Affymetrix Expression Profiling


Ocean Ridge Biosciences offers gene expression analysis in human, mouse, rat, and other species using the Affymetrix GeneChip system. Recognized as the gold standard for microarrays, the Affymetrix GeneChip system is comprised of 25-mer oligonucleotide probes synthesized on quartz chips and assembled into cartridges. The use of multiple probes per exon and gene on microarrays produced in a well-developed and controlled manufacturing process offers high data reliability. For a detailed description of the Affymetrix GeneChip technology click here.

Affymetrix GeneChip users can take advantage of ORB's superior customer support and experimental design consultation without having to switch gene expression analysis platforms. ORB will also assist you with compiling and directly comparing your new Affymetrix data sets with archived data from previous Affymetrix studies. ORB provides service for all Affymetrix microarrays with a focus on the cost-effective "Gene ST" chips, which provide comprehensive information about alternative splicing in addition to data on gene-level changes in transcript abundance, giving researchers much of the same information that sequencing provides, but for less time, expense, and complexity. ORB's scientists are particularly experienced at obtaining quality data from unusual sample types and difficult or low-quantity samples.

Obtain pricing information for Affymetrix transcriptome-level arrays.

Clariom D assay (Datasheet)
Affymetrix’s Clariom D assay is designated as next-generation transcriptome-level expression analysis tool. This array uses a novel design to provide unprecedented coverage of transcriptome-wide gene- and exon- level expression profiles. Clariom D incorporates full coverage of all known coding and non-coding splice variants. The Clariom D assay is most comparable to RNA sequencing because it offers strand specific hybridization and the ability to detect low expressing transcripts, but unlike sequencing, this array does not require globin or rRNA removal. Clariom D assays are available for human, mouse, and rat. This array is validated with several common biospecimens, such as blood, cells, and snap-frozen, RNAlater-preserved, and FFPE tissues to facilitate the discovery of informative biomarkers.

Table I. Coverage of the Clariom D assay

Array content Human Mouse Rat
Genes (transcript clusters) >134,700 >66,100 >68,900
Transcripts >542,500 >214,900 >495,200
Exons >948,300 >498,500 >320,400
Exon-exon splice junctions >484,900 >282,500 >293,700
Total Probes >6,765,500 >6,022,300 >5,946,400

For further information see the ThermoFisher Scientific product page for the Clariom D array.

Gene 2.0 ST Arrays (Datasheet)
The Affymetrix GeneChip Gene 2.0 ST Array is an improvement to the existing GeneChip Gene 1.0 ST Array. The latest version 2.0 was re-designed in 2012 and therefore is based on very current annotation covering >30,000 coding transcripts and >11,000 long intergenic non- coding transcripts. These arrays are designed with a median of 21 unique probes per transcript. Each unique probe is 25 bases in length measuring a median of 525 bases per transcript. This design strategy combined with the ability to evaluate whole-transcriptome gene expression at the gene and exon levels allowing the study of transcript variants and alternative splicing events. ORB offers high quality hybridization and analysis service for all of Affymetrix GeneChip Gene 2.0 ST arrays with the assurance of superior performance and data confidence. We also provide pathway analysis using Gene Set Analysis Toolkit as described under 3' Gene Expression Analysis Arrays. For other custom analyses such as exon level analysis, please inquire. ORB continues to offer complete service for the previous version, GeneChip Gene 1.0 ST Array at the special pricing.


Special Offer for the processing of Gene 2.0 ST arrays

$385 per sample for complete gene expression profiling service on Gene ST arrays (minimum of 6 samples per order-- does not include cost of array chip). Please contact us to initiate service.


Table II. Coverage of GeneChip - Gene 2.0 ST Arrays

Array content Human Gene 2.0 ST Mouse Gene 2.0 ST Rat Gene 2.0 ST
Total RefSeq transcripts 40,716 35,240 28,407
NM – RefSeq coding transcript, well-established annotation 30,654 26,191 16,771
NR – RefSeq non-coding transcript, well-established annotation 5,638 3,391 442
XM – RefSeq coding transcript, provisional annotation 996 1,946 10,376
XR – RefSeq non-coding transcript, provisional annotation 3,428 3,712 818
lincRNA transcripts 11,086 ~2000 NA
RS (Entrez) gene count 24,838 26,515 23,586

For further information see the ThermoFisher Scientific product page for the Gene 2.0 ST array.

GeneChip Human Transcriptome Array 2.0 (Datasheet)
The Affymetrix GeneChip Human Transcriptome Array 2.0 is designed to measure and analyze the transcript isoforms produced by the different modes of alternative splicing. This high-resolution array contains >6.0 million distinct probes, of which 70% of the probes cover exons for coding transcripts, and the remaining 30% cover exon-exon splice junctions and non-coding transcripts. This array was designed with approximately ten probes per exon and four probes per exon-exon splice junction providing the deepest insight available into all coding and non-coding transcripts available. Affymetrix's TAC Software allows users to perform a variety of analyses on their data, such as perform statistical tests for differential expression, identify alternative splicing events, and visualize gene models. To view a sample data set from the human transcriptome array 2.0, click here. ORB offers hybridization services at competitive prices for the Human Transcriptome Array 2.0 with the assurance of complete, accurate, and reproducible data with every experiment.

