Shop All DNA & RNA Microarray Analysis

GeneChip™ Rat Genome 230 2.0 Assay (Applied Biosystems™)

The GeneChip™ Rat Genome 230 2.0 Assay is a powerful tool for toxicology, neurobiology, and other applications using rat as a model organism.

• Provides comprehensive coverage of the transcribed rat genome on a single array
• Comprised of more than 31,000 probe sets, analyzing over 30,000 transcripts and variants from over 28,000 well-substantiated rat genes
• Sophisticated bioinformatics tools available through the NetAffx™ Analysis Center to rapidly obtain biologically meaningful results
• Publicly available drafts of the rat genome and leading public rat databases were used to refine sequences and provide a higher quality of data output

Assay Profile
All probe sets represented on the GeneChip Rat Expression Set 230 are included on the GeneChip Rat Genome 230 2.0 Assay. Sequences used in the design of the GeneChip Rat Genome 230 2.0 Assay were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 99, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the rat genome from the Baylor College of Medicine Human Genome Sequencing Center (June 2002).

The GeneChip Rat Genome 230 2.0 Assay includes representation of the RefSeq database sequences and probe sets related to sequences and refined EST clusters previously represented on the GeneChip Rat Genome U34 Set.

Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Eleven pairs of oligonucleotide probes are used to measure the level of transcription of each sequence represented on the GeneChip Rat Genome 230 2.0 Assay.

GeneChip™ miRNA 4.1 Array Strip (Applied Biosystems™)

Many diseases, including cancer, are frequently described as diseases of disordered gene expression. It is estimated that more than 30% of protein translation of coding genes is regulated by miRNA. There is also a large amount of growing evidence suggesting miRNA interacts with long non-coding RNA in the signaling networks that regulate alternative splicing events, which impacts cellular processes such as apoptosis, proliferation, and differentiation – all of which have shown to be causative elements in diseases such as cancer.

Measuring the changes in these critical nodes of regulation is extremely important for deciphering the biological context of differentially expressed genes. This array design is a powerful tool for studying the role of small non-coding RNAs and their involvement in a broad spectrum of developmental and physiological mechanisms.

To account for known miRNAs, we are pleased to offer the miRNA 4.1 Array Strips within our growing catalog of miRNA arrays. This array offers updated content with the same high performance as the previous generation array.

Applied Biosystems™ miRNA 4.1 Array Strips help bring you closer to biology with:
Comprehensive coverage – Designed to interrogate all mature miRNA sequences in miRBase Release 20
Easily correlate miRNA results – Analysis files contain host gene ID, predicted and validated miRNA target genes, and clustered miRNA information
Easy analysis – Analyze human, mouse, rat, or every miRNA for all species using the same array
Low sample input – Requires as little as 130 ng total RNA
Simple, fast, and free analysis solutionCoupled with Expression Console™ Software and Transcriptome Analysis Console (TAC) Software, researchers have a complete solution from data to decision-making in minutes.

Related Links
GeneChip™ miRNA 3.1 Array Strip
B2 Control Oligo (3nM)
FlashTag™ Biotin HSR RNA Labeling Kits
FlashTag™ Biotin HSR RNA Labeling Kits
GeneAtlas™ Hybridization, Wash, and Stain Kit for miRNA Arrays
GeneAtlas™ Fluidics Tray Filling Guide for miRNA (laminated)
GeneChip™ Hybridization Control Kit

Axiom™ 2.0 Reagent Kit (Applied Biosystems™)

Axiom™ 2.0 Reagent Kits are designed for use with Axiom pre-designed and Axiom myDesign™ Arrays.

These kits are available in 96-, 384-, and 24- reaction formats. The kits include the reagents and control DNA required to produce hybridization-ready targets for Axiom pre-designed and Axiom myDesign Arrays. Axiom Reagent Kits can be used for genotyping of SNPs and indels on Axiom Genotyping Arrays and for the detection of microbial targets on Axiom Microbiome Arrays.

