Adequate design of customized cDNA macroarray for convenient multiple gene expression analysis

Journal of Bioscience and Bioengineering

Volumn 103, Issue 1, 2007, Pages 74-81

  Sugiyama, Shunpei ^a   Yamamoto, Kimiko ^b   Nishimura, Norihiro ^c   Nakagawa, Miki ^a   Maruta, Yukio ^a   Ando, Joji ^b  

^a GeneticLab Co Ltd   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c MIE UNIVERSITY   (Japan)

Author keywords

cDNA macroarray; human coronary artery endothelial cells; real time polymerase chain reaction; shear stress

Indexed keywords

BIOLOGICAL MEMBRANES; ENZYMES; GENES; GENETIC ENGINEERING; REAL TIME SYSTEMS; RNA; SHEAR STRESS;

CDNA MACROARRAY; HUMAN CORONARY ARTERY ENDOTHELIAL CELLS; OLIGONUCLEOTIDE PROBES; REAL TIME POLYMERASE CHAIN REACTION;

DNA;

COMPLEMENTARY DNA; MESSENGER RNA;

ACCURACY; ARTERY ENDOTHELIUM; ARTICLE; CELL MEMBRANE; COMPARATIVE STUDY; CONTROLLED STUDY; CORONARY ARTERY; DNA MICROARRAY; GENE EXPRESSION; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYSIS; HUMAN; HUMAN CELL; IMMOBILIZED CELL; MEASUREMENT; MONITORING; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; REAL TIME POLYMERASE CHAIN REACTION; SHEAR STRESS; VASCULAR ENDOTHELIUM;

CELLS, CULTURED; ENDOTHELIAL CELLS; EQUIPMENT DESIGN; EQUIPMENT FAILURE ANALYSIS; GENE EXPRESSION PROFILING; HUMANS; MECHANOTRANSDUCTION, CELLULAR; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; PROTEOME;

EID: 33846827086     PISSN: 13891723     EISSN: None     Source Type: Journal    
DOI: 10.1263/jbb.103.74     Document Type: Article

References (57)

