Abstract
cDNA arrays are a powerful tool for discovering gene expression patterns. Nylon arrays have the advantage that they can be re-used several times. A key issue in high throughput gene expression analysis is sensitivity. In the case of nylon arrays, signal detection can be affected by the plastic bags used to keep membranes humid. In this study, we evaluated the effect of five types of plastics on the radioactive transmittance, number of genes with a signal above the background, and data variability. A polyethylene plastic bag 69 μm thick had a strong shielding effect that blocked 68.7% of the radioactive signal. The shielding effect on transmittance decreased the number of detected genes and increased the data variability. Other plastics which were thinner gave better results. Although plastics made from polyvinylidene chloride, polyvinyl chloride (both 13 μm thick) and polyethylene (29 and 7 μm thick) showed different levels of transmittance, they all gave similarly good performances. Polyvinylidene chloride and polyethylene 29 mm thick were the plastics of choice because of their easy handling. For other types of plastics, it is advisable to run a simple check on their performance in order to obtain the maximum information from nylon cDNA arrays.
Highlights
ABSTRACT cDNA arrays are a powerful tool for discovering gene expression patterns
We have successfully identified several genes that are induced by cold stress in sugarcane (Nogueira et al, 2003), and several recent studies on gene expression profiling have used macroarrays, including the identification of angiogenesis factors in lung cancer tissues (Ohira et al, 2002), the response to sulfur starvation in Arabidopsis thaliana (L.) Heynh. plants (Hirai et al, 2003), and the identification of genes involved in ceramidedependent neuronal apoptosis (Decraene et al, 2002)
One of the key issues in cDNA array analysis is the detection of genes that are expressed at low levels, because these correspond to the largest part of the transcriptome in most cells (Bishop et al, 1974; Jongeneel et al, 2003)
Summary
ABSTRACT cDNA arrays are a powerful tool for discovering gene expression patterns. Nylon arrays have the advantage that they can be re-used several times. One of the key issues in cDNA array analysis is the detection of genes that are expressed at low levels, because these correspond to the largest part of the transcriptome in most cells (Bishop et al, 1974; Jongeneel et al, 2003). We have compared several plastics to determine which one provides the best transmittance and evaluated their effect on the detection of gene expression and other aspects of cDNA array analysis.
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