We found that microarray cDNA preparation methods have a profound impact on this analysis, in particular demonstrating that the comparison of microarrays hybridized to random-primed and oligo-dT-primed cDNA enabled the distinction between transcripts that were degraded, deadenylated, or cleaved in a sequence specific manner.
Differentially expressed genes can be investigated using a multitude of methods, such as cDNA microarray, cDNA-AFLP, RDA, SAGE, and SSH [ 13– 17].
In order to evaluate the microarray results obtained with this method, we labelled two S. cerevisiae total RNA samples with the NimbleGen-recommended double-stranded cDNA method, the indirect (aminoallyl) method and our direct random method, each in triplicate.
With current studies of cell mixtures, transcript expression levels are measured relative to each other using methods such as quantitative PCR, microarrays, cDNA sequencing (RNA-Seq, etc).
Three established methods of measuring gene expression used in biological research are microarrays, cDNA and Serial Analysis of Gene Expression (SAGE) libraries.
These factors may introduce a bias that improves the correlation between qPCR and microarrays that used oligo dT -primed cDNA labeling metholigo dT -primedindirecDNAnd the ds-cDNA methods.
There are other, more comprehensive cDNA microarray methods available, which produce copious amounts of data.
Since SSH specifically amplified the difference of gene expression, the SSH/microarray approach should also be able to identify more differentially expressed genes between hepatoma and non-hepatoma liver tissues, which were originally undetectable by the regular cDNA microarray methods.
The cDNA microarray hybridization method is now widely used to analyze simultaneously the expression of thousands of genes in cancer tissues [ 5, 21], but the contamination of tumors by epithelial, stromal or immune cells presents problems for obtaining accurate expression profiles.
It is worth noting that 96% of the 470 genes identified as overexpressed by the cDNA microarray method [ 13] were included within the total set of elements in the oligonucleotide microarray platform [ 12].