Clariom™ S Pico Assay, human (Applied Biosystems™)

Obtain a gene-level view of the human transcriptome with Clariom S Pico Assays for human samples. Clariom S Pico Assays serve as a next generation transcriptome-wide gene-level expression profiling tool, which allows for the fastest, simplest, and most scalable path to generating the results you need for your research. Based on industry-leading microarray technology, the novel Human Clariom S Assay design provides extensive coverage of all known well-annotated genes, compatibility with research sample types, scalable formats, and flexible data analysis software. Clariom S Pico Assays are the tools of choice to find expression biomarkers with known function as quickly, easily, and cost-effectively as possible.

Find answers, move on
Although the number of known transcribed genes has expanded rapidly in recent years, knowledge of the function of each gene is still evolving. Many genes and transcripts found in databases are poorly annotated or unannotated, which can complicate and prolong data analysis and interpretation. Human Clariom S Pico Assays focus on well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies and to quickly assess changes in key genes and pathways. With less time required for data analysis, Clariom S Pico Assays for human help researchers reach conclusions more rapidly.

Simple, swift biomarker discovery
• Accurately measure gene-level expression from >20,000 well-annotated genes to get to answers quickly.
• Choose a format that suits your throughput needs, processing from 1 to 192 samples a day.
• Go from data to insight in minutes with intuitive, highly visual, free analysis software designed for the biologist.

When you have precious samples, get it right the first time
• Generate robust expression profiles from as little as 100 pg of total RNA–as few as 10 cells.
• Utilize RNA from various sample types including blood, cells, and fresh/fresh-frozen or FFPE tissues.
• Preserve sample integrity and reduce data variability with an assay that does not require a globin or rRNA removal step.
• Save time and money with fully automated sample preparation options.

Clariom S solutions are available formats for single-sample (cartridge array) processing on the GeneChip™ 3000 instrument system and high-throughput automated processing (plate array) on the GeneTitan™ Microarray System, offering the flexibility to accommodate both small and large cohort studies. The complete solution comes with reagents and fast, simple Transcriptome Analysis Console (TAC) software to analyze and visualize global expression patterns of genes, pathways, and network interactions in minutes.

Get the truest level of gene-level expression
To generate robust gene-level expression, Human Clariom S Assays detect only the exons present in all known transcript isoforms expressed from a single gene locus-constitutive exons. This differs from other gene-level array technologies and shallow RNA-Seq, which provide either a biased view of gene expression or data that are complicated by variation in expression of transcript variants. By detecting only constitutive exons throughout the length of each known gene, Human Clariom S Assays generate the most accurate and truest measurement of gene-level expression available today.

Keeping biomarker identification across the transcriptome simple and swift, Clariom S Pico Assays for human provide you with the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.

Axiom™ HLA Typing Analysis Services (Applied Biosystems™)

High-resolution HLA typing on large-scale sample sets over thousands of markers
The human leukocyte antigen (HLA) complex is the human version of the major histocompatibility complex (MHC); this complex includes genes responsible for immune function. Variations in these genes affect immune response, including transplant rejection as well as disease susceptibility.

The highly polymorphic nature of this region and the prevalence of pseudogenes create challenges in traditional genotyping methods. Combining the use of direct genotyping with advanced imputation methods over the extended MHC region allows accurate HLA typing from SNP genotype data.

4-digit HLA types for 11 major loci
•With Axiom HLA Analysis 1.2, you will now be able to produce accurate HLA types from any genotyping data set from Affymetrix containing high-quality genotypes of a select number of predetermined markers.

Coverage of major HLA genes
•Determine the HLA type of 11 major MHC Class I and Class II loci (see Fig. 1) with 2-digit and 4-digit resolution.
•Integrate HLA typing with genotyping data for insight into immune system variation associations with genome-wide association studies (GWAS).

