Affymetrix GeneChip

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Affymetrix

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.

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.

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, 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 GENMAPP and 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 GENMAPP or Gene Set Analysis Toolkit web server. To see if your model organism is covered, click here.

Table 1: Coverage of 3' Expression Analysis Arrays

For other model organisms, click here.

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Gene 1.0 ST Arrays (Datasheet)

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 using GENMAPP and Gene Set Analysis Toolkit as described under 3' Gene Expression Analysis Arrays. For other custom analyses such as exon level analysis, please inquire.

ORB is currently offering special pricing of $375 per sample for complete gene expression profiling service on Gene ST arrays (minimum of 6 samples per order). Please Contact Us to initiate service.

Table2: Coverage of GeneChip - Gene 1.0 ST Arrays

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Exon 1.0 ST Arrays (Datasheet)

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 predicted gene structures. This design 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, hybridization, preliminary data processing, and quality control report of your array results. We provide both gene level and exon level processed datasets generated using Expression Console software. Pathway analysis of the differentially expressed genes as described under 3' Gene Expression Analysis Arrays and custom analysis for detection of alternatively spliced genes are also offered.

Table3: Coverage of GeneChip - Exon 1.0 ST Arrays

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Specialty arrays

• Human X3P Array Specifically designed in collaboration between Affymetrix & Arcturus, for whole genome profiling of formalin fixed, paraffin embedded samples
• Human Genome U95 Set
• Murine Genome U74v2 Set
• Rat ToxFX 1.0 Array
• Rat Toxicology U34 Array For a list of all the different specialty arrays from Affymetrix, click here.

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3' Gene Expression Analysis Arrays from Other Model organisms

Table4: Coverage of Other Arrays

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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