Research Highlight: The MicroArray Quality Control Project
MicroArray Quality Control (MAQC) Project
The MAQC Consortium consists of scientists and statisticians from over 50 regulatory, academic, and industrial groups (including Ambion, an Applied Biosystems Business, and Applied Biosystems), who analyzed the data from more than 1,300 arrays. Their data, results, and protocols are freely available—see the sidebar, Links to Articles, Data Sets, and SOPs, to obtain this information.
Reproducibility of Gene Expression Measurements 
Validation of Microarray Results 
Microarray Performance and Normalization Techniques 
External RNA Controls 
Comparison of One- and Two-Color Microarray Platforms 
Microarray Platform Consistency in a Toxicogenomic Study 
1. Shi L, Reid LH, Jones WD, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24(9):1151–1161.
2. Canales RD, Luo Y, Willey JC, et al. (2006) Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 24(9):1115–1122.
3. Shippy R, Fulmer-Smentek S, Jensen RV, et al. (2006) Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nat Biotechnol 24(9):1123–1131.
4. Tong W, Lucas AB, Shippy R, et al. (2006) Evaluation of external RNA controls for the assessment of microarray performance. Nat Biotechnol 24(9):1132–1139.
5. Patterson TA, Lobenhofer EK, Fulmer-Smentek SB, et al. (2006) Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nat Biotechnol 24(9):1140–1150.
6. Guo L, Lobenhofer EK, Wang C, et al. (2006) Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol 24(9):1162–1169.
The FirstChoice® Human Brain Reference RNA is a high-quality standard for human microarray analysis, pooled from multiple donors and several brain regions to ensure unbiased coverage. This RNA was one of two samples used to generate data in the MAQC studies [1–5], making this FirstChoice RNA a valuable reference for microarray experiments.
Ambion MessageAmp™ II-Biotin Enhanced Kit and Illumina® TotalPrep™ RNA Amplification Kit use the Eberwine T7 linear amplification method [Van Gelder et al. (1990) Proc Natl Acad Sci USA 87:1663-1667] for RNA amplification that most accurately represents the initial mRNA profile. The IVT reaction and an NTP mix containing biotinylated UTP provide ease of use and optimal labeling. Sufficient amounts of amplified RNA are generated for array analysis after a single round of amplification with only 50 ng of input RNA. These kits have a high sensitivity and increase the percent of Present Calls.
The MessageAmp II-Biotin Enhanced Kit is used for target preparation on Affymetrix® GeneChip® Microarrays, while the Illumina TotalPrep RNA Amplification Kit is used only with Illumina Sentrix® Microarrays.
Applied Biosystems NanoAmp™ RT-IVT Labeling Kit is an in vitro transcription amplification protocol for labeling very low amounts of RNA for hybridization to Applied Biosystems Genome Survey Microarrays. One round of in vitro transcription amplifies as little as 200 ng of RNA; two rounds amplify as little as 5 ng. The RNA is converted to digoxigenin (DIG)-labeled amplified RNA (aRNA, or cRNA).
Genome Survey Microarrays are available from Applied Biosystems for human (32,878 probes for 29,098 genes), mouse (~32,000 genes), and rat (~27,000 genes) genes. Each is made with 60-mer DNA probes for optimal sensitivity and specificity. Chemiluminescence technology requires no excitation, dramatically improving signal-to-noise values and enabling low-level detection not achievable with other arrays.
Quantitative Reverse Transcription PCR Platform
Quantitative RT-PCR provides microarray verification and allows further study of specific gene expression results. TaqMan® Gene Expression Assays comprise >741,000 probe/primer sets for quantitative analysis of human, mouse, rat, Arabidopsis, Drosophila, C. elegans, dog, and Rhesus Macaque genes. Universal cycling conditions enable any assay combination to be run on Applied Biosystems instruments, including the 7300, 7500/7900HT (standard and FAST) Real-Time PCR Systems, and the ABI PRISM® 7700/7000 Sequence Detection Systems.
~1000 MAQC TaqMan Assays can be found on the TaqMan Gene Expression Assay search page (under Set Membership --> Collaborator Sets).