Direct genotyping and imputation
•Utilize an ancestry-enriched reference panel (see Fig. 2) for populations of interest to improve accuracy of HLA typing. The current reference panel is enriched for Caucasian populations.
•Leverage allele frequency patterns and linkage disequilibrium through imputation and direct genotyping in the extended MHC region to generate accurate HLA haplotypes.
•Overcome challenges in multi-ethnic populations for high-accuracy typing of HLA loci, see the publication on Multi-Population Classical HLA Type Imputation.

Easy-to-use software
•Select and import a genotyping file in the Axiom HLA Analysis window (see Fig. 3). The software supports our array genotyping output files in .vcf format.
•Analyze HLA loci of interest: select from 11 major MHC Class I and Class II HLA loci.
•Export selected loci results for all samples in "Full Report" for 4-digit or 2-digit resolution or for selected samples in "Per Sample Report."

HLA analysis of genotyping data from systems other than our genotyping arrays
Affymetrix Research Service Laboratory (ARSL) provides direct HLA analysis of any high-quality genotyping data set with sufficient coverage of markers within the extended MHC region. Please inquire for more information.

Download information and instructions
Download the latest version of the Axiom HLA Analysis 1.2 (64-bit) and install the software by following the installation instructions found in the Axiom™ HLA Analysis User Guide. This version is supported on Microsoft Windows®7 Professional (SP 1) with Quad Core Processor and can be used for analyzing data from Axiom™ Human Genotyping Solution and Genome-Wide Human SNP Array 6.0 genotyping arrays.

Please note that while any population can be analyzed with this software, lower accuracy may be observed for some loci and alleles depending on their frequency in the reference panel. The current reference panel is optimized for Caucasian populations; we are continuing to improve coverage of additional ethnicities to improve call rates and accuracy.

For a list of features and system requirements, please download the latest release notes.

Click here to download a copy of Axiom™ HLA Analysis software.
Download software

Additional software files and analysis solutions from Affymetrix
Axiom™ Analysis Suite
Affymetrix Power Tools (APT)
Genotyping Console™ (GTC) Software
SNPolisher

GeneChip™ Porcine Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ Porcine Gene 1.0 ST Arrays enable you to:
• Measure expression, across the entire gene, with higher resolution and accuracy than with classical 3'-biased microarray solutions
• Get accurate and reproducible data by using multiple independent measurements for each transcript

Background
Model and applied research organisms are valuable for comparative genomics research, evolutionary biology, and continue to play a critical role in deciphering the molecular mechanisms underlying human disease, and agricultural crop improvement. The GeneChip Gene 1.0 ST Arrays have been developed for the analysis of a wide range of model and applied research organisms. These organisms are the latest additions to the growing family of Gene Expression Microarrays offering whole-transcript coverage. The GeneChip Gene 1.0 ST Arrays were designed in collaboration with influential researchers, such as Alan Archibald, Head of the Division of Genetics and Genomics at the Roslin Institute (Porcine Array design), Leonard Zon, Director of Stem Cell Research Program, and Yi Zhou, Genomic Core Director of the Stem Cell Research Program at Children's Hospital Boston and Harvard Medical School in Boston (Zebrafish Array design).

Key benefits
Highest transcript coverage – get confident expression measurements of well-annotated content with up to 26 probes per transcript
Whole-transcriptome analysis – capture the transcript isoforms you may miss with 3'-biased expression designs
High data correlation – achieve high inter- and intra-array strip signal correlation (R >0.99)

Proven performance from the industry standard
GeneChip Gene 1.0 ST Arrays offer whole-transcriptome coverage for selected model and applied research organisms. All designs are based on the most recent genomic content and offer the highest probe coverage (up to 26 probes across the full length of the gene). This allows for accurate detection for whole-transcriptome microarray analysis and provides higher resolution and accuracy than other classical 3'-biased microarray solutions on the market. The whole-transcriptome analysis approach enables researchers to detect multiple transcript isoforms, including those that might be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.

