Effects of Atmospheric Ozone on Microarray Data Quality

Fare, Thomas L.; Coffey, Ernest M.; Dai, Hongyue; He, Yudong; Kessler, Deborah A.; Kilian, Kristopher A.; Koch, John E.; LeProust, Eric; Marton, Matthew J.; Meyer, Michael; Stoughton, Roland; Tokiwa, George; Wang, Yanqun

doi:10.1021/ac034241b

Cited by 196 publications

(132 citation statements)

References 4 publications

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“…To overcome these disadvantages, image analysis methods were developed [20,21]. Additionally, Fare et al described deteriorating effects of atmospheric ozone on microarray data quality [22]. The homogeneous signal distribution on APTES/PDC could also be a reason for the higher sensitivity for lower capture DNA concentrations.…”

Section: Discussionmentioning

confidence: 99%

Optimization of Gold Nanoparticle-Based DNA Detection for Microarrays

Festag¹,

Steinbrück²,

Wolff³

et al. 2005

J Fluoresc

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DNA microarrays are promising tools for fast and highly parallel DNA detection by means of fluorescence or gold nanoparticle labeling. However, substrate modification with silanes (as a prerequisite for capture DNA binding) often leads to inhomogeneous surfaces and/or nonspecific binding of the labeled DNA. We examined both different substrate cleaning and activating protocols and also different blocking strategies for optimizing the procedures, especially those for nanoparticle labeling. Contact angle measurements as well as fluorescence microscopy, atomic force microscopy (AFM), and a flatbed scanner were used to analyze the multiple-step process. Although the examined different cleaning and activating protocols resulted in considerably different contact angles, meaning different substrate wettability, silanization led to similar hydrophobic surfaces which could be revealed as smooth surfaces of about 2-4 nm roughness. The two examined silanes (3-glycidoxypropyltrimethoxysilane (GOPS) and 3-aminopropyltriethoxysilane (APTES)) differed in their DNA binding homogeneity, maximum signal intensities, and sensitivity. Nonspecific gold binding on APTES/PDC surfaces could be blocked by treatment in 3% bovine serum albumin (BSA).

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Section: Discussionmentioning

confidence: 99%

Optimization of Gold Nanoparticle-Based DNA Detection for Microarrays

Festag¹,

Steinbrück²,

Wolff³

et al. 2005

J Fluoresc

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“…Values <1 and >2 are considered poor. It has also been demonstrated that environmental ozone levels affect Cy5 signal intensities, thus reducing data quality [Fare et al, 2003]. To overcome this issue, a novel dye "Hyper5" was developed, which is more ozone stable and photo stable than Cy5 [Dar et al, 2008].…”

Section: Signal Intensity Ratiomentioning

confidence: 99%

Genome-wide arrays: Quality criteria and platforms to be used in routine diagnostics

et al. 2012

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Whole-genome analysis using genome-wide arrays, also called "genomic arrays," "microarrays," or "arrays," has become the first-tier diagnostic test for patients with developmental abnormalities and/or intellectual disabilities. In addition to constitutional anomalies, genomic arrays are also used to diagnose acquired disorders. Despite the rapid implementation of these technologies in diagnostic laboratories, external quality control schemes (such as CEQA, EMQN, UK NEQAS, and the USA QA scheme CAP) and interlaboratory comparisons show that there are huge differences in quality, interpretation, and reporting among laboratories. We offer guidance to laboratories to help assure the quality of array experiments and to standardize minimum detection resolution, and we also provide guidelines to standardize interpretation and reporting.

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“…On occasion, there was considerable variability between microarray experiments done at different locations, or done at the same location on different days of the year. Careful analysis of the environmental factors found that the dyes used in microarray analysis are differentially sensitive to ozone, with Cy5/Alexa647 affected by 5-10 parts per billion ozone, whereas Cy3/Alexa555 are not affected until ozone levels reach >100 parts per billion [58]. Introduction of air purifiers to reduce ozone levels has improved the consistency of microarray data.…”

Section: Discussionmentioning

confidence: 99%

Limitations of Mass Spectrometry-Based Peptidomic Approaches

Fricker

2015

J. Am. Soc. Mass Spectrom.

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Abstract. Mass spectrometry-based peptidomic approaches are powerful techniques to detect and identify the peptide content of biological samples. The present study investigated the limitations of peptidomic approaches using trimethylammonium butyrate isotopic tags to quantify relative peptide levels and Mascot searches to identify peptides. Data were combined from previous studies on human cell lines or mouse tissues. The combined databases contain 2155 unique peptides ranging in mass from 444 to 8765 Da, with the vast majority between 1 and 3 kDa. The amino acid composition of the identified peptides generally reflected the frequency in the Eukaryotic proteome with the exception of Cys, which was not present in any of the identified peptides in the free-SH form but was detected at low frequency as a disulfide with Cys residues, a disulfide with glutathione, or as S-cyanocysteine. To test if the low detection rate of peptides smaller than 500 Da, larger than 3 kDa, or containing Cys was a limitation of the peptidomics procedure, tryptic peptides of known proteins were processed for peptidomics using the same approach used for human cell lines and mouse tissues. The identified tryptic peptides ranged from 516 to 2418 Da, whereas the theoretical digest ranged from 217 to 7559 Da. Peptides with Cys were rarely detected and, if present, the Cys was usually modified S-cyanocysteine. Additionally, peptides with mono-and di-iodo Tyr and His were identified. Taken together, there are limitations of peptidomic techniques, and awareness of these limitations is important to properly use and interpret results.

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Effects of Atmospheric Ozone on Microarray Data Quality

Cited by 196 publications

References 4 publications

Optimization of Gold Nanoparticle-Based DNA Detection for Microarrays

Optimization of Gold Nanoparticle-Based DNA Detection for Microarrays

Genome-wide arrays: Quality criteria and platforms to be used in routine diagnostics

Limitations of Mass Spectrometry-Based Peptidomic Approaches

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