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| Status |
Public on May 20, 2008 |
| Title |
Exon Level Expression Profiling: a Novel Unbiased Transcriptome Analysis for Body Fluids |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
Transcriptome analysis of partially degraded and fragmented RNA samples from body fluids
Global gene expression profiling has shown great promise in high-throughput biomarker discovery for early disease detection in body fluids such as saliva, which is accessible, cost-effective, and non-invasive. However, this goal has not been fully realized because saliva, like many clinical samples, contains partially fragmented and degraded RNAs that are difficult to amplify and detect with prevailing technologies. Here, using nanogram scale salivary RNA as a proof-of-principle example, we describe our progress with a novel poly-A tail independent mRNA amplification strategy combined with the Affymetrix GeneChip Exon arrays. We defined a Salivary Exon Core Transcriptome (SECT) with highly similar expression profiles in healthy individuals verified by quantitative PCR. Informatics analysis of SECT provided important mechanistic insight to their potential origin and function. Finally we demonstrated the diagnostic potential of true exon level expression profiling approach with salivary exon biomarkers that accurately discriminated gender in healthy individuals.
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| Overall design |
We analyzed saliva from 18 healthy subjects (7 males, 11 females) using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Exon Array Computational Tool. No techinical replicates were performed.
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| Contributor(s) |
Hu Z, Zhou H, Zimmermann BG, Henson BS, Yu W, Elashoff D, Krupp G, Wong DT |
| Citation(s) |
18356245, 20717777 |
| Submission date |
May 08, 2007 |
| Last update date |
Nov 01, 2019 |
| Contact name |
David T.W. Wong |
| E-mail(s) |
dtww@ucla.edu, mikehu@ucla.edu
|
| Organization name |
University of California, Los Angeles
|
| Department |
Dental Research Institute
|
| Street address |
10833 Le Conte Ave, CHS 73-017
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL5175 |
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version] |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA99889 |
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