Complete Reagents, Software and Instrumentation Solution for Optimal Array Performance
For convenience and complete support, the Gene 1.0 ST Array is provided as part of a comprehensive solution that includes GeneChip reagents and instrumentation:
• GeneChip WT Sense Target Labeling and Control Reagents. For detailed information on the procedure of the assay and performance information, please refer to the WT Sense Target Labeling Assay Manual
• GeneChip Fluidics Station 450 for complete walk-away array processing to obtain the highest levels of reproducibility
• GeneChip Scanner 3000 7G with the optional Autoloader for array image acquisition

We offer several tools to help you in your data analysis, including GeneChip Expression Console; software, the NetAffx Analysis Center, and the Integrated Genome Browser (IGB).

Expression Console Software is an easy-to-use application that enables probe set summarization as well as preliminary data quality evaluation. A simple workflow enables the user to quickly analyze the data (see figure). The resulting data can be further analyzed using software applications from GeneChip-compatible™ software providers.

The NetAffx Analysis Center, with regularly updated biological and functional annotations of probe sets, is the most comprehensive resource for array annotations and probe sequence information. Flexible query tools and external links allow researchers to drill down into genes and annotations of interest. This resource makes it easy to interpret microarray results and quickly design downstream studies.

Workflow
Researchers can also use IGB to visualize results in a genomic context. Genomic annotations including RefSeq sequences, SNPs and genomic locations from various sources can be viewed alongside microarray gene expression signal data.

The Gene 1.0 ST Array data analysis workflow is similar to the workflow for 3' gene expression analysis, utilizing Expression Console 1.1, third-party GeneChip-compatible software and annotation tools in the NetAffx Analysis Center and IGB.

Content profile
GeneChip Gene 1.0 ST Arrays provide the latest coverage of the transcribed genome. We use a comprehensive collection of information sources to design probes that interrogate up to 26 unique sequences of each transcript. Together these 26 unique 25-mer probes interrogate up to 650 bases per transcript. This high probe coverage across the entire transcript results in superior performance and data confidence as well as the ability to update your experimental data as the understanding of each genome and transcriptome grows.

Axiom™ Biobank Genotyping Array, 96 array plate (Applied Biosystems™)

The Axiom™ Biobank Genotyping Array was designed by and for thought leaders in the human genetics community for high-throughput, high-value genotyping of large sample cohorts to explore the genetics of complex diseases and translational research with a single comprehensive low-cost solution. This array contains one 96-array plate that allows for genome-wide genotyping of large sample collections such as those screened at biobanks, genome centers, and core labs.

GWAS
• Intelligent marker selection enables imputation of millions of additional SNPs
• The genomic content module of each array is optimized for specific populations and is customizable to any 1000 Genomes population study by adding additional markers of your choosing

• Immune function, including content covering the major histocompatibility complex (MHC), human leukocyte antigen (HLA), and killer-cell immunoglobulin-like receptors (KIR)

Pharmacogenomic markers
• Markers were selected to represent phases of absorption, distribution, metabolism, and excretion (ADME)

Inflammation and HLA
• Contains markers with evidence for association with autoimmune and inflammation
• Covers variants in genes in the HLA and KIR regions known to be important in immune response

Exome
• Rare, non-synonymous coding SNPs and indels in protein coding regions of the genome
• A majority of variants are rare with minor allele frequency (MAF) <1%
• Newly discovered loss-of-function content
• SNPs and indels identified from a sequencing initiative of 26,000 individuals
• Known disease-causing mutations

eQTLs
• Markers that have known associations to RNA expression traits
• Captures unique eQTLs contained in the NCBI Genotype-Tissue Expression (GTEx) eQTL database, GEUVIDAS project, and several other discovery projects

Human disease
• Blood phenotypes
• Cancer common variants
• Cardiometabolic

Choose your content
• Order the pre-designed array and customize it with markers of your choice
• Custom markers may be de novo or selected from the Axiom Genomic Database of genotype-tested markers

Please note: Reagent kits do not include plastic consumables required to run the assay on the Beckman Biomek™ FXP Target Prep Express System. Please contact us for a list of required plastic consumables.

