Abstract
The GeneChip system (Affymetrix) utilizes polyadenylation complementary oligonucleotides as a primer for labeling of ribonucleic acid (RNA). The polyadenylation usually locates at a downstream of the 3’ end of transcripts. When RNA is somehow degenerated, 5’ moiety of a transcript will not be well labeled. On the other hand, its 3’ moiety may relatively well be labeled even though RNA is degenerated. Thus 3’/5’ ratio of housekeeping genes may represent RNA quality. In the previous study, we experienced difficulties in confirming the microarray data by real-time polymerase chain reaction. During the analysis of this problem using 3’/5’ ratio of the housekeeping genes, we found suggestive and general concern which should be considered before an analysis of microarray data using any clinical samples.
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