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Updated: Aug 9, 2026
07:27
Transcriptome Analysis of Single Cells
Published on: April 25, 2011
Whole transcriptome amplification for gene expression profiling and development of molecular archives
Scott A Tomlins1, Rohit Mehra, Daniel R Rhodes
1Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109-0602, USA.
Neoplasia (New York, N.Y.)
|April 14, 2006
Summary
Whole transcriptome amplification (WTA) offers a fast, versatile method to profile minute tumor samples. This technique amplifies cDNA from nanograms of RNA, creating a molecular archive compatible with degraded RNA, overcoming limitations of in vitro transcription methods.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Microgram quantities of RNA are typically needed for expression profiling of tumor specimens.
- In vitro transcription (IVT)-based amplification is a common but limited method for amplifying small RNA quantities for microarray analysis.
Purpose of the Study:
- To validate whole transcriptome amplification (WTA) as an alternative RNA amplification method.
- To assess WTA's compatibility with limited and degraded RNA samples.
- To demonstrate WTA's utility as a molecular archive for cDNA samples.
Main Methods:
- Whole transcriptome amplification (WTA) was employed to generate cDNA libraries and amplified targets from nanogram quantities of total RNA.
- Quantitative polymerase chain reaction (PCR) and cDNA microarrays were used in conjunction with WTA.
- WTA was combined with laser capture microdissection for profiling frozen prostate tissues.
Main Results:
- WTA successfully amplified cDNA from nanogram quantities of total RNA within 3 to 4 hours.
- WTA-generated cDNA libraries can be amplified through multiple PCR rounds, serving as a molecular archive.
- WTA is compatible with artificially degraded RNA and RNA from formalin-fixed paraffin-embedded tissues, unlike many IVT-based methods.
Conclusions:
- Whole transcriptome amplification (WTA) is a versatile method for profiling and archiving cDNA from minute tumor samples.
- WTA overcomes the limitations of IVT-based amplification and is compatible with partially degraded RNA.
- The ability to create a bankable cDNA resource from minimal, degraded RNA significantly advances molecular profiling capabilities.
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