Affymetrix GeneChip

Affymetrix GeneChip


Ocean Ridge Biosciences offers gene expression analysis in Human, Rat, Mouse 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 more 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.

GeneChip Human Transcriptome Array 2.0 (Datasheet)

Affymetrix’ newly introduced GeneChip Human Transcriptome Array 2.0 has been 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 Human Transcriptome Array 2.0 with the assurance of complete, accurate, and reproducible data with every experiment.

Table 1: Coverage of Human Transcriptome Array 2.0

Array content Protein coding contentNon-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

Exons 339,146 0

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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 provides 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.

Table 2: Coverage of GeneChip - Gene 2.0 ST Arrays

Transcript coverage of the array Human Gene 2.0 ST Array Mouse Gene 2.0 ST Array Rat Gene 2.0 ST Array

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

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ORB is currently offering special pricing of $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.

ORB continues to offer complete service for the previous version, GeneChip Gene 1.0 ST Array at the special pricing.

3' Gene Expression Analysis Arrays

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. For a complete list of all available 3' expression arrays, click here. 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, labelling, 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 (no additional charge for order of 12 or more samples). This is available for all model organisms listed on the Gene Set Analysis Toolkit web server. To see if your model organism is covered, click here.

System Rev_630

Table 3: Coverage of 3' Expression Analysis Arrays

Genechip System # of genes # of transcripts # of 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 other model organisms, click here.

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3' Gene Expression Analysis Arrays from Other Model organisms

Table 4: Coverage of Other Arrays

Genechip System # of annotated genes / Unigene clusters # of transcripts # of Probe sets Probe pairs / sequence

Arabidopsis ATH1 Genome Array (Datasheet) >24000 >22,500 11

Bovine Genome Array (Datasheet) >19,000 ~23000 24,072 11

Canine Genome 2.0 Array Φ (Datasheet) >17,200 >18,000 42,870 11

Chicken Genome Array † (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

Φ also covers >20,000 predicted genes
† also covers 684 avian viral transcripts
For other organisms not listed here please inquire.

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Specialty arrays

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Contact Us

Ocean Ridge Biosciences, LLC
394 SW 12th Ave
Deerfield Beach, Florida 33442
Phone: 754-600-5128
Fax: 561-427-7845