GeneChip™ E. coli Genome 2.0 Array (Applied Biosystems™)

The GeneChip™ E. coli Genome 2.0 Array contains probe sets to detect transcripts from the K12 strain of E. coli and three pathogenic strains of E. coli. Using the E. coli Genome 2.0 Array, researchers can gain a comprehensive view of three pathogenic forms of E. coli while continuing ongoing research projects with the K12 strain.

The GeneChip E. coli Genome 2.0 Array includes approximately 10,000 probe sets for all 20,366 genes present in four strains of E. coli. Due to the high degree of similarity between the E. coli strains, whenever possible, a single probe set is tiled to represent the equivalent ortholog in all four strains. The GeneChip E. coli Genome 2.0 Array tiles probe sets over the entire open reading frame (ORF) of E. coli, includes over 700 intergenic regions, probes for various antibiotic resistance markers, and incorporates additional control and reporter genes from the previous generation E. coli array.

PrimeView Human Genome U219 Array Plate (Applied Biosystems™)

Proven performance from the industry standard
The PrimeView Human Genome U219 96-array Plate and Trays enables high-throughput expression profiling of 96 samples at a time using probe sets with an emphasis on established, well-annotated content. Sequences used in the design of the array were selected from the UniGene database 219, RefSeq version 36, and full-length human mRNAs from GenBank™.

The Human Genome U219 Array enables you to:
• Measure gene expression of more than 36,000 transcripts and variants per sample
• Get accurate and reproducible gene expression data by using multiple independent measurements for each transcript

Key benefits
• Enables increased productivity and efficiency through parallel processing
• Process 16, 24, or 96 samples on a single array plate
• Offers excellent gene expression accuracy and reproducibility
• Multiple independent measurements per transcript for increased confidence in your results
   - 11 probes per set for well-annotated sequences
   - 9 probes per set for the remainder
• Provides complete coverage of the annotated genome

Content profile
• The Human Genome U219 Array is comprised of more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through UniGene or via RefSeq annotation.
• The EST and mRNA sequences used in the design were clustered and assembled to create consensus sequences that represent alternative splice forms. Each assembly was then analyzed for orientation and alternative 3' end evidence.
• Content was chosen to cover all well-annotated genes and transcripts from RefSeq v36 and by leveraging all available EST and mRNA evidence that fall into the same clusters, to rigorously detect alternate 3' ends of those
well-annotated genes.
• More than 1,000 probe sets represent transcripts that have no official gene symbol in UniGene, but are based on predicted RefSeq sequences and UniGene clusters with good evidence of actual transcription.

GeneChip™ Citrus Genome Array (Applied Biosystems™)

The GeneChip™ Citrus Genome Array is designed specifically to monitor gene expression in Citrus. This array was created in collaboration with leading Citrus researchers through the Affymetrix GeneChip™ Consortia Program. The array contains 30,171 probe sets representing up to 33,879 Citrus transcripts based on EST sequences obtained from several Citrus species and Citrus hybrids. Because Citrus has relatively long generations and times-to-production, it will be especially useful for researchers to identify the genetic mechanisms critical to:

•High crop yield
•Disease and insect resistance
•Growth response to environmental factors

The GeneChip™ Citrus Genome Array provides a tool that enables researchers to elucidate these complex genetic traits in Citrus to determine how crop production can be improved. The array includes 46 probe sets representing several Citrus pathogens, and 60 probe sets representing various reporters, selectable markers, and transgenes. Also included are sequences from Poncirus and Poncirus crosses with Citrus hybrids.

The GeneChip™ Citrus Genome Array was designed in close collaboration with the Citrus Research Community as part of the Affymetrix™ GeneChip Consortia Program.

