Gene Expression Microarrays

The SMF performs gene expression microarray services using Affymetrix and Illumina platforms.   

Affymetrix has three main types of gene expression arrays, Exon 1.0 ST arrays ,Gene 1.0 ST arrays and 3’IVT Expression arrays. Human, mouse, rat and other eukaryotic organisms can be profiled using these arrays.  

  • Affymetrix Exon 1.0 ST is a whole-transcript (WT) array. This array detects both polyadenylated and non-polyadenylated transcript RNA samples as well as being able to detect alternative splicing sites.  It uses multiple probes per exon to enable an exon-level analysis and allows an investigator to distinguish between different isoforms of a gene.  In addition, multiple probes on different exons are summarized into an expression value of all transcripts from the same gene to offer gene-level analysis.  Exon Arrays provide the most comprehensive coverage of the genome.
  • Affymetrix Gene 1.0 ST -The Gene 1.0 ST Array uses a subset of probes from the Exon 1.0 ST array and covers only well-annotated content. Like the Exon 1.0 ST Array, “gene-level” analysis of multiple probes on different exons is summarized into an expression value representing all transcripts from the same gene.
  • The Affymetrix 3' IVT Express kit is used for visualization of 3' biased eukaryotic expression. This platform utilizes oligo-dT primers to produce cDNA, then in vitro transcription to generate biotin-labeled cRNA, which is hybridized to 3' targeting probes on the array.

Illumina provides human, mouse, and rat BeadArray-based technology arrays for whole-genome gene expression analysis.  Illumina gene expression arrays allow multiple samples to be processed ranging from six to twelve samples per one microarray.   This allows for higher throughput and cost savings over some other platforms.   

Illumina also offers the ability to detect partially degraded samples from archival human tissues such as formalin fixed paraffin embedded (FFPE) tissues using a modified protocol.