| Experiment Id | E-GEOD-7574 | Series Id | GSE7574 |
| Name | Analysis of on-chip hybridization kinetics for optimization of gene expression experiments | Experiment Type | transcription profiling by array |
| Study Type | Baseline | Source | ArrayExpress |
| Curation Date | 2017-11-30 |
| description | DNA microarray technology is a powerful tool for getting the overview of gene expression in biological samples. Although the successful application of microarray-based expression analysis was demonstrated in a number of applications, the main problem with this approach is the fact that expression levels deduced from hybridization experiments do not necessarily correlate with RNA concentrations. Moreover, oligonucleotide probes corresponding to the same gene can give different hybridization signals. Apart from cross-hybridizations and differential splicing, this could be due to secondary structures of probes or targets. In addition, for low copy genes, hybridization equilibrium may be reached after hybridization times much longer than the one commonly used (overnight, 15 hours). Thus, hybridization signals could depend on kinetic properties of the probe, which may vary between different oligonucleotide probes immobilized on the same microarray. To validate these hypothesis, on-chip hybridization kinetics and duplexes thermostability analysis were performed using oligonucleotide microarrays containing 50-mer probes corresponding to mouse genes. We demonstrate that differences in hybridization kinetics between the probes can influence the interpretation of expression data. Ways to improve the reliability of microarray-based expression analysis are discussed. Keywords: kinetics, gene expression, microarrays Total RNA were extracted from 5 thymus and 6 cortex of B10D2 mice. For each tissue, equal amounts of each RNA were pooled and 15 µg were labeled by reverse-transcription and hybridized on neurotransmission microarrays. Three replicates of each experiment have been performed. |
