Peer Reviewed

1

Document Type

Article

Publication Date

2009

Keywords

Animals, DNA, Complementary, Gene Library, Humans, Nucleic Acid Hybridization, RNA, Reverse Transcriptase Polymerase Chain Reaction

Comments

The original publication is available at http://www.springerprotocols.com

Abstract

The comparison of two RNA populations that differ from the effects of a single-independent variable, such as a drug treatment or a specific genetic defect, can identify differences in the abundance of specific transcripts that vary in a population-dependent manner. There are a variety of methods for identifying differentially expressed genes, including microarray, SAGE, qRT-PCR, and DDGE. This protocol describes a potentially less sensitive yet relatively easy and cost-effective alternative that does not require prior knowledge of the transcriptomes under investigation and is particularly applicable when minimal levels of starting material, RNA, are available. RNA input can often be a limiting factor when analyzing RNA from, for example, rigorously purified blood cells. This protocol describes the use of SMART-PCR to amplify cDNA from sub-microgram levels of RNA. The amplified cDNA populations under comparison are then subjected to suppression subtractive hybridization (SSH-PCR), a technique that couples subtractive hybridization with suppression PCR to selectively amplify fragments of differentially expressed genes. The final products are cDNA populations enriched for significantly over-represented transcripts in either of the two input RNA preparations. These cDNA populations may then be cloned to make subtracted cDNA libraries and/or used as probes to screen subtracted cDNA, global cDNA, or genomic DNA libraries.

Disciplines

Life Sciences

Citation

Hillmann A, Dunne E, Kenny D. cDNA amplification by SMART-PCR and suppression subtractive hybridization (SSH)-PCR. Methods in Molecular Biology 2009;496:223-43.

PubMed ID

18839114

DOI Link

10.1007/978-1-59745-553-4_15

Included in

Life Sciences Commons

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