• Array Types and Quality Control Parameters

    Affymetrix Exon and Gene Arrays

    The Affymetrix Exon and Gene Arrays are the most recently released expression arrays. The Affymetrix Gene Arrays offer complete genome coverage, based on the most recent data. For each gene transcript there are at least 26 unique oligonucleotide probes, whose sequences are scattered across the exons of the entire gene.

    The Affymetrix Exon Arrays assay expression of every exon of every gene, allowing global analysis of alternate exon usage. Most investigators use the Affymetrix Gene 1.0 ST Arrays for their projects. Affymetrix has developed a Mouse, a Human and a Rat Gene 1.0 ST Array.

    Illumina BeadChip  

    The Illumina BeadChip is a commercially manufactured microarray that utilizes BeadArray technology.  These microarrays provide genome-wide gene expression data by using one unique 50-mer gene-specific sequence for each gene transcript.

    Affymetrix  3’ Expression Arrays

    The Affymetrix  3’ Expression Arrays also offer complete genome coverage for many organisms. For these arrays, gene transcript expression is determined by using 11 unique oligonucleotide probes, whose sequences are located near the 3’ end of the gene transcript.

    Remember that all samples must use the same target amplification procedure, and the same microarray type for a single project.

    Array Quality Control Parameters

    For each sample hybridized to an Affymetrix Expression array, a number of quality controls are checked after the data analysis file is created. An analysis of all quality control parameters indicate whether there was efficient target amplification, labeling and hybridization to the array.

    Evaluated expression data is then transferred back to the researcher via a CD or a network drive. Statisticians in the Biomedical Informatics Core are available to provide more in-depth analysis.