensity of the red channel over the green channel for the Alexa Fluor 3 and 5 dye set at 0 minutes (A–C) and 200 minutes (D–F) of exposure. A and D: Microarray images for two dye-swap experiments. Probes are arranged as in Figure 1. B and E: Block intensity charts comparing the average intensity of all features for a given block of the ratio of the red and green channels. C and F: Plot of microarray results for experiment. Probes are arranged as in Figure 1. The Journal of Molecular Diagnostics 2009 11, 590-597DOI: (10.2353/jmoldx.2009.090009) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 5 Total intensity of the red channel over the green channel for the Alexa Fluor 555 and 647 dye set at 0 minutes (A–C) and 200 minutes (D–F) of exposure. A and D: Microarray images for two dye-swap experiments. Probes are arranged as in Figure 1. B and E: Block intensity charts comparing the average intensity of all features for a given block of the ratio of the red and green channels. C and F: Plot of microarray results for experiment. Probes are arranged as in Figure 1. The Journal of Molecular Diagnostics 2009 11, 590-597DOI: (10.2353/jmoldx.2009.090009) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 6 Total intensity of the red channel over the green channel for the Cy3 and Cy5 dye set at 0 minutes (A–C) and 200 minutes (D–F) of exposure. A and D: Microarray images for two dye-swap experiments. Probes are arranged as in Figure 1. B and E: Block intensity charts comparing the average intensity of all features for a given block of the ratio of the red and green channels. C and F: Plot of microarray results for experiment. Probes are arranged as in Figure 1. The Journal of Molecular Diagnostics 2009 11, 590-597DOI: (10.2353/jmoldx.2009.090009) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions