Expression Analysis :: The Research Institute at Nationwide Children's Hospital

Expression Analysis

Using a wide range of expression arrays, we enable researchers to simultaneously monitor gene-wide expression profiles. To see a detailed comparison of our expression array platform click here.

Standard Expression Profiling

For standard expression profiling, as little as 100 nanograms of total RNA (down to as low as 500 picograms) is sufficient for reliable expression.

Agilent Dual-Mode Expression Arrays

These long oligo arrays provide a low cost, robust and highly sensitive solution for genome-wide expression analysis. Choose from an array catalog for over 20 different species, or have Agilent custom print your array for under $200.

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Starting January 2009

We now offer our clients the option of using Agilent Technologies commercially available arrays. This dual-mode technology (one or two color) provides the flexibility to choose the optimum detection method for your research needs:

  • Greater sensitivity conferred by high-quality, significantly longer probes
  • A linear dynamic range that spans more than four orders of magnitude
  • Enhanced resolving power in two-color mode
  • Simplified experimental design in one-color mode
  • Substantially lower cost


Agilent-designed 60-mer oligonucleotide microarrays are processed through a powerful combination of probe design algorithms coupled with Agilent's probe selection process. The most commonly used expression arrays:

Each contains 44,000 elements, with over 41,000 human, mouse or rat transcripts. Choose from an array catalog for over 20 different species, or have Agilent custom print your array for under $200.

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Affymetrix GeneChip Gene ST Arrays

The latest product in the family of Affymetrix expression arrays offering whole-transcript coverage. Genes are represented by probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than the legacy 3' array designs.

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The small format of these arrays makes them a cost-effective expression profiling solution for new microarray users. Sense DNA targets (ST) are generated from as little as 100ng of total RNA. Each of the well-annotated genes is represented by approximately 26 probes spread across the full length of the gene, providing a more complete and accurate picture of gene expression than 3'-based expression array designs. All 26 probes are summarized into a single expression value per gene.

GeneChip® Human Gene 1.0 ST Array
Each of the 28,869 genes on this array are represented by approximately 26 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3' based expression array designs.

GeneChip® Mouse Gene 1.0 ST Array
Each of the 28,853 genes on this array are represented by approximately 27 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3’-based expression array designs.

GeneChip® Rat Gene 1.0 ST Array
Each of the 27,342 genes is represented on the array by approximately 26 probes spread across the full length of the gene, providing a more complete and more accurate picture of gene expression than 3’-based expression array designs.

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Affymetrix Legacy 3' Arrays

The Legacy 3' arrays represent Affymetrix's traditional approach to gene expression analysis. Genes are represented by probe sets designed to the 3' end of a given target mRNA. The content of these arrays has not changed since the early 2000's.

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These legacy arrays were designed with Probe Sets (8-15 perfect match and mis-match probes per gene) being biased towards the 3' end of the gene.

Human Genome U133 Plus 2.0 Array
Comprised of more than 54,000 probe sets representing over 18,000 well-characterized human genes. The sequence clusters were created from the UniGene database (Build 133, April, 2001). An additional 9,921 new probe sets representing approximately 6,500 new genes were created from the UniGene database (Build 159, January, 2003).

GeneChip® Mouse Genome 430 2.0 Array
Comprised of over 45,000 probe sets representing over 21,000 well-substantiated mouse genes. The sequence clusters were created from the UniGene database (Build 107, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute for Genome Research (MGSC, April 2002).

GeneChip® Rat Genome 230 2.0 Array
Comprised of more than 31,000 probe sets, analyzing over 30,000 transcripts and variants from over 15,000 well-substantiated rat genes. The sequence clusters were created from the UniGene database (Build 99, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the rat genome from the Baylor College of Medicine Human Genome Sequencing Center (June 2002).

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Exon and Transcript Discovery

Expression profiling at the Exon level can be obtained from 1-2 µg of total RNA.

Affymetrix GeneChip Exon ST Arrays

A powerful tool to look at splice variants with Probe Sets returning data at the Exon level or as a summery per gene.

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GeneChip Exon Arrays provide the most comprehensive coverage of the genome and enable two complementary levels of analysis: gene expression and alternative splicing. Multiple probes per exon enable "exon-level" analysis and allow you to distinguish between different isoforms of a gene. This exon-level analysis on a whole-genome scale opens the door to detecting specific alternative splicing events that may play a central role in disease mechanism and etiology. You can also perform "gene-level" analysis, in which multiple probes on different exons are summarized into a single expression value of all transcripts from the same gene, enabling similar analysis workflows to 3'-gene expression.

GeneChip® Human Exon 1.0 ST Array
For the highest resolution expression analysis, the Human Exon ST array interrogates over 1 million exon clusters within the known and predicted transcribed regions of the entire genome. These arrays contain approximately four probes per exon and roughly 40 probes per gene.

GeneChip® Mouse Exon 1.0 ST Array
For the highest resolution expression analysis, the Mouse Exon ST array interrogates over 1 million exon clusters within the known and predicted transcribed regions of the entire genome. These arrays contain approximately four probes per exon and roughly 40 probes per gene.

GeneChip® Rat Exon 1.0 ST Array
For the highest resolution expression analysis, the Rat Exon ST array interrogates over 850,000 exon clusters within the known and predicted transcribed regions of the entire genome. These arrays contain approximately four probes per exon and roughly 40 probes per gene.

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Affymetrix GeneChip® Tiling Arrays

For discovery of unknown transcripts, human and mouse tiling arrays interrogating the entire genome can be utilized.

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