Northwestern University Feinberg School of Medicine

Center for Genetic Medicine

Microarray Processing


Microarray is the first high-throughput genome technology developed in the mid-1990s. Over the years, this technology has seen tremendous growth and maturation. At the beginning it was mainly used for gene expression profiling. Its application soon diversified into other areas, including genotyping, DNA methylation analysis, and copy number variation analysis with comparative genomic hybridization (CGH). Attested by the large amounts of data deposited in databases such as Gene Expression Omnibus (GEO), microarray technology has supported the biomedical research community for over two decades and is still being employed today.

Different from next-gen sequencing, microarray is based on hybridization of nucleic acid molecules. To achieve genome- or transcriptome-wide coverage, tens or hundreds of thousands of probes are immobilized and arrayed onto a solid matrix surface. These arrays, or chips, are then used for hybridization with DNA or RNA prepared from biological samples. Signal readouts from the hybridization are then used to analyze genomic DNA sequence polymorphism, epigenetic modification, gene expression changes, etc.

Over the years, based on how probes are generated and immobilized, different microarray platforms are developed. The NUSeq Core provides support to two of the most widely adopted microarray platforms, i.e., the Affymetrix GeneChip and the Illumina BeadChip systems. NUSeq also provides bioinformatics services to data generated on both platforms.

Affymetrix GeneChip

The probes used by the Affymetrix GeneChip technology are oligonucleotide DNA probes synthesized in situ using photolithography, a process that is very similar to the manufacture of semiconductor chips.

Affymetrix offers a wide array of GeneChips for different applications, including transcriptome gene expression profiling, genome-wide genotyping, cytogenetics, copy number variation (CNV) and loss of heterozygosity (LOH) analysis. On transcriptome gene expression profiling, Affymetrix offers the following arrays:

For genome-wide genotyping, the Genome-Wide Human SNP Array 6.0 can be used.

For a whole list of Affymetrix, please visit the Affymetrix Microarray Solution website.

Affymetrix GeneChip Processing Pricing
ServicesNU/CBCExternalIndustrialUnit
Affymetrix GeneChip Processing$375.00$412.50$468.80Sample

*GeneChip costs are additional and billed as pass-through. As chip prices vary please enquire for your particular chip. We provide free consultation for your project if you are unsure.


Illumina BeadChip

Illumina BeadChip microarray offers solutions for DNA methylation profiling, whole-genome genotyping, and gene expression analysis. Using a different approach invented by Dr. David Walt and colleagues at Tufts University, the Illumina BeadArray technology creates an array using specially prepared microbeads, which self-assemble into microwells etched into a substrate. Each microbead, 3 microns in diameter and spaced 5.7 microns apart, carries on its surface hundreds of thousands of copies of a particular oligonucleotide sequence that act as probes.

Since each Illumina BeadArray is formed from random assembly of microbeads into microwells, to identify which bead type is in which microwell requires a decoding process. This process is based on hybridization of oligonucleotides that are complementary to the probes on the beads. These oligonucleotides, called decoders, are labeled with multiple fluorophors. Different sets of these differentially labeled oligonucleotides are used in the decoding process. The ingenuity of this decoding process lies in the fact that only a small number of fluorophors and a small number of steps are needed to achieve the decoding of an extremely large number of beads in the array.

To produce detection signal from experimental samples, different BeadArrays use different assays. For example, genotyping BeadArrays use the Infinium HD assay to differentiate different alleles. Also different from the Affymetrix GeneChip, the Illumina BeadArray accommodates multiple samples on each array.

Commonly used Illumina BeadChip microarrays include:

View a full list of human genotyping arrays.

(Illumina discontinues supply of this array at the end of 2016)

Illumina BeadChip Processing Pricing
ServicesNU/CBCExternalIndustrialUnit
Illumina Human Methylation EPIC Array Analysis: < 384 samples$50.00$55.00$62.50Sample
Illumina Human Methylation EPIC Array Analysis: >=384 samples$45.00$49.50$56.30Sample
Illumina Genotyping Array Analysis: < 96 samples$56.20$61.80$70.30Sample
Illumina Genotyping Array Analysis: >=96 samples$41.50$45.70$51.90Sample
Illumina Human Gene Expression BeadChip Analysis$115.00$126.50$144.00Sample

*BeadChip array costs are additional and billed as pass-through. As chip prices vary please enquire for your particular chip. We provide free consultation for your project if you are unsure.