Immobilized probe and glass surface chemistry as variables in microarray fabrication
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- 作者：Martin J Hessner (1) (2)
Lisa Meyer (2)
Jennifer Tackes (2)
Sanaa Muheisen (2)
Xujing Wang (1) (2) - 刊名：BMC Genomics
- 出版年：2004
- 出版时间：December 2004
- 年：2004
- 卷：5
- 期：1
- 全文大小：1155KB
- 参考文献：1. Hessner MJ, Wang X, Khan S, Meyer L, Schlicht M, Tackes J, Datta MW, Jacob HJ, Ghosh S: Use of a three-color cDNA microarray platform to measure and control support-bound probe for improved data quality and reproducibility. / Nucleic Acids Res 2003, 31:e60. CrossRef
2. Hessner MJ, Wang X, Hulse K, Meyer L, Wu Y, Nye S, Guo SW, Ghosh S: Three color cDNA microarrays: quantitative assessment through the use of fluorescein-labeled probes. / Nucleic Acids Res 2003, 31:e14. CrossRef
3. Hessner MJ, Singh VK, Wang X, Khan S, Tschannen MR, Zahrt TC: Utilization of a labeled tracking oligonucleotide for visualization and quality control of spotted 70-mer arrays. / BMC Genomics 2004, 5:12. CrossRef
4. Winzeler EA, Schena M, Davis RW: Fluorescence-based expression monitoring using microarrays. / Methods Enzymol 1999, 306:3鈥?8. CrossRef
5. Yue H, Eastman PS, Wang BB, Minor J, Doctolero MH, Nuttall RL, Stack R, Becker JW, Montgomery JR, Vainer M, Johnston R: An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression. / Nucleic Acids Res 2001, 29:E41鈥?1. CrossRef
6. MacMurray AJ, Moralejo DH, Kwitek AE, Rutledge EA, Van Yserloo B, Gohlke P, Speros SJ, Snyder B, Schaefer J, Bieg S, Jiang J, Ettinger RA, Fuller J, Daniels TL, Pettersson A, Orlebeke K, Birren B, Jacob HJ, Lander ES, Lernmark A: Lymphopenia in the BB Rat Model of Type 1 Diabetes is Due to a Mutation in a Novel Immune-Associated Nucleotide (Ian)-Related Gene. / Genome Res 2002, 12:1029鈥?039. CrossRef
7. Wang X, Ghosh S, Guo S-W: Quantitative quality control in microarray image processing and data acquisition. / Nucleic Acids Research 2001, 29:E75鈥?2. CrossRef
8. Wang X, Hessner MJ, Wu Y, Pati N, Ghosh S: Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction. / Bioinformatics 2003, 19:1341鈥?347. CrossRef
9. Diehl F, Grahlmann S, Beier M, Hoheisel J: Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. / Nucleic Acids Research 2001, 29:e38. CrossRef
10. Wang HY, Malek RL, Kwitek AE, Greene AS, Luu TV, Behbahani B, Frank B, Quackenbush J, Lee NH: Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays. / Genome Biol 2003, 4:R5. CrossRef
11. Rees W, Yager T, Korte J, Von Hippel P: Betaine can eliminate the base pair composition dependence of DNA melting. / Biochemistry 1993, 32:137鈥?44. CrossRef
12. Henke W, Herdel K, Jung K, Schnorr D, Loening S: Betaine improves the PCR amplification of GC-rich sequences. / Nucleic Acids Research 1997, 25:3957鈥?958. CrossRef
13. Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS: 'Touchdown' PCR to circumvent spurious priming during gene amplification. / Nucleic Acids Res 1991, 19:4008. CrossRef
14. Hecker KH, Roux KH: High and low annealing temperatures increase both specificity and yield in touchdown and stepdown PCR. / Biotechniques 1996, 20:478鈥?85.
15. Roux KH, Hecker KH: One-step optimization using touchdown and stepdown PCR. / Methods Mol Biol 1997, 67:39鈥?5.
16. Eisen M, Brown P: DNA arrays for analysis of gene expression. / Methods in Enzymology 1999, 303:179鈥?05. CrossRef
17. Wang X, Jiang N, Feng X, Xie Y, Tonellato P, Ghosh S, Hessner MJ: A novel approach for high quality microarray processing using third-dye array visualization technology. / IEEE Transactions on Nanoscience 2003, 2:193鈥?01. CrossRef - 作者单位：Martin J Hessner (1) (2)
Lisa Meyer (2)
Jennifer Tackes (2)
Sanaa Muheisen (2)
Xujing Wang (1) (2)
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, The Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
文摘
Background Global gene expression studies with microarrays can offer biological insights never before possible. However, the technology possesses many sources of technical variability that are an obstacle to obtaining high quality data sets. Since spotted microarrays offer design/content flexibility and potential cost savings over commercial systems, we have developed prehybridization quality control strategies for spotted cDNA and oligonucleotide arrays. These approaches utilize a third fluorescent dye (fluorescein) to monitor key fabrication variables, such as print/spot morphology, DNA retention, and background arising from probe redistributed during blocking. Here, our labeled cDNA array platform is used to study, 1) compression of array data using known input ratios of Arabidopsis in vitro transcripts and arrayed serial dilutions of homologous probes; 2) how curing time of in-house poly-L-lysine coated slides impacts probe retention capacity; and 3) the retention characteristics of 13 commercially available surfaces. Results When array element fluorescein intensity drops below 5,000 RFU/pixel, gene expression measurements become increasingly compressed, thereby validating this value as a prehybridization quality control threshold. We observe that the DNA retention capacity of in-house poly-L-lysine slides decreases rapidly over time (~50% reduction between 3 and 12 weeks post-coating; p < 0.0002) and that there are considerable differences in retention characteristics among commercially available poly-L-lysine and amino silane-coated slides. Conclusions High DNA retention rates are necessary for accurate gene expression measurements. Therefore, an understanding of the characteristics and optimization of protocols to an array surface are prerequisites to fabrication of high quality arrays.