1. MacDonald M.J., and Rosbash M. Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107 (2001) 567-578
2. Ohki R., Yamamoto K., Mano H., Lee R.T., Ikeda U., and Shimada K. Identification of mechanically induced genes in human monocytic cells by DNA microarrays. J. Hypertens. 20 (2002) 685-691
3. Yoshimoto H., Saltsman K., Gasch A.P., Li H.X., Ogawa N., Botstein D., Brown P.O., and Cyert M.S. Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J. Biol. Chem. 277 (2002) 31079-31088
4. Middleton F.A., Mirnics K., Pierri J.N., Lewis D.A., and Levitt P. Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia. J. Neurosci. 22 (2002) 2718-2729
5. Lockhart D.J., and Winzeler E.A. Genomics, gene, expression and DNA arrays. Nature 405 (2000) 827-836
6. Duggan D.J., Bittner M., Chen Y., Meltzer P., and Trent J.M. Expression profiling using cDNA microarrays. Nat. Genet. 21 (1999) 10-14
7. Velculescu V.E., Zhang L., Vogelstein B., and Kinzler K.W. Serial analysis of gene expression. Science 270 (1995) 484-487
8. Donaldson L., Vuocolo T., Gray C., Strandberg Y., Reverter A., McWilliam S., Wang Y., Byrne K., and Tellam R. Construction and validation of a bovine innate immune microarray. BMC Genomics 6 (2005) 135
9. Livak K.J., and Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-delta delta C(T)). Methods 25 (2001) 402-408
10. Schena M., Shaon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
11. Relogio A., Schwager C., Richter A., Ansorge W., and Valcarcel J. Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res. 30 (2002) e51
12. Saiki R.K., Walsh P.S., Levenson C.H., and Erlich H.A. Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc. Natl. Acad. Sci. USA 86 (1989) 6230-6234
13. Martin C., Roberts D., van Der Weide M., Rossau R., Jannes G., Smith T., and Maher M. Development of a PCR-based line probe assay for identification of fungal pathogens. J. Clin. Microbiol. 38 (2000) 3735-3742
14. Kasai S., and Tomita T. Male specific expression of a cytochrome P450 (Cyp312a1) in Drosophila melanogaster. Biochem. Biophys. Res. Commun. 300 (2002) 894-900
15. Okuno K., Yasutomi M., Nishimura N., Arakawa T., Shiomi M., Hida J., Ueda K., and Minami K. Gene expression analysis in colorectal cancer using practical DNA array filter. Dis. Colon Rectum 44 (2001) 295-299
16. Gemma A., Takenaka K., Hosoya Y., Matuda K., Seike M., Kurimoto F., Ono Y., Uematsu K., Takeda Y., Hibino S., Yoshimura A., Shibuya M., and Kudoh S. Altered expression of several genes in highly metastatic subpopulations of a human pulmonary adenocarcinoma cell line. Eur. J. Cancer 37 (2001) 1554-1561
17. Hughes T.R., Mao M., Jones A.R., Burchard J., Marton M.J., Shannon K.W., Lefkowitz S.M., Ziman M., Schelter J.M., Meyer M.R., and other 14 authors. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19 (2001) 342-347
18. Cheng-Chung C., Chun-Houh C., Te-Tsui L., and Konan P. Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res. 32 (2004) e99
19. Xu W., Bak S., Dcker A., Paquette S.M., Feyereisen R., and Galbraith D.W. Microarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana. Gene 272 (2001) 61-74
20. Evertsz E.M., Au-Young J., Ruvolo M.V., Lim A.C., and Reynolds M.A. Hybridization cross-reactivity within homologous gene families on glass cDNA microarrays. Biotechniques 31 (2001) 1182 1184, 1186
21. Kane M.D., Jatkoe T.A., Stumpf C.R., Lu J., Thomas J.D., and Madore S.J. Assessment of the sensitivity and specificity of oligonucleotide (50 mer) microarrays. Nucleic Acids Res. 28 (2000) 4552-4557
22. Tijssen P. Hybridization with nucleic acid probes, part 1: theory and nucleic acid preparation (1993), Elsevier Science Publisher, NY
23. Lockhart L.J., Dong H., Byrne M.C., Follettie M.T., Gallo M.V., Chee M.S., Mittmann M., Wang C., Kobayashi M., Horton H., and Brown E.L. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14 (1996) 1675-1680
24. Selinger D.W., Cheung K.J., Mei R., Johansson E.M., Richmond C.S., Blattner F.R., Lockhart D.J., and Church G.M. RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 18 (2000) 1262-1268
25. Kosaki K., Ando J., Korenaga R., Kurokawa T., and Kamiya A. Fluid shear stress increases the production of granulocyte-macrophage colony stimulating factor by endothelial cells via mRNA stabilization. Circ. Res. 82 (1998) 794-802
26. Pfaffl M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29 (2001) 2002-2007
27. Shieh J., To C., Carramao J., Nishimura N., Maruta Y., Hashimoto Y., Wright D., Wu H.C., and Azarani A. High-throughput array production using precision glass syringes. Biotechniques 32 (2002) 1360-1365
28. Freeman W.M., Walker S.J., and Vrane K.E. Quantitative RT-PCR: pitfalls and potential. Biotechniques 26 (1999) 112-122 124-125
29. Walker N.J. Real-time and quantitative PCR: applications to mechanism-based toxicology. J. Biochem. Mol. Toxicol. 15 (2001) 121-127
30. Draghici S., Khatri P., Eklund A.C., and Szallasi Z. Reliability and reproducibility issues in DNA microarray measurements. Trends Genet. 22 (2005) 101-109
31. Bammler T., Beyer R.P., Bhattacharya S., Boorman G.A., Boyles A., Bradford B.U., Bumgarner R.E., Bushel P.R., Chaturvedi K., Choi D., and other 54 authors. Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods 2 (2005) 351-356
32. Jenssen T.K., Langaas M., Kuo W.P., Smith-Sorensen B., Myklebost O., and Hovig E. Analysis of repeatability in spotted cDNA microarrays. Nucleic Acids Res. 30 (2002) 3235-3244
