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Ocean Ridge Biosciences
Affymetrix Array Hybridization Services
 
 

ORB's Affymetrix Array Hybridization Services

Ocean Ridge Biosciences Logo Affymetrix Logo
Ocean Ridge Biosciences now offers gene expression analysis in Human, Rat, Mouse and other species using Affymetrix GeneChip system. Being recognized as the gold standard for microarrays, Affymetrix GeneChip system comprises of 25-mer oligonucleotide probes synthesized on quartz chips and assembled into cartridges. Pairs of perfect match and mismatch probes (probe set) and multiple probes per gene offer a high reliability on the Affymetrix microarray data. For a more detailed description of the Affymetrix GeneChip technology click here.
Affymetric Bench Setup
Affymetrix GeneChip users can now take advantage of ORB's superior customer support and experimental design consultation with out 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 will provide 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.
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 hybridization and analysis service package for 3' Expression Arrays includes sample quality control, labeling & data analysis using Affymetrix Expression Console. We also include a free of cost (for 6 or more samples) pathway analysis using GENMAPP and Gene Set Analysis Toolkit to identify pathways enriched with differentially expressed genes from your study. This is available for all model organisms listed on the GENMAPP or Gene Set Analysis Toolkit web server. To see if your model organism is covered, click here.
Affymetrix System Illustration
Table1: Coverage of GeneChip — Gene 1.0 ST 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
The Affymetrix GeneChip — Gene 1.0 ST Array System detects the expression of well-annotated genes, with approximately 26 probes (perfect match only) per gene designed to scan the entire length of the gene. The use of multiple probes covering the entire length of the gene ensures an accurate measurement of the gene expression than the conventional 3' biased gene expression analysis and also provides information about alternative splicing. To view a sample data set from Gene 1.0 ST Arrays, click here. ORB offers high quality hybridization and analysis service for all of Affymetrix GeneChip — Gene 1.0 ST arrays. We also provide pathway analysis of the differentially expressed genes as described under 3' Gene Expression Analysis Arrays.
Table2: Coverage of GeneChip — Gene 1.0 ST Arrays
Genechip System # of genes # of probe sets Probes per gene
Human Gene 1.0 ST Array 28,869 764,885 ~26
Mouse Gene 1.0 ST Array 28,853 770,317 ~27
Rat Gene 1.0 ST Array 27,342 722,254 ~26
The Affymetrix GeneChip — Exon 1.0 ST Array System scans the complete genome at an exon level, with 4 probes per exon and approximately 40 probes per gene. The Exon 1.0 ST Array System probe sets were designed based on Genbank & Refseq transcripts, ESTs, synteny maps and also predicted gene structures, and this ensures the most comprehensive coverage of the whole genome suited for studying well characterized genes and also novel genes. To view a sample data set from Exon 1.0 ST Arrays, click here. ORB offers complete service for all Affymetrix GeneChip — Exon 1.0 ST arrays. Our comprehensive package includes sample quality control, labeling & data analysis. Our data analysis provides gene level and also exon level analysis, which enables detection of alternative splicing and isoform detection. We also provide pathway analysis of the differentially expressed genes as described under 3' Gene Expression Analysis Arrays.
An Affymetrix Gene Chip
Table3: Coverage of GeneChip — Exon 1.0 ST Arrays
Genechip System # of probe
sets for transcripts
# of probe
sets for ESTs
# of probe
sets (in millions)
Probes
per gene
Total no. of features
Human Exon 1.0 ST Array 306,583 665,175 1.4 ~40 >5,500,000
Mouse Exon 1.0 ST Array 266,791 554,003 1.2 ~40 >4,500,000
Rat Exon 1.0 ST Array 195,943 211,451 1.0 ~40 ~4,000,000
Human X3P Array
Specifically designed in collaboration between Affymetrix & Arcturus, for whole genome profiling of formalin fixed, paraffin embedded samples
For a list of all the different specialty arrays from Affymetrix, click here.
3' Gene Expression Analysis Arrays (Other Model organisms)
Table4: 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

Ocean Ridge Biosciences
10475 Riverside Drive, Suite 1
Palm Beach Gardens, FL 33410
Updated 03-09-10
Phone: 561-427-7845
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