Axiom™ Transplant Genotyping Array (Applied Biosystems™)

Axiom™ Transplant Genotyping Array, one of the Axiom™ Biobank Genotyping Arrays, is designed for high-powered, genome-wide genotyping of large sample collections such as those screened at biobanks, genome centers, and core labs.

Axiom Transplant Genotyping Array was designed by and for thought leaders in the human genetics community for high-throughput, high-value genotyping of large sample cohorts to explore the genetics of complex diseases and translational research with a single comprehensive low-cost solution.

GWAS

•Intelligent marker selection enables imputation of millions of additional SNPs
•The genomic content module of each array is optimized for specific populations and is customizable to any 1000 Genomes population study by adding additional markers of your choosing

Transplant

•Content specific for transplantation research including functional variants, loss-of-function markers, and copy number
•Immune function, including content covering the major histocompatibility complex (MHC), human leukocyte antigen (HLA), and killer-cell immunoglobulin-like receptors (KIR)

Pharmacogenomic markers

•Markers were selected to represent phases of absorption, distribution, metabolism, and excretion (ADME)

Inflammation and HLA

•Contains markers with evidence for association with autoimmune and inflammation
•Covers variants in genes in the HLA and KIR regions known to be important in immune response

Exome

•Rare, non-synonymous coding SNPs and indels in protein coding regions of the genome
•A majority of variants are rare with minor allele frequency (MAF) <1%
•Newly discovered loss-of-function content
•SNPs and indels identified from a sequencing initiative of 26,000 individuals
•Known disease-causing mutations

eQTLs

•Markers that have known associations to RNA expression traits
•Captures unique eQTLs contained in the NCBI Genotype-Tissue Expression (GTEx) eQTL database, GEUVIDAS project, and several other discovery projects

Human disease

•Alzheimer's disease, including coverage of ApoE
•Blood phenotypes
•Cancer common variants
•Cardiometabolic

Choose your content

•Order the pre-designed array and customize it with markers of your choice
•Custom markers may be de novo or selected from the Axiom™ Genomic Database of genotype-tested markers

Please note: Reagent kits do not include plastic consumables required to run the assay on the Beckman Biomek™ FXP Target Prep Express System. For a list of required Beckman consumables, please see the Axiom™ 2.0 Automated Assay User Guide below.


Axiom™ 2.0 384HT Reagent Kit (Applied Biosystems™)

Axiom™ 2.0 384HT Reagent Kit includes all reagents to process one Axiom 384HT Array Plate.

GeneChip™ Rice Gene 1.0 ST Array, China (Applied Biosystems™)

The GeneChip™ Rice (Cn) Gene 1.0 ST Arrays enable you to:
• Measure expression, across the entire gene, with higher resolution and accuracy than with classical 3'-biased microarray solutions
• Get accurate and reproducible data by using multiple independent measurements for each transcript

Background
Model and applied research organisms are valuable for comparative genomics research, evolutionary biology, and continue to play a critical role in deciphering the molecular mechanisms underlying human disease, and agricultural crop improvement. The GeneChip Gene 1.0 ST Arrays have been developed for the analysis of a wide range of model and applied research organisms. These organisms are the latest additions to the growing family of Gene Expression Microarrays offering whole-transcript coverage. The GeneChip Gene 1.0 ST Arrays were designed in collaboration with influential researchers, such as Alan Archibald, Head of the Division of Genetics and Genomics at the Roslin Institute (Porcine Array design), Leonard Zon, Director of Stem Cell Research Program, and Yi Zhou, Genomic Core Director of the Stem Cell Research Program at Children's Hospital Boston and Harvard Medical School in Boston (Zebrafish Array design).

