Microarray-Related Products Microarrays have become a routine tool used in many labs for applications ranging from quantitative analysis of gene expression profiles to SNP genotyping. IDT offers a variety of products to support microarray-based research needs. Oligonucleotide-based microarrays offer greater specificity than long cDNA or PCR-product arrays. IDT can provide single oligonucleotides in tubes or thousands of oligonucleotides in plates and can meet the needs of any array experiment. Generally, arrays intended for use in expression profiling will employ oligos that are 60-70 bases long. Only IDT offers mass spectrometry QC on all oligos to assure that only the right oligos are spotted on a printed array. Further, IDT offers a variety of modifications that can be used for covalent attachment of array oligos, including Amino modifications, I-LinkerTM, and AcryditeTM. Many facilities print their own microarray slides using cDNA/PCR products or oligonucleotides. Quality control is essential to ensure data integrity. It is crucial to verify that all spots have good morphology and that nucleic acid was deposited for all features on slides produced in a print run. Spot drop out is a commonly encountered problem in printed arrays that can lead to false negatives. SpotQC is a hybridization-based product that can be used to QC printed arrays. Many users print arrays using 50% DMSO or 3X SSC-based solutions. While using DMSO is a good strategy for long cDNA or PCR products where the high concentration of DMSO helps denature double-stranded probes, oligonucleotide probes do not need denaturation and a simple 50% DMSO buffer can lead to suboptimal spotting. Print buffers containing 3X SSC have been routinely used for spotting oligo probes; however, additives are needed to help reduce evaporation during extended print runs. IDT offers two spotting buffer formulations for optimal printing on amine-surface slides (OSB) and epoxide-surface slides (ESB). Both spotting buffer formulations are specifically designed for reduced evaporation and suitable for either short or overnight microarray print runs. IDT's Epoxide Spotting Buffer (ESB) improves both probe attachment density and spot morphology when printing oligos probes on epoxide slides, and IDT's Oligo Spotting Buffer (OSB) improves both spot morphology and signal uniformity when printing oligo probes on amine slides. Most microarray experiments examine cellular RNA for gene expression. RNase contamination in the lab can ruin these experiments. IDT offers RNaseAlertTM Substrate, which can be used to identify reagents or equipment that are contaminated with RNases. IDT also offers Nuclease Decontamination Solution, which can be used to clean contaminated surfaces. Finally, we offer water and buffers which are guaranteed to be free of nuclease contamination. Correct design of oligonucleotides used in microarray experiments requires that a variety of parameters be considered. Oligos must be screened for Tm, self-dimer potential, hairpin potential, location within the transcript, and cross-reactivity with other transcripts. IDT Bioinformatics offers a free microarray oligo design tool on the web in the Workbench section of SciTools. This design tool allows for batch processing of thousands of probes or single oligos and is available at http://www.idtdna.com/Scitools/Applications/WorkBench/. Call Technical Support at 800-328-2661 to consult with a bioinformatics specialist who can assist with design of microarray oligonucleotides. |