Expression Analysis

The core facility provides expression analysis services for the Affymetrix, Agilent and Illumina platforms. We have a long experience in expression analysis and can offer extensive data analysis support and bioinformatics.

Affymetrix Arrays

Affymetrix provide four generations of expression arrays, Clariom D and S arrays, Transcriptome arrays (HTA) and 3' (IVT) arrays. Affymetrix Transcriptome arrays and Clariom D arrays are Affymetrix highest resolution micro arrays for gene expression profiling, the array design is based on 15 data sources and both coding and noncoding RNAs can be detected. The IVT 3' and ST arrays are applicable for a large number of species, Transcriptome and Clariom arrays are available for human, mouse and rat. The Affymetrix arrays are available in two formats: cartridge arrays for individual samples and Array plates, available in 16, 24 and 96 sample format.

Agilent Arrays

The Agilent Gene Expression Microarray Platform provides a flexible and affordable solution for gene expression studies. Catalog arrays across 30 species are available for whole-genome studies with superior 60-mer oligonucleotide probes, printed using SurePrint technology. The flexibility of this technology means that unlimited custom arrays can also be created, designed using Agilent's online application eArray. Small amounts of RNA can be accessed, as low as 10 ng total input RNA.

Agilent also supply SurePrint G3 Exon Microarrays, giving the possibility to get the same level of performance and sensitivity but with comprehensive coverage down to the exon level. Exon arrays are available for human, mouse, and rat to enable multiple experiments from the same dataset: gene-level, exon-level and splicing analysis.

Illumina Arrays

The Illumina expression beadarray probes are bound to beads and randomly distributed onto arrays. Each array is individual and provided with a decoding sequence specifying the position of each probe. For the moment expression analysis is possible with human, mouse and rat arrays containing a very high feature redundancy. Multi sample formats provide effective handling and lower sample pricing allowing bigger experimental scale than other systems. The sample requirement for the Ambion amplification and labelling protocol that we use are approximately between 100ng -1µg (Vmax - 10ul) of pure total RNA.

Probe Design Comparison