Key benefits
Highest transcript coverage – get confident expression measurements of well-annotated content with up to 26 probes per transcript
Whole-transcriptome analysis – capture the transcript isoforms you may miss with 3'-biased expression designs
High data correlation – achieve high inter- and intra-array strip signal correlation (R >0.99)

Proven performance from the industry standard
GeneChip Gene 1.0 ST Arrays offer whole-transcriptome coverage for selected model and applied research organisms. All designs are based on the most recent genomic content and offer the highest probe coverage (up to 26 probes across the full length of the gene). This allows for accurate detection for whole-transcriptome microarray analysis and provides higher resolution and accuracy than other classical 3'-biased microarray solutions on the market. The whole-transcriptome analysis approach enables researchers to detect multiple transcript isoforms, including those that might be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.

Complete Reagents, Software and Instrumentation Solution for Optimal Array Performance
For convenience and complete support, the Gene 1.0 ST Array is provided as part of a comprehensive solution that includes GeneChip reagents and instrumentation:
• GeneChip WT Sense Target Labeling and Control Reagents. For detailed information on the procedure of the assay and performance information, please refer to the WT Sense Target Labeling Assay Manual
• GeneChip Fluidics Station 450 for complete walk-away array processing to obtain the highest levels of reproducibility
• GeneChip Scanner 3000 7G with the optional Autoloader for array image acquisition

We offer several tools to help you in your data analysis, including GeneChip Expression Console; software, the NetAffx Analysis Center, and the Integrated Genome Browser (IGB).

Expression Console Software is an easy-to-use application that enables probe set summarization as well as preliminary data quality evaluation. A simple workflow enables the user to quickly analyze the data (see figure). The resulting data can be further analyzed using software applications from GeneChip-compatible™ software providers.

The NetAffx Analysis Center, with regularly updated biological and functional annotations of probe sets, is the most comprehensive resource for array annotations and probe sequence information. Flexible query tools and external links allow researchers to drill down into genes and annotations of interest. This resource makes it easy to interpret microarray results and quickly design downstream studies.

Workflow
Researchers can also use IGB to visualize results in a genomic context. Genomic annotations including RefSeq sequences, SNPs and genomic locations from various sources can be viewed alongside microarray gene expression signal data.

The Gene 1.0 ST Array data analysis workflow is similar to the workflow for 3' gene expression analysis, utilizing Expression Console 1.1, third-party GeneChip-compatible software and annotation tools in the NetAffx Analysis Center and IGB.

Content profile
GeneChip Gene 1.0 ST Arrays provide the latest coverage of the transcribed genome. We use a comprehensive collection of information sources to design probes that interrogate up to 26 unique sequences of each transcript. Together these 26 unique 25-mer probes interrogate up to 650 bases per transcript. This high probe coverage across the entire transcript results in superior performance and data confidence as well as the ability to update your experimental data as the understanding of each genome and transcriptome grows.

GeneChip™ Rabbit Gene 1.1 ST Array Strip (Applied Biosystems™)

The Rabbit Gene 1.1 ST Array Strips enable you to:
• Measure expression, across the entire gene, with higher resolution and accuracy than with classical 3'-biased microarray solutions
• Get accurate and reproducible data by using multiple independent measurements for each transcript
• Process four samples on a single array strip with the cost-effective GeneAtlas™ System

Background
Model and applied research organisms are valuable for comparative genomics research, evolutionary biology, and continue to play a critical role in deciphering the molecular mechanisms underlying human disease, and agricultural crop improvement. Gene 1.1 ST Array Strips have been developed for the analysis of a wide range of model and applied research organisms. These organisms are the latest additions to the growing family of Gene Expression Microarrays offering whole-transcript coverage. The Gene 1.1 ST Array Strip were designed in collaboration with influential researchers, such as Alan Archibald, Head of the Division of Genetics and Genomics at the Roslin Institute (Porcine Gene 1.1 ST array design), Leonard Zon, Director of Stem Cell Research Program, and Yi Zhou, Genomic Core Director of the Stem Cell Research Program at Children's Hospital Boston and Harvard Medical School in Boston (Zebrafish Gene 1.1 ST Array design).

