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affymetrix: expression at gene and exon level
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The UHNMAC is an Authorised Service Provider of the Affymetrix GeneChip® platform. Affymetrix offers the flexibility to study expression at the gene, exon or whole-genome level on a single system.

Gene–level Expression Profiling

  • Available for Human, Mouse and Rat in standard 3' GeneChip® catalog array format and any organisms in CustomExpress® array solutions.
  • Gene level profiling is used to investigate numerous biological processes such as tumour classification, regulatory pathways and validating drug targets.

Alternative splicing and Biomarker research at the Exon Level

  • One array, two functions - available for human, mouse and rat.
  • Enables most robust gene-level analysis with 30-40 probes representing most genes for higher sensitivity and genome-wide alternative splicing analysis on a single array. This adds a new dimension to your research by adding all coding genes on a single array.

GeneChip® 1.0ST Whole–Genome Level

  • The Gene 1.0 ST Array is a perfect match (PM)-only design with probes that hybridize to sense target.
  • Offers whole-transcript coverage. Each of the 28,869 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.
  • The small format of the array makes it a cost-effective expression profiling solution for new microarray users.

Expression service includes:

  • Total RNA Quality Checked with Agilent BioAnalyzer ($10 fee is charged if RNA quality deemed too low quality to proceed with the experiment)
  • cRNA generation
  • Hybridisation, washing and scanning of arrays
  • Generation of .dat, .cel, .chp and .rpt files
  • .dat, .cel and .chp files sent to customer (CD/DVD or FTP)
We also offer an optional data analysis service.

Key differences between Exon 1.0 ST and 3' Expression GeneChips:

The human arrays are used as an example; refer to the GeneChip Exon Array Design technical note and the Design and Performance of the GeneChip Human Genome U133 Plus 2.0 and Human Genome U133A 2.0 Array technical note.

Human Exon 1.0 ST Array
GeneChip Human Genome U133 Plus 2.0 Array GeneChip
Human 1.0ST Gene Array
Probe sets 1.4 million 54,000 760,000 (~2.5 probes/exon)
# perfect match
probes for each probe selection region
4 11 array contains perfect match probes only
subtraction strategy
median intensity of up to 1,000 background probes with the same GC content one mismatch probe for every PM probe estimated using a set of 20,000 generic background probes
Probe selection
region location
along the entire length of the transcripts mostly 3' end along the entire length of the transcripts
Probe selection
region length
median 123 bp 600 bp entire length
# probes for each RefSeq Sequence 30 - 40 11 26
Interrogated strand sense antisense sense
Labelling method random priming oligo T7 priming from the 3'-end random priming
Nuclei acid hybridised cDNA cRNA cDNA
Background detection surrogate probes perfect and mismatch probes perfect match only
Analysis software Expression Console™ Expression Console™ Expression Console™

Protocols used for 3' expression arrays and 1.0ST gene arrays:

  • 3' IVT Expression Labeling Protocol (Affymetrix)
  • Whole Transcript Labeling Protocol (Affymetrix)
  • Ovation™ RNA Amplification System V2 (NuGEN)
  • WT-Ovation™ Pico RNA Amplification System V2 (NuGEN)
  • FL-Ovation™ cDNA Biotin Module V2 (NuGEN)
  • Applause WT-Amp ST-RNA Amplification System (NuGEN)
Protocols used for Exon 1.0ST arrays:
  • Whole Transcript Labeling Protocol(Affymetrix)
  • WT-Ovation™ Exon Module (NuGEN)
  • WT-Ovation™ Pico RNA Amplification System V2 (NuGEN)
  • FL-Ovation™ cDNA Biotin Module V2 (NuGEN)
  • Applause WT-Amp Plus ST-RNA Amplification System (NuGEN)

Pricing: Download (Last updated: September 2011)
Please note that this pricing is for academic groups. Commercial customers should contact us for a quote.

Contact: Affymetrix Service at

Reduced cost for Test-3 arrays: Test-3 arrays are available at a much lower cost per array for studies involving NuGEN's WT-Pico kit for sample labelling. Contact us for details.

Gene expression profiling is also available on the Agilent and Illumina array platforms.