The Affymetrix Expression Unit provides users with the necessary equipment for the hybridisation, staining and scanning of Affymetrix Expression arrays and offers support and technical advice to those users who request it.
Affymetrix expression arrays measure the expression signal at the genomic-transcriptomic level and/or at the exonic level of thousands of genes simultaneously from a given sample thanks to the specific RNA-DNA or DNA-DNA hybridisation technique.
These are high-density oligonucleotide microarrays that include thousands of probe sets (probesets) with sequences of the transcriptome of the species studied arranged on the base of the array. Each probe is an oligonucleotide (typically 25 nucleotides) complementary to the region under study represented thousands of times in microcells of the array.
The signal obtained from the hybridisation of the sample (labelled and fragmented RNA or DNA) with the oligo-probes arranged on the microarrays provides the measure of the expression level of the sample analysed.
Classically, Affymetrix microarrays place the oligonucleotide probes at the 3‘ end of the genes they interrogate and use the expression level at this location to estimate the expression level of the gene (3’ gene expression arrays).
In addition to these arrays, Affymetrix currently has arrays with probes distributed along the entire length of the gene (Whole-Transcript arrays) allowing the detection of expression in genes with a truncated 3‘ end (due to splicing, non-polyadenylation, genomic deletions or other events that alter the 3’ end of the gene). Likewise, within the Whole-Transcript arrays, Affymetrix designed a model of arrays, the so-called Exon Arrays, capable of identifying splicing events thanks to the fact that they present probes in each of the exons of the genes they interrogate.
Affymetrix has a vast catalogue of arrays for expression analysis of both genes and exons:
1. 3' Gene Expression Analysis Arrays
These are the classic Affymetrix arrays that allow expression studies at gene level thanks to perfect match and mismatch probes located at the 3' end of the gene. There are different types of 3' arrays, both in humans and in other model organisms in research (prokaryotes and eukaryotes) as well as in species of commercial interest.
The 3’ IVT Express kit is used, to process the samples with the 3‘ arrays, following the instructions described in the 3' IVT Express Kit User Manual.
2. Whole-Transcript Expression Arrays
These arrays allow expression studies with probes distributed throughout the entire gene, not only located at the 3‘ end, thus detecting expression in genes with a truncated 3’ end (due to splicing, non-polyadenylation, genomic deletions or other events that alter the 3' end of the gene). In addition, within the Whole-Transcript arrays, Affymetrix designed a model of arrays, the so-called Exon Arrays, capable of identifying splicing events thanks to the fact that they present probes in each of the exons of the genes they interrogate.
To process the samples with these arrays, the GeneChip® Whole-Transcript (WT) Sense Target Labelling and Control Reagents kit is used, following the instructions described in the WT Sense Target Labelling Assay manual.
Recently, Affymetrix and Ambion developed a new protocol for sample processing, The Ambion® WT Expression Protocol, which combines the Ambion WT Expression and GeneChip® WT Terminal Labelling kits.
- GeneChip® Command Console® Software.
- Expression Console® Software.
Platform for Sequencing and Functional Genomics
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