33. Tan P.K., Downey T.J., Spitznagel Jr. E.L., Xu P., Fu D., Dimitrov D.S., Lempicki R.A., Raaka B.M., and Cam M.C. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31 (2003) 5676-5684
34. Kuo W.P., Jenssen T.K., Butte A.J., Ohno-Machado L., and Kohane I.S. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18 (2002) 405-412
35. Irizarry R.A., Warren D., Spencer F., Kim I.F., Biswal S., Frank B.C., Gabrielson E., Garcia J.G., Geoghegan J., Germino G., and other 15 authors. Multiple-laboratory comparison of microarray platforms. Nat. Methods 2 (2005) 345-350
36. Chen X.L., Varner S.E., Rao A.S., Grey J.Y., Thomas S., Cook C.K., Wasserman M.A., Medford R.M., Jaiswal A.K., and Kunsch C. Laminar flow induction of antioxidant response element-mediated genes in endothelial cells. J. Biol. Chem. 278 (2003) 703-711
37. De Keulenaer G.W., Chappell D.C., Ishizaka N., Nerem R.M., Alexander R.W., and Griendling K.K. Oscillatory and steady laminar shear stress differentially affect human endothelial redox state: role of a superoxide-producing NADH oxidase. Circ. Res. 82 (1998) 1094-1101
38. Tsuboi H., Ando J., Korenaga R., Takada Y., and Kamiya A. Flow stimulates ICAM-1 expression time and shear stress dependently in cultured human endothelial cells. Biochem. Biophys. Res. Commun. 206 (1995) 988-996
39. Nagel T., Resnick N., Atkinson W.J., Dewey Jr. C.F., and Gimbrone Jr. M.A. Shear stress selectively upregulates intercellular adhesion molecule-1 expression in cultured human vascular endothelial cells. J. Clin. Invest. 94 (1994) 885-891
40. Sampath R., Kukielka G.L., Smith C.W., Eskin S.G., and McIntire L.V. Shear stress-mediated changes in the expression of leukocyte adhesion receptors on human umbilical vein endothelial cells in vitro. Ann. Biomed. Eng. 23 (1995) 247-256
41. Lin M.C., Almus-Jacobs F., Chen H.H., Parry G.C.N., Mackman N., and Shyy J.Y.J. Shear stress induction of the tissue factor gene. J. Clin. Invest. 99 (1997) 737-744
42. Akimoto S., Mitsumata M., Sasaguri T., and Yoshida Y. Shear stress markedly elevated the mRNA level of p21, and this elevation in mRNA faded after the release of cells from shear stress, concomitant with a recovery of DNA synthesis. Circ. Res. 86 (2000) 185-190
43. Korenaga R., Yamamoto K., Ohura N., Sokabe T., Kamiya A., and Ando J. Sp1-mediated downregulation of P2X4 receptor gene transcription in endothelial cells exposed to shear stress. Am. J. Physiol. Heart Circ. Physiol. 280 (2001) H2214-H2221
44. Inoue H., Taba Y., Miwa Y., Yokota C., Miyagi M., and Sasaguri T. Transcriptional and posttranscriptional regulation of cyclooxygenase-2 expression by fluid shear stress in vascular endothelial cells. Arterioscler. Thromb. Vasc. Biol. 22 (2002) 1415-1420
45. Chun T.H., Itoh H., Ogawa Y., Tamura N., Takaya K., Igaki T., Yamashita J., Doi K., Inoue M., Masatsugu K., Korenaga R., Ando J., and Nakao K. Shear stress augments expression of C-type natriuretic peptide and adrenomedullin. Hypertension 29 (1997) 1296-1302
46. Okahara K., Kambayashi J.-I., Ohnishi T., Fujiwara Y., Kawasaki T., and Monden M. Shear stress induces expression of CNP gene in human endothelial cells. FEBS Lett. 373 (1995) 108-110
47. Redmond E.M., Cullen J.P., Cahill P.A., Sitzmann J.V., Stefansson S., Lawrence D.A., and Okada S.S. Endothelial cells inhibit flow-induced smooth muscle cell migration: role of plasminogen activator inhibitor-1. Circulation 103 (2001) 597-603
48. Kawai Y., Matsumoto Y., Watanabe K., Yamamoto H., Satoh K., Murata M., Handa M., and Ikeda Y. Hemodynamic forces modulate the effects of cytokines on fibrinolytic activity of endothelial cells. Blood 87 (1996) 2314-2321
49. Yoshizumi M., Kurihara H., Sugiyama T., Takaku F., Yanagisawa M., Masaki T., and Yazaki Y. hemodynamic shear stress stimulates endothelin production by cultured endothelial cells. Biochem. Biophys. Res. Commun. 161 (1989) 859-864
50. Sharefkin J.B., Diamond S.L., Eskin S.G., McIntire L.V., and Deffenbach C.W. Fluid flow decreases preproendothelin mRNA levels and suppresses endothelin-1 peptide release in cultured human endothelial cells. J. Vasc. Surg. 14 (1991) 1-9
51. Malek A., and Izumo S. Physiological fluid shear stress causes downregulation of endothelin-1 mRNA in bovine aortic endothelium. Am. J. Physiol. 263 (1992) C389-C396
52. 2+ and protein kinase C in shear stress-induced actin depolymerization and endothelin 1 gene expression. Circ. Res. 75 (1994) 630-636
53. Shinoki N., Kawasaki T., Minamino N., Okahara K., Ogawa A., Ariyoshi H., Sakon M., Kambayashi J., Kangawa K., and Monden M. Shear stress down-regulates gene transcription and production of adrenomedullin in human aortic endothelial cells. J. Cell Biochem. 71 (1998) 109-115
54. Makalowski W., Zhang J., and Boguski M.S. Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequence. Genome Res. 6 (1996) 846-857
55. Yulug I.G., Yulug A., and Fisher E.M. The frequency and position of Alu repeats in cDNAs, as determined by database searching. Genomics 27 (1995) 544-548
56. Yuen T., Wurmbach E., Pfeffer R.L., Ebersole B.J., and Sealfon S.C. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res. 30 (2002) e48
57. Dorris D.R., Nguyen A., Gieser L., Lockner R., Lublinsky A., Patterson M., Touma E., Sendera T.J., Elghanian R., and Mazumder A. Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios. BMC Biotechnol. 3 (2003) 6