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Resources Genomics Core Facility Microarrays

Microarrays

DNA microarrays are a well established technology for genome-wide characterization of gene transcription, single nucleotide variation, copy number variation and epigenetic cytosine methylation. The genomics core employs the most robust and accurate method on the market: the Illumina BeadArray platform. Traditionally, microarrays were glass slides printed with short DNA strands. This method has serious drawbacks, such as uneven spot morphology, signal bias due to spot position and low design flexibility. BeadArrays are a unique approach to microarray technology, using glass slides with micrometer sized holes to house oligonucleotide coated beads. The BeadArrays are used as a standard array would be, with the exception of a molecular decoding step that is performed by the scanner.

The three major applications of the BeadArray platform are for genotyping, gene transcription quantification, and cytosine methylation.

As of March 2012, more than 4,000 genotyping samples have been processed with an average call rate of >0.99%. Human genotyping studies are most often performed using the Infinium HD using OmniExpress (750k SNPs) or Omni2.5-8 arrays (2.4M SNPs). These chips are also capable of copy number variant estimation (CNV). Custom content chips for Genome Wide Association Studies (GWAS) are also available; please contact us with details of your project.

See details on all genotyping and CNV arrays from Illumina

Learn more about Formalin Fixed, paraffin embedded samples that can be used for genotyping studies using a specialized kit from Illumina [PDF]

Gene expression analysis chips are available for Human, Mouse and Rat; all chips contain all known genes and many regulatory RNAs. As of March 2012, microRNA chips and custom gene expression services have been discontinued by Illumina. Find out more about the composition of gene expression chips

Genome-wide methylation scanning in human samples (including stem cells and tumor cells) can be accomplished with the Human Methylation 450K array. This array covers CpG islands, sites known to be methylated in promoters, DNase hypersensitive sites and miRNA promoter regions. Learn more

High Throughput Capacity for Large Projects


Micrometer diameter beads positioned in etched silica holes

The Institute for Genomics and Multiscale Biology has made a substantial investment in high-throughput processing equipment for large BeadArray projects. We operate two TECAN Evo liquid handling robots, capable of processing 24 chips per run. Our Illumina HiScan microarray scanner is a top-of-the-line system with a robotic arm enabling 24-hour microarray data acquisition. With the existing equipment and facilities, the genomics core can process up to 600 samples per week.

If you would like to submit samples for BeadArray analysis, please see sample submission page for location and pricing. Guidance for experimental design is also available. Please feel free to contact us with any question.

For more information, see details on Illumina's site or view specification sheet [PDF].


BeadArray Technology Sample Submission Guidelines