Expression Analysis Arrays

Affymetrix provides a broad range of expression, whole genome, and custom arrays. Please visit http://www.affymetrix.com/products/arrays/index.affx for a complete, up-to-date listing of arrays available.

 

 

Released in early 2007, the new Human Gene 1.0 ST Array represents the next generation in gene expression profiling. Using a subset of probes from the Human Exon Array, the Human Gene 1.0 Array makes use of the Whole Transcript Target Protocol to interrogate along the entire length of 28869 well annoted genes. By using the Whole Transript method, 26 probes are used to identify each gene, allowing a much higher degree of accuracy over the previous generation's 3' approach.  The smaller format, made possible by the new 5um feature size, allows for reduced cost without reducing content.

 

 

All probe sets represented on the GeneChip® Human Genome U133 Set are identically replicated on the GeneChip® Human Genome U133 Plus 2.0 Array with the addition of 9,921 new probe sets representing approximately 6,500 new genes. The sequences from which these probe sets were derived were selected from GenBank®, dbEST, and RefSeq. The sequence clusters were created from the UniGene database, and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository, UC Santa Cruz Golden-Path human genome database, and the NCBI human genome assembly .

 

 

The Human Genome U133 (HG-U133) Set, consisting of two GeneChip® arrays, contains almost 45,000 probe sets representing more than 39,000 transcripts derived from approximately 33,000 well-substantiated human genes. The HG-U133A Array includes representation of the RefSeq database sequences and probe sets related to sequences previously represented on the Human Genome U95Av2 Array. The U133A Array analyses the expression level of 18,400 transcripts and variants, including 14,500 well-characterized human genes that can be used to explore human biology and disease processes. The HG-U133B Array contains primarily probe sets representing EST clusters.

 

 

The Human Genome U95 (HG-U95) Set, consisting of five GeneChip® arrays, contains almost 63,000 probe sets interrogating approximately 54,000 clusters derived from the UniGene database. Based on this build and associated annotations, the HG-U95Av2 Array represents approximately 10,000 full-length genes, while arrays B through E represent EST clusters.

 

 

The GeneChip® Human Genome Focus Array represents over 8,500 verified human sequences from the NCBI RefSeq database. Both the probe sets and normalization genes on the Focus Array are also represented on the Human Genome U133A Array. The Human Genome Focus Array is an ideal tool for researchers with limited resources and those just getting started with GeneChip technology. As your research efforts grow, you can directly compare data collected with the Human Genome Focus Array to the Human Genome U133 Set with no loss in quality.

 

 

The Mouse Genome 430 2.0 Array combines all of the probesets from the original Mouse Expression Set 430, onto a single array. By using a smaller feature size, you get the same content in half the package.

 

 

The GeneChip® Mouse Expression Set 430 is a powerful tool that analyzes the transcribed mouse genome in order to explore human biology and disease processes using the widely used mouse model organism. Coverage of over 39,000 transcripts on a single array.

 

 

The Rat Genome U34 Set monitors the expression of >24,000 genes and EST clusters. The sequences include all rat sequence clusters from the UniGene Database and supplemented with additional annotated gene sequences from Genbank. The Rat Genome U34 Set contains 3 arrays (RG-U34A, RG-U34B and RG-U34C). The A array contains probes derived from all full-length or annotated genes as well as thousands of EST clusters. The B and C arrays contain only EST clusters. In addition, all sequences analyzed on the Rat Toxicology U34 Array are also analyzed on the A array of this set.

 

 

The GeneChip® Yeast Genome S98 Array contains probe sets for approximately 6,400 S. cerevisiae (S288C strain) genes identified in the Saccharomyces Genome Database (December 1998). This array also contains approximately 600 additional probe sets representing putative open reading frames (ORFs) identified by SAGE analysis, mitochondrial proteins, TY proteins, plasmids, and a small number of ORFs for strains other than S288C.

 

 

Sequences chosen for your design can use genes, ESTs, or EST clusters. Custom arrays offer the flexibility of accessing information specific to your scientific areas of interest. Specific model organisms, proprietary sequence, or genes of interest can be used.

 

 

The GenFlex Tag Array uses nucleic acid hybridization to interrogate as many as 2000 individual reaction products from complex pooled mixtures. These allow custom designing of probe sets represented on arrays.

 

 

 

 

Images reproduced with permission from Affymetrix, Inc.

 

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