Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Whole Transcriptome Amplification for Gene Expression Profiling and Development of Molecular Archives


ABSTRACT: Type of experiment: This study used microarray experiments to evaluate the reproducibility and fidelity of Whole Transcriptome Amplification (WTA). Experimental factors: This study contains multiple categories of microarray experiments. Self-self hybridizations from WTA amplified total RNA were performed to evaluate the reproducibility of WTA. To evaluate the fidelity of WTA, the same total RNA, isolated from tissue samples or cell lines, was either directly used for microarray analysis or subjected to WTA amplification before hybridization. The amount of input total RNA for WTA amplification was varied for different hybridizations. To demonstrate the usefulness of WTA, benign epithelia, cancerous epithelia and stroma isolated by laser capture microdissection from frozen prostate tissue specimens were subjected to WTA and hybridized. To demonstrate the fidelity of WTA with degraded samples, total RNA from cell lines was artificially degraded before WTA and hybridization. Total RNA isolated from formalin-fixed paraffin-embedded (FFPE) tissues containing benign and cancerous prostate tissue were also subjected to WTA and hybridized.

ORGANISM(S): Homo sapiens

SUBMITTER: Arul Chinnaiyan 

PROVIDER: E-GEOD-2618 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Whole transcriptome amplification for gene expression profiling and development of molecular archives.

Tomlins Scott A SA   Mehra Rohit R   Rhodes Daniel R DR   Shah Rajal B RB   Rubin Mark A MA   Bruening Eric E   Makarov Vladimir V   Chinnaiyan Arul M AM  

Neoplasia (New York, N.Y.) 20060201 2


Expression profiling of clinically obtainable tumor specimens has been hindered by the need for microgram quantities of RNA. In vitro transcription (IVT)-based amplifications are most commonly used to amplify small quantities of RNA for microarray analysis. However, significant drawbacks exist with IVT-based amplification, and the need for alternative amplification methods remains. Herein, we validate whole transcriptome amplification (WTA), an exponential amplification technique that produces c  ...[more]

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