DNA arrays for low gene expression ? - (Jul/25/2004 )
Has anyone some experience in the validity of using micro or macroarray techniques to detect weak gene expression levels? in other word, are DNA arrays suitable to study a low gene expression levels ? which is the more convenient and sensitive methode to measure a low gene expression?
any idea would be appreciated.
In microarray experiment, reliable measurement is more achievable for highly expressed genes in a target sample than for those expressed at low levels. Accurate measurement of low-expressing genes is challenging because the low-intensity signals are not only weaker, but also more variable
Actually, compared to non-PCR based detection such as Northern and RPA, PCR amplification in microarray introduces a bias toward boosting the presence of low copy number genes in the resulted cDNA population.
Generally speaking, oligonucleotide-based DNA microarrays is better than cDNA based microarray for detecting low expression genes, because the generation of cDNA microarrays involves many laborious and error-prone steps, including bacterial culturing, PCR amplification and purification, and DNA sequence validation. In addition, cDNA microarrays are prone to cross-hybridization with gene family members that have 70% or more sequence homology. Long oligonucleotide microarrays perform better than short ones for the same purpose.
Also read this paper:
Optimization of oligonucleotide-based DNA microarrays