Table III. Coverage of the Human Transcriptome Array 2.0

Array content Protein coding content Non-protein coding content
Genes (transcript clusters) 44,699 22,829
Transcripts 245,349 40,914
Exons 560,472 109,930
Exon clusters 296,058 82,444

For further information see the ThermoFisher Scientific product page for the Human Transcriptome 2.0 array.

Obtain pricing information for Affymetrix gene-level arrays.


Clariom S assay (Datasheet)
The Clariom S assay is based on a sub-set of probes derived from the Clariom D assay and provides a the most intricate transcriptome-wide gene- and exon-level expression profiles, including the ability to detect alternative splicing events of coding and long non-coding RNA, in a single experiment. Interrogating >20,000 genes, the Clariom S array is designed to select the best 10 probes from most constitutive exons in order to provide the best estimate of gene-level expression. Similar to other Affymetrix GeneChip solutions, the Clariom S is available for single-sample or cartridge array processing on the GeneChip® 3000 instrument system and is compatible with rapid, straight-forward analysis using Affymetrix's Transcriptome Analysis Console (TAC) Software.

Table IV. Coverage of the Clariom S assay

Array content Human Mouse Rat
Genes (transcript clusters) >20,800 >22,100 >22,900
Transcripts >337,100 >150,300 >129,800
Total Probes >211,300 >221,900 >231,800
Probes targeting genes >205,800 >221,300 >231,800

For further information see the ThermoFisher Scientific product page for the Clariom S array.


PrimeView (Datasheet)
The PrimeView Human Gene Expression array U219 3’ expression array was created using a recent genome annotation build (UniGene database 219 and RefSeq version 36) and is focused on high confidence gene content. The PrimeView array includes >553,000 probes to detect in total > 43,000 well established coding transcripts. This array was designed to provide the highest transcript coverage in the industry for well-annotated genes and transcripts from RefSeq. PrimeView produces reliable results obtained from multiple independent measurements per transcript using 11 probes per set for well annotated sequences and 9 probes per set for the remainder.

Table V. Coverage of PrimeView Array

Array content PrimeView Array
RefSeq probe sets (total) 48,658
UniGene probe sets not covered by RefSeq probe sets 419
Other probe sets (controls and other sequence sources) 318
Total probe sets 49,395

For further information see the ThermoFisher Scientific product page for the PrimeView array.

GeneChip 3’ Expression (Datasheet)
ORB offers high quality hybridization and analysis service for all of Affymetrix GeneChip 3' expression arrays. Affymetrix 3' expression arrays are available for a wide variety of species including human, mouse, rat and much more. With multiple probes per gene and built in control features, Affymetrix 3' expression arrays offer superior coverage of the genes in the model organism of interest. A list of all model organisms that are available for 3' microarray analysis, can be found here, and for additional details on 3' expression arrays for other model organisms, view Table VII below. To view a sample data set from 3' expression arrays for your organism of interest, click here.

Our comprehensive Gene Expression Analysis service package for 3' Expression Arrays includes sample quality control, labeling, hybridization, preliminary data processing, and quality control report of your array results. We also offer a statistical analysis package including ANOVA, principle component analysis, hierarchical clustering, fold-change calculations, and Power Point summary for a minimal additional charge. In addition, ORB provides pathway analysis using Web Gestalt software to identify pathways enriched with differentially expressed genes from your study.

Table VI. Coverage of 3' Expression Analysis Arrays

GeneChip System Genes Transcripts Probe Sets Probe pairs/
Probe set
Human Genome U133 Plus 2.0 Array (Datasheet) 38,500 ~47,400 ~54,000 11
Mouse Genome 430 2.0 Array (Datasheet) >34,000 >39,000 >45,000 11
Rat Genome 230 2.0 Array (Datasheet) 28,757 30,248 31,042 11

For further information see the ThermoFisher Scientific product page for the Gene 3' Expression array.

Table VII. 3' Gene Expression Analysis Arrays from Other Model Organisms

GeneChip System # of annotated gene / Unigene clusters # of transcripts # of probe sets Probe pairs/
Arabidopsis ATH1 Genome Array (Datasheet) >24,000 >22,500 11  
Bovine Genome Array (Datasheet) >19,000 ~23,000 24,072 11
Canine Genome 2.0 Array1 (Datasheet) >17,200 >18,000 42,870 11
Chicken Genome Array2 (Datasheet) 28,416 32,773 37,703 11
C. elegans Genome Array (Datasheet) 22,150 22,500 11  
Drosophila Genome 2.0 Array (Datasheet) >18,500 18,880 14  
Zebrafish Genome Array (Datasheet) ~14,900 15,509 16  

1, Covers >20,000 predicted genes. 2, Covers 684 avian viral transcripts.
For other organisms not listed here, please inquire.

Specialty arrays

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