Gene expression analysis is currently carried out using three methods that provide complementary data: microarrays, RNA-Seq, and RT-qPCR. Microarrays provide comprehensive whole-genome coverage in single experiments, with rapid data acquisition and results at a low price per sample.
This document describes a study validating the reliability of Agilent SurePrint G3 Gene Expression Microarrays. The authors compare microarray data against two complementary techniques: reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and next-generation sequencing (RNA-Seq). The goal is to demonstrate that the microarray platform provides accurate, reproducible results consistent with other established methods.
The study utilized specific Agilent reagents and systems, including the Low Input Quick Amp Labeling Kit for sample preparation and the Mx3005P QPCR System for RT-qPCR analysis. Results showed a correlation of R > 0.99 between microarray signals across technical replicates and a high concordance (R > 0.99) between microarray ratios and RT-qPCR predictions, confirming the accuracy of the SurePrint G3 arrays.
Twenty-five ng of total RNA was amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit.
The reproducibility demonstrated a correlation of R > 0.99 for signals across technical replicates in one-color assays.
The single end sequencing was performed with short 36 bp reads.