Detecting Antisense Transcription Using Affymetrix Exon Arrays
Author Information
Author(s): Ge Xijin, Rubinstein Wendy S, Jung Yong-chul, Wu Qingfa
Primary Institution: South Dakota State University
Hypothesis
Can Affymetrix Exon arrays be modified to detect antisense transcription across mammalian genomes?
Conclusion
The modified Affymetrix Exon arrays can effectively detect a large number of natural antisense transcripts in human Jurkat cells.
Supporting Evidence
- The modified protocol identified antisense transcription at 2,088 exonic loci of 1,516 UniGene clusters.
- Many antisense transcripts were validated by orientation-specific RT-PCR.
- The study detected 1,026 potentially novel antisense transcripts not previously reported.
Takeaway
Scientists found a way to use special DNA chips to see if there are hidden messages in our genes that go in the opposite direction.
Methodology
The study used a modified cDNA synthesis protocol to label single-strand cDNA in reverse orientation for detection of antisense transcripts.
Potential Biases
The absence of mismatch probes in the Exon array may lead to less reliable detection calls.
Limitations
The method requires a large amount of total RNA and is limited to known or predicted exonic loci.
Participant Demographics
Human Jurkat cells derived from T-cell leukemia.
Statistical Information
P-Value
0.01
Statistical Significance
p<0.01
Digital Object Identifier (DOI)
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