Nucleic Acids Research, 2003, Vol. 31, No. 11 e60
© 2003 Oxford University Press
Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility
1 The Max McGee National Research Center for Juvenile Diabetes, Department of Pediatrics, The Medical College of Wisconsin and Children’s Hospital of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, 2 The Human and Molecular Genetics Center, 3 The Department of Pathology and 4 The Department of Physiology, The Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
*To whom correspondence should be addressed at The Max McGee National Research Center for Juvenile Diabetes, Department of Pediatrics, The Medical College of Wisconsin and Children’s Hospital of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA. Tel: +1 414 456 4496; Fax: +1 414 456 6663; Email: mhessner{at}mcw.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Construction methodologies for cDNA microarrays lack the ability to determine array integrity prior to hybridization, leaving the array itself a source of uncontrolled experimental variation. We solved this problem through development of a three-color cDNA array platform whereby printed probes are tagged with fluorescein and are compatible with Cy3 and Cy5 target labeling dyes when using confocal laser scanners possessing narrow bandwidths. Here we use this approach to: (i) develop a tracking system to monitor the printing of probe plates at predicted coordinates; (ii) define the quantity of immobilized probe necessary for quality hybridized array data to establish pre-hybridization array selection criteria; (iii) investigate factors that influence probe availability for hybridization; and (iv) explore the feasibility of hybridized data filtering using element fluorescein intensity. A direct and significant relationship (R2 = 0.73, P < 0.001) between pre-hybridization average fluorescein intensity and subsequent hybridized replicate consistency was observed, illustrating that data quality can be improved by selecting arrays that meet defined pre-hybridization criteria. Furthermore, we demonstrate that our three-color approach provides a means to filter spots possessing insufficient bound probe from hybridized data sets to further improve data quality. Collectively, this strategy will improve microarray data and increase its utility as a sensitive screening tool.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. Mori, A. Polichnowski, P. Glocka, M. Kaldunski, Y. Ohsaki, M. Liang, and A. W. Cowley Jr. High Perfusion Pressure Accelerates Renal Injury in Salt-Sensitive Hypertension J. Am. Soc. Nephrol., August 1, 2008; 19(8): 1472 - 1482. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. J. Hessner, B. Xiang, S. Jia, R. Geoffrey, S. Holmes, L. Meyer, S. Muheisen, and X. Wang Three-color cDNA microarrays with prehybridization quality control yield gene expression data comparable to that of commercial platforms Physiol Genomics, March 13, 2006; 25(1): 166 - 178. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. E. Knoll, J. L. Pietrusz, and M. Liang Tissue-specific transcriptome responses in rats with early streptozotocin-induced diabetes Physiol Genomics, April 14, 2005; 21(2): 222 - 229. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Morrison, K. Knoll, M. J. Hessner, and M. Liang Effect of high glucose on gene expression in mesangial cells: upregulation of the thiol pathway is an adaptational response Physiol Genomics, May 19, 2004; 17(3): 271 - 282. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. L. Gunderson, S. Kruglyak, M. S. Graige, F. Garcia, B. G. Kermani, C. Zhao, D. Che, T. Dickinson, E. Wickham, J. Bierle, et al. Decoding Randomly Ordered DNA Arrays Genome Res., May 1, 2004; 14(5): 870 - 877. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. A. C. 't Hoen, R. Turk, J. M. Boer, E. Sterrenburg, R. X. de Menezes, G.-J. B. van Ommen, and J. T. den Dunnen Intensity-based analysis of two-colour microarrays enables efficient and flexible hybridization designs Nucleic Acids Res., February 24, 2004; 32(4): e41 - e41. [Abstract] [Full Text] [PDF]
|
|