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Cerebrospinal Fluid MicroRNA Profiling Using Quantitative Real Time PCR
Published on: January 22, 2014
Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA
Zhining Wen1, Charles Wang, Quan Shi
1Division of Systems Biology, National Center for Toxicological Research (NCTR), US Food and Drug Administration (FDA), 3900 NCTR Road, Jefferson, AR 72079, USA.
BMC Bioinformatics
|October 16, 2010
Summary
Expired microarrays can still yield reliable gene expression data, showing high concordance with unexpired arrays. Human reference RNA samples remained stable for at least four years when stored properly.
Area of Science:
- Molecular Biology
- Genomics
- Bioinformatics
Background:
- The Affymetrix GeneChip® system is a costly microarray platform.
- Expired microarrays may pose a challenge for researchers due to cost and sample availability.
- The long-term stability of reference RNA samples for gene expression analysis was uncertain.
Purpose of the Study:
- To determine the utility of expired Affymetrix GeneChip® microarrays for gene expression analysis.
- To assess the transcriptome integrity of human reference RNA samples stored for four years.
- To compare gene expression data from expired and unexpired microarrays.
Main Methods:
- Microarray data generation using expired and unexpired Affymetrix U133A and U133Plus2 microarrays.
- Comparison of gene expression data from 2009 with 2005 MAQC project data.
- Analysis of differentially expressed genes (DEGs) and fold change compression.
Main Results:
- High overlap (96.99%) in DEGs between expired and unexpired microarrays.
- 97.44% overlap in DEGs between U133Plus2 microarray data from 2009 and 2005.
- Microarray data from expired U133A arrays showed high concordance with MAQC project data.
Conclusions:
- Expired microarrays (U133A) are suitable for identifying DEGs with high specificity and consistency.
- Expired microarrays may exhibit fold change compression and reduced sensitivity.
- MAQC reference RNA samples stored at -80°C are stable for at least four years.
