CDNA arrays

Array types There are two main types of arrays (i) oligonucleotide and (ii) cDNA arrays. In the first type short 20-25mers are synthesized on a silica chip... 

The abundant expression of a variety of transporters in Caco-2 cells also makes it attractive to apply functional genomics tools, such as cDNA arrays in order to map the expression [31] and relative abundance of these transporters [32], Also, genomic mapping of surface receptors on Caco-2 cells can be performed to study receptor-mediated endocytosis and other endocytotic pathways for larger molecules in enterocytes [33-36]. 

Luo L et al. Gene expression profiles of laser-captured adjacent neuronal sub-types. Nature Med 1999 5 117-122. Chiang LW et al. An orchestrated gene expression component of neuronal programmed cell death revealed by cDNA array analysis. Proc Nat Acad Sci USA 2001 98 2814-2819. 

O Shaughnessy RF et al. PA-FABP, a novel marker of human epidermal transit amplifying cells revealed by 2D protein gel electrophoresis and cDNA array hybridisation. FEBS Lett 2000 486 149-154. 

Zeytun, A., et. al., Analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced gene expression profile in vivo using pathway-specific cDNA arrays, Toxicology, 178, 241, 2002. 

The normal gene expression in the rat nasal epithelium has been studied by using cDNA array technology (Hester et al. 2001). 

Hester, S.D., G.B. Benavides, M. Sartor, L. Yoon, K.T. Morgan, and D.C. Wolf 2001. Studies of normal gene expression in the rat nasal epithelium using cDNA array technology. Nature Genetics 27 59-60. 

Miki R, Kadota K, Bono H et al. Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci USA 2001 98 2199-2204. 

Baker YA, Harries HM, Waring JF et al. Clofibrate-induced gene expression changes in rat liver a cross-laboratory analysis using membrane cDNA arrays. Environ Health Perspect 2004 112 428-438. Waring JF, Ulrich RG, Flint N et al. Interlaboratory evaluation of rat hepatic gene expression changes induced by methapyrilene. Environ Health Perspect 2004 112 439 48. 

Microarrays based on cDNA or oligonucleotides differ fundamentally in how their experimental outputs are analyzed. Typical cDNA arrays are hybridized with differentially labeled cDNA pools generated from two separate RNA sources. For example, RNA may be harvested from untreated cells grown under a standard set of conditions and the cDNA produced from this RNA pool may be labeled with one fluorescent dye. A second RNA sample is then harvested from the same cell type after it is treated with a chemical or grown under a different set of conditions, and the cDNA is labeled with a second dye. Once the two cDNAs can be distinguished by their labels, equal amounts are mixed and hybridized competitively to the same cDNA array. The ratio of one dye signal to the other at each probe will reflect relative differences in abundance between the two RNA samples for the gene represented. 

Rather than describing changes in expression of a known class of genes, several studies have utilized unbiased approaches to determine changes in expression of a large number of genes in association with arousal state using cDNA arrays, DNA chips, or other molecular techniques. Subtractive hybridization was used to isolate two mRNAs whose expression was altered in forebrain after 24-hr SD... 

We shall describe here some of the approaches used for computation of data from two-dye comparative gene expression profiling analyses carried out with cDNA arrays. 

Malaspina A, Kaushik N, de Belleroche J. Differential expression of 14 genes in amyotrophic lateral sclerosis spinal cord detected using gridded cDNA arrays. J Neurochem 2001 77(1) 132-145. 

Bezchlibnyk YB, Wang JF, McQueen GM, Young LT. Gene expression differences in bipolar disorder revealed by cDNA array analysis of post-mortem frontal cortex. J Neurochem 2001 79(4) 826-834. 

Chong VZ, Young LT, Mishra, RK. 2002. cDNA array reveals differential gene expression following chronic neuroleptic administration Implications of synapsin II in haloperidol treatment. J Neurochem 82 1533-1539. 

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