Stripping custom microRNA microarrays and the lessons learned about probe-slide interactions

Analytical Biochemistry

Volumn 386, Issue 2, 2009, Pages 222-227

  Zhang, Xiaoxiao ^a   Xu, Wayne ^a   Tan, Jiankang ^a   Zeng, Yan ^a,b  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Custom microarray; GAPSII slide; microRNA; Oligonucleotide probe

Indexed keywords

BIOCHIPS; GENE EXPRESSION; OLIGONUCLEOTIDES; PROBES;

DNA MICRO-ARRAY; GAPSII SLIDE; GENE EXPRESSION PROFILING; GENOME WIDE ANALYSIS; MICROARRAY EXPERIMENTS; MICRORNA EXPRESSION; MICRORNAS; OLIGONUCLEOTIDE PROBES;

RNA;

BUFFER; DNA; MICRORNA; NUCLEIC ACID; OLIGONUCLEOTIDE; SODIUM CHLORIDE;

ARTICLE; DNA PROBE; MICROARRAY ANALYSIS; OLIGONUCLEOTIDE PROBE; PARAMETER; PRIORITY JOURNAL;

EID: 59749102883     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2008.12.008     Document Type: Article

References (30)

1. Meister G., and Tuschl T. Mechanisms of gene silencing by double-stranded RNA. Nature 431 (2004) 343-349
2. Valencia-Sanchez M.A., Liu J., Hannon G.J., and Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20 (2006) 515-524
3. Zeng Y. Principles of microRNA production and maturation. Oncogene 25 (2006) 6156-6162
4. Berezikov E., Guryev V., van de Belt J., Wienholds E., Plasterk R.H., and Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 (2005) 21-24
5. Lewis B.P., Burge C.B., and Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 (2005) 15-20
6. Xie X., Lu J., Kulbokas E.J., Golub T.R., Mootha V., Lindblad-Toh K., Lander E.S., and Kellis M. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434 (2005) 338-345
7. Miranda K.C., Huynh T., Tay Y., Ang Y.S., Tam W.L., Thomson A.M., Lim B., and Rigoutsos I. A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126 (2006) 1203-1217
8. Ambros V. The functions of animal microRNAs. Nature 431 (2004) 350-355
9. Carthew R.W. Gene regulation by microRNAs. Curr. Opin. Genet. Dev. 16 (2006) 203-208
10. Calin G.A., and Croce C.M. MicroRNAs and chromosomal abnormalities in cancer cells. Oncogene 25 (2006) 6202-6210
11. Hammond S.M. MicroRNAs as oncogenes. Curr. Opin. Genet. Dev. 16 (2006) 4-9
12. Babak T., Zhang W., Morris Q., Blencowe B.J., and Hughes T.R. Probing microRNAs with microarrays: tissue specificity and functional inference. RNA 10 (2004) 1813-1819
13. Barad O., Meiri E., Avniel A., Aharonov R., Barzilai A., Bentwich I., Einav U., Gilad S., Hurban P., Karov Y., Lobenhofer E.K., Sharon E., Shiboleth Y.M., Shtutman M., Bentwich Z., and Einat P. MicroRNA expression detected by oligonucleotide microarrays, system establishment, and expression profiling in human tissues. Genome Res. 14 (2004) 2486-2494
14. Esau C., Kang X., Peralta E., Hanson E., Marcusson E.G., Ravichandran L.V., Sun Y., Koo S., Perera R.J., Jain R., Dean N.M., Freier S.M., Bennett C.F., Lollo B., and Griffey R. MicroRNA-143 regulates adipocyte differentiation. J. Biol. Chem. 279 (2004) 52361-52365
15. Liu C.G., Calin G.A., Meloon B., Gamliel N., Sevignani C., Ferracin M., Dunmitru C.D., Shimizu M., Zupo S., Dono M., Alder H., Bullrich F., Negrini M., and Croce C.M. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc. Natl. Acad. Sci. USA 101 (2004) 9740-9744
16. Miska E.A., Alvarez-Saavedra E., Townsend M., Yoshii A., Sestan N., Rakic P., Constantine-Paton M., and Horvitz H.R. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 5 (2004) R68
17. Thomson J.M., Parker J., Perou C.M., and Hammond S.M. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1 (2004) 47-53
18. Baskerville S., and Bartel D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11 (2005) 241-247
19. Goff L.A., Yang M., Bowers J., Getts R.C., Padgett R.W., and Hart R.P. Rational probe optimization and enhanced detection strategy for microRNAs using microarrays. RNA Biol. 2 (2005) 93-100
20. Strother T., Hamers R.J., and Smith L.M. Covalent attachment of oligodeoxyribonucleotides to amine-modified Si (001) surfaces. Nucleic Acids Res. 28 (2000) 3535-3541
21. Dolan P.L., Wu Y., Ista L.K., Metzenberg R.L., Nelson M.A., and Lopez G.P. Robust and efficient synthetic method for forming DNA microarrays. Nucleic Acids Res. 29 (2001) E107-E117
22. Consolandi C., Castiglioni B., Bordoni R., Busti E., Battaglia C., Berbardi L.R., and De Bellis G. Two efficient polymeric chemical platforms for oligonucleotide microarray preparation. Nucleosides Nucleotides Nucleic Acids 21 (2002) 561-580
23. Bao Z., Wenli W., Rong S., Ling L., Qiuye G., and Wenling Z. Re-use of a stripped cDNA microarray. Br. J. Biomed. Sci. 59 (2002) 118-119
24. Benters R., Niemeyer C.M., Drutschmann D., Blohm D., and Wohrle D. DNA microarrays with PAMAM dendritic linker systems. Nucleic Acids Res. 30 (2002) e10
25. Hu Z., Troester M., and Perou C.M. High reproducibility using sodium hydroxide-stripped long oligonucleotide DNA microarrays. BioTechniques 38 (2005) 121-124
26. Hahnke K., Jacobsen M., Gruetzkau A., Gruen J.R., Koch M., Emoto M., Meyer T.F., Walduck A., Kaufmann S.H.E., and Mollenkopf H. Striptease on glass: validation of an improved stripping procedure for in situ microarrays. J. Biotechnol. 128 (2007) 1-13
27. Pellis L., Franssen-van Hal N.L., Burema J., and Keijer J. The intraclass correlation coefficient applied for evaluation of data correction, labeling methods, and rectal biopsy sampling in DNA microarray experiments. Physiol. Genomics 16 (2003) 99-106
28. Ehrenreich A. DNA microarray technology for the microbiologist: an overview. Appl. Microbiol. Biotechnol. 73 (2006) 255-273
29. Cook M.A., Chan C.-K., Jorgensen P., Ketela T., So D., Tyers M., and Ho C.-Y. Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays. PLoS ONE 3 (2008) e1546
30. Call D.R., Chandler D.P., and Brockman F. Fabrication of DNA microarrays using unmodified oligonucleotide probes. BioTechniques 30 (2001) 368-376