Transcriptomics,Multiomics

Dataset Information

5

Exon Level Expression Profiling: a Novel Unbiased Transcriptome Analysis for Body Fluids


ABSTRACT: 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. 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.

OTHER RELATED OMICS DATASETS IN: PRJNA99889

ORGANISM(S): Homo sapiens  

SUBMITTER: Bradley S Henson   David Elashoff  Weixia Yu  David T Wong  Zhanzhi Hu  Guido Krupp  David T.W. Wong  Bernhard G Zimmermann  Hui Zhou 

PROVIDER: E-GEOD-7760 | ArrayExpress | 2008-05-19

SECONDARY ACCESSION(S): GSE7760PRJNA99889

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-7760.README.txt Txt
E-GEOD-7760.eSet.r Other
E-GEOD-7760.idf.txt Idf
E-GEOD-7760.processed.1.zip Processed
E-GEOD-7760.raw.1.zip Raw
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Publications

Exon-level expression profiling: a comprehensive transcriptome analysis of oral fluids.

Hu Zhanzhi Z   Zimmermann Bernhard G BG   Zhou Hui H   Wang Jianghua J   Henson Bradley S BS   Yu Weixia W   Elashoff David D   Krupp Guido G   Wong David T DT  

Clinical chemistry 20080320 5


<h4>Background</h4>The application of global gene expression profiling to saliva samples is hampered by the presence of partially fragmented and degraded RNAs that are difficult to amplify and detect with the prevailing technologies. Moreover, the often limited volume of saliva samples is a challenge to quantitative PCR (qPCR) validation of multiple candidates. The aim of this study was to provide proof-of-concept data on the combination of a universal mRNA-amplification method with exon arrays  ...[more]

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