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J Biomol Tech. 2010 September; 21(3 Suppl): S43.
PMCID: PMC2918120

Evaluation of Microarray Performance for Two RNA Amplification Methodologies

G. Miyada and V. Sementchenko
NuGEN Technologies, San Carlos, CA, United States



Advances in high-throughput gene expression technologies such as microarrays have transformed our understanding of the molecular mechanisms underlying various types of biological processes and diseases. The Applause™ line of products (3'-Amp, WT-Amp ST, and WT-Amp Plus ST) addresses requirements of gene expression microarray users with high-quality RNA (50 nanograms) that want a low-cost, single-day, and reliable sample preparation solution. A comparison was made between the Applause line of amplification products and available vendor data for the GeneChip® WT cDNA Synthesis and Amplification and GeneChip3' IVT Express products. Data generated from 50 ng HeLa, MAQC A, and MAQC B RNA using the Applause 3'-Amp kit were compared to equivalent reported vendor data for the GeneChip 3' IVT Express amplification kit. NuGEN's Applause 3'-Amp outperformed the GeneChip 3' IVT Express with amplifications and labeling completed within 6 hours. It also did better than the GeneChip 3' IVT Express platform on HGU133 Plus 2.0 by percent Present Calls (%P). Differential expression analysis of MAQC samples demonstrated high correlation between the Applause 3'-Amp array data and data generated by quantitative PCR (qPCR) for the MAQC Project (Nature Biotech, 24:1151-1161 (2006)), with an R value of 0.96. Data generated from 50 ng brain and skeletal muscle RNA with the Applause WT-Amp ST and WT-Amp Plus ST kits were compared to equivalent 1 μg vendor data for GeneChip WT cDNA Synthesis and Amplification Kit. In addition to the improved speed (9 hours), the Applause WT-Amp kits also showed better QC array metrics (Pos-vs-Neg AUC, All-Probe-Set-Mean, All-Probe-Set-RLE-Mean) than the GeneChip WT cDNA Synthesis and Amplification kit. The Applause amplification system provides researchers with a fast, economical, and high-quality solution to everyday microarray needs.

Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities