DNA, microarrays

DNA microarrays, or DNA chips consist of thousands of individual DNA sequences arrayed at a high density on a single matrix, usually glass slides or quartz wafers, but sometimes on nylon substrates. Probes with known identity are used to determine complementary binding, thus allowing the analysis of gene expression, DNA sequence variation or protein levels in a highly parallel format. 

Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 20 467-470... 

Spike-ins are usually RNA transcripts used to calibrate measurements in a DNA microarray experiment. Each spike-in is designed to hybridize with a specific control probe on the target array. Manufacturers of commercially available microarrays typically offer companion RNA spike-ins kits . Known amounts of RNA spike-ins are mixed with the experiment sample during preparation. Subsequently the measured degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements of the sample RNA. 

Nambiar S, Mirmohammadsadegh A, Doroudi R, Gustrau A, Marini A, Boeder G, et al. Signaling networks in cutaneous melanoma metastasis identified by complementary DNA microarrays. Arch Dermatol 2005 141 165-73. 

Ise R, Han D, Takahashi Y, Terasaka S, Inoue A, Tanji M, et al. Expression profiling of the estrogen responsive genes in response to phytoestrogens using a customized DNA microarray. FEBS Lett 2005 579 1732-40. 

Khan J et al DNA microarray technology the anticipated impact on the study of human disease. Biochim Biophys Acta 1999 1423 M17. 

IHC, IF, real-time PCR (mRNA), ELISA, RT-PCR, DNA microarray Real-time PCR (mRNA), IF, ELISA, RT-PCR Real-time PCR (mRNA), RT-PCR, Northern, ISH, IHC, IF, ELISA RT-PCR, IHC, ISH (mRNA)... 

SF, synovium DNA microarray, RT-PCR, ELISA, ISH (mRNA) Higher levels compared with OA and traumatic joint injury. Increased expression compared with OA but not PA. 38, 159, 160, 190... 

CXCR1 Synovium DNA microarray, RT-PCR, WB Higher levels compared with OA. 159... 

Lettieri, T., Recent applications of DNA microarray technology to toxicology and ecotoxicology,... 

It should be possible to extend the DNA microarray-binding experiment to whole-genome analysis of transcription factor binding sites. The authors suggest that a microarray spotted with 12,000 one-kilobase sequences would span the entire Saccharomyces cerevisiae genome (Bulyk et al., 2001). Such an array could be used to characterize the sequence specificity of S. cerevisiae transcription factors. These experiments would be useful for predicting functions of previously uncharacterized transcription... 

Bulyk, M. L., Huang, X., Choo, Y., and Church, G. M. (2001). Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 98, 7158-7163. 

Shalon, D., Smith, S. J., and Brown, P. O. (1996). A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639-645. 

Al-Khaldi, S. F. Martin, S. A. Rasooly, A. Evans, J. D. DNA microarray technology used for studying foodborne pathogens and microbial habitats Minireview. J. AOAC Int. 2002,85, 906-910. 

Call, D. R. Bakko, M. K. Krug, M. J. Roberts, M. C. Identifying antimicrobial resistance genes with DNA microarrays. Antimicrob. Agents Chemother. 2003,47, 3290-3295. 

Call, D. R. Borucki, M. K. Loge, F. J. Detection of bacterial pathogens in environmental samples using DNA microarrays. J. Microbiol. Meth. 2003, 53, 235-243. 

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