Key benefits
Highest transcript coverage – get confident expression measurements of well-annotated content with up to 26 probes per transcript
Whole-transcriptome analysis – capture the transcript isoforms you may miss with 3'-biased expression designs
High data correlation – achieve high inter- and intra- array strip signal correlation (R >0.99)
Convenient format – process four samples at the same time with minimal manual array handling
Simple workflow – streamline your work, from target preparation through pathway analysis, and use intuitive software for data interpretation

Proven performance from the industry standard
Gene 1.1 ST Array Strips offer whole-transcriptome coverage for selected model and applied research organisms. All designs are based on the most recent genomic content and offer the highest probe coverage (up to 26 probes across the full length of the gene). This allows for accurate detection for whole-transcriptome microarray analysis and provides higher resolution and accuracy than other classical 3'-biased microarray solutions on the market. The whole-transcriptome analysis approach enables researchers to detect multiple transcript isoforms, including those that might be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.

Gene 1.1 ST Array Strips are designed exclusively for the GeneAtlas System – the first personal microarray system to allow four samples to be processed in parallel. It combines affordability, simplified workflow, ease of use, intuitive software, and excellent performance. For more information on the GeneAtlas System, please visit here.

Gene 1.1 ST Array Strips are supported by our easy-to-use and integrated data analysis software pipeline, which includes GeneAtlas Instrument Control Software for instrument processing of array strips, Partek™ Express™ Software for quality control and statistical analysis, and an Ariadne Pathway Studio™ Explore Software for pathway analysis, visualization, and other features that allow you to put your data into a biological context.

Please note that Pathway Studio Explore includes the ResNet™ Mammalian Database, which supports analysis of human, mouse, and rat sequences. The software also offers access to the ResNet Plant Database, which has gene definitions from Entrez for Arabidopsis, rice, and soybean, but other than Arabidopsis, only has relationship data for those species-specific genes. You may contact Ariadne to obtain the ResNet Plant Database on DVD free of charge. For all other organisms, contact Ariadne to explore possibilities for creating a custom database.

Content profile
Gene 1.1 ST Array Strips provide the latest coverage of the transcribed genome. We use a comprehensive collection of information sources to design probes that interrogate up to 26 unique sequences of each transcript. Together these 26 unique 25-mer probes interrogate up to 650 bases per transcript. This high probe coverage across the entire transcript results in superior performance and data confidence as well as the ability to update your experimental data as the understanding of each genome and transcriptome grows.

GeneChip™ HT RG-230 PM Array Plate (Applied Biosystems™)

Description: Proven performance from the industry standard
The GeneChip™ HT RG-230 PM 24-Array Plate enables high-throughput expression profiling of multiple samples using the same industry-standard content as the GeneChip Rat Genome 230 2.0 Array.*

The HT RG-230 PM Array Plate enables you to:
• Measure gene expression of more than 30,000 transcripts and variants from more than 28,000 well-substantiated rat genes on a single array
• Get accurate and reproducible data by using multiple independent measurements for each transcript

Key Benefits
• Enables increased productivity and efficiency through parallel processing
   - Process 16, 24, or 96 samples on a single array plate
• Same industry-leading performance and content as the Rat Genome 230 2.0 Array in cartridge format
   - Strong signal and correlation to previous designs
• Multiple independent measurements per transcript for increased confidence in your results
   - Interrogates more sequence than a single probe measurement
•Conveniently packaged
   - Individual 16-, 24-, and 96-array plates available
   - All processing trays included

Content Profile
Sequences used in the design of the array were selected from GenBank™ dbEST and RefSeq. The sequence clusters were created from the UniGene database (Build 107, June 2002) and refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute Center for Genome Research (MGSC, April 2002).

*The HT RG-230 PM Array Plate only retains perfect match (PM) probes from the cartridge design. Mismatch (MM) probes were removed.