Related Experiment Videos
Moderate degradation does not preclude microarray analysis of small amounts of RNA
Oliver Schoor1, Toni Weinschenk, Jörg Hennenlotter
1University of Tübingen, Tübingen, Germany.
Biotechniques
|December 20, 2003
Summary
Even partially degraded RNA samples can yield reliable gene expression profiles, especially when ribosomal bands are visible. Careful analysis allows meaningful results from suboptimal RNA quality in gene expression studies.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Gene expression analysis using microarrays is increasingly vital for small RNA samples obtained via methods like laser microdissection.
- RNA quality is a frequent challenge in analyzing degraded samples.
Purpose of the Study:
- To evaluate how varying degrees of RNA degradation affect gene expression profiles.
- To determine the usability of partially degraded RNA for microarray analysis.
Main Methods:
- Induced RNA degradation in human tumor and healthy tissues using endogenous ribonucleases.
- Amplified degraded RNA (20 ng total RNA) through two rounds of in vitro transcription.
- Analyzed amplified RNA using Affymetrix oligonucleotide microarrays.
- Confirmed expression differences via real-time quantitative PCR.
Main Results:
- Gene expression profiles from partially degraded RNA samples (with visible ribosomal bands) showed high similarity to intact samples.
- RNA degradation had a limited impact on the overall expression profile under tested conditions.
Conclusions:
- Partially degraded RNA samples can produce meaningful gene expression data.
- Suboptimal RNA quality does not necessarily preclude successful microarray analysis if samples are handled carefully.