Shop All DNA & RNA Microarray Analysis

Axiom™ Genome-Wide EUR, 96 array plate (Applied Biosystems™)

Axiom™ Genome-Wide EUR 1 Array Plate is designed for European ancestry genome-wide imputation analysis with a focus in disease-associated genes. The arrays include additional markers that are specific to multiple HapMap populations. These arrays have the industry-s highest coverage of rare variants to replicate studies of specific loci and/or genes that have been identified in previous genome-wide association studies. The use of imputation enables a highly cost-effective, budget conscious alternative to other commercially available arrays.

We also offer the following Maximum Genome-Wide Coverage Arrays:

Axiom Genome-Wide ASI 1 Array Plate - The first array designed to maximize genomic coverage of rare alleles (MAF >1%) of a consensus East Asian (JPT+CHB) genome

Axiom Genome-Wide CHB 1 & CHB 2 Array Plate - The Genome-Wide CHB 1 Array Plate maximizes genomic coverage of common alleles (MAF >5%) of the Han Chinese genome. The Genome-Wide CHB 2 Array Plate is designed to target rare variants (MAF 2-5%) as a complement to Axiom Genome-Wide CHB 1 Array Plate. The Genome-Wide CHB 1 & CHB 2 Array Set Bundle enables the most comprehensive commercially available genome-wide coverage in CHB populations.

Axiom Genome-Wide PanAFR Array Plate Set - The first array to offer pan-African genomic coverage, with ˜90% genetic coverage of common and rare variants (MAF >2%) of the Yoruba (West African) genome and >85% coverage of common and rare variants (MAF >2%) of the Luhya and Maasi (East African) genomes. This array set also offers high genomic coverage (>85%) in admixed populations with West African ancestry.

Axiom Genome-Wide CEU 1 Array Plate Our first cost-effective array to maximize coverage of rare variants (MAF >1%) for European populations.

Axiom Genome-Wide EAS 1 Array Plate - East Asian ancestry

Axiom Genome-Wide AFR 1 Array Plate - Admixed population of West African and European ancestry

Axiom Genome-Wide LAT 1 Array Plate - Admixed population of Native American, European, and West African ancestry

Don't see what you-re looking for? Please contact us for assistance in choosing a product or to request an array design consulatation.

Benefits of Axiom Genome-Wide Population-Optimized Arrays:

Each array plate was designed to achieve ˜90% genomic coverage (r2 >0.8) in each target population, while covering markers with MAF of 1-5% in areas such as:
• Critical biological categories (e.g., coding SNPs)
• Biological processes (e.g., drug metabolizing genes)
• Disease categories (e.g., cardiovascular disease, cancer, immunity/inflammation, MHC, and CNS)
• Common and rare SNPs and insertions/deletions (indels) from the International HapMap Project, 1000 Genomes Project, and published disease associations
• Genotype-tested genomic content proven to give informative and reliable results
• Markers preselected for coverage in critical biological categories, such as coding SNPs, and biological pathways, such as drug metabolizing or cardiovascular genes
• High sample pass rate, call rate, and reproducibility
• Compatible with the Axiom 2.0 Reagent Kit, GeneTitan™ MC Instrument, automated or manual workflow, and Genotyping Console™ Software

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

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

Axiom™ Genome-Wide Human Origins 1 Array Plate (Applied Biosystems™)

Axiom Genome-Wide Human Origins 1 Array is a unique genotyping panel optimized for population geneticists that has been designed in collaboration with leading investigators, solely for studying human history, migration, and natural selection. The Array has genomic markers from 11 different modern human populations and archaic hominids. Each marker has been cleanly ascertained in samples of known ancestry, is well annotated and genotype-tested, enabling robust statistical analysis and avoiding the confounding biases that can be introduced by use of GWAS arrays for population genetic studies.

Benefits of Axiom Genome-Wide Human Origins 1 Array:
• Establishes a common set of ~629,000 SNPs that can be typed in diverse populations
• Includes markers from 11 modern human populations, making it a valuable tool for population geneticists and evolutionary biologists as well as for consumer genomic firms that offer ancestry testing
• SNPs were selected from sites with read coverage from Neanderthals, Denisovans, and chimpanzees, enabling the users to compare data from modern humans to archaic hominids and apes
• Includes SNPs that were cleanly ascertained and well-documented, overcoming the limitations and drawbacks of SNP arrays otherwise designed for use in medical genetics and GWAS studies
• Each marker is high-quality and genotype-tested for high sample pass rate, call rate, and reproducibility
• Supports diverse sample inputs including blood, saliva, cell line, and whole-genome amplified DNA
• Compatible with the Axiom 2.0 Reagent Kit, GeneTitan MC Instrument's automated or manual workflow, and Axiom Analysis Suite

Reference genotyped data was generated against 943 unrelated individuals from the Human HGDP-CEPH (Human Genome Diversity Cell Line Panel). This genotype dataset (Harvard HGDP-CEPH Genotypes) is available as Dataset 11 at http://www.cephb.fr/en/hgdp_panel.php

Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

GeneChip™ Porcine Gene 1.1 ST Array (Applied Biosystems™)

The GeneChip™ Porcine Gene 1.1 ST 24-Array Plate enables 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 up to 96 samples on a single array plate with the GeneTitan™ Instrument

Development of the Gene Expression Microarrays
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 Plates 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 Plates 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 up to 96 samples at the same time with minimal manual array handling

Proven performance from the industry standard
Gene 1.1 ST Array Plates 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.

Content profile
Gene 1.1 ST Array Plates 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™ Mouse Genome 430A 2.0 Array (Applied Biosystems™)

The GeneChip™ Mouse Genome 430A 2.0 Array is a single array representing approximately 14,000 well-characterized mouse genes.

The GeneChip™ Mouse Genome 430A 2.0 Array is a single array representing approximately 14,000 well-characterized mouse genes that can be used to explore biology and disease processes. New, reduced feature size means that you can use smaller sample volumes than the previous Mouse Expression Array 430A without compromising performance.

•Provides coverage of well-substantiated genes in the transcribed mouse genome on a single array
•Analyzes the expression level of approximately 14,000 well-characterized mouse genes
•The Power of the Probe Set - offering multiple independent measurements for each transcript delivering the greatest accuracy and reproducibility of any microarray platform
•All probe sets represented on the GeneChip™ Mouse Expression Array 430A are included on the GeneChip Mouse Genome 430A 2.0 Array

Array 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 then refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute for Genome Research (MGSC, April 2002).

Axiom™ Porcine Breeders Array, mini-96 format (Applied Biosystems™)

The Applied Biosystems Axiom Porcine Breeders Array includes markers focused on genomic selection of commercial porcine breeds, including Large White, Landrace, Duroc, and Pietrain. Core markers for the array were selected from markers on the Axiom Porcine High-Density Array that were evaluated using samples from multiple commercial and domestic breeds, including European wild boars. The inclusion of the most informative and well-performing markers from existing porcine arrays ensures that this array can be used for comparison with data generated by previous studies. With the availability of the Axiom Long Format Export Tool, which converts Axiom array data into long format, the array also provides the ability to continue existing projects with no change to the current bioinformatics infrastructure and pipeline.

Features include:
• 55,150 markers for genomic and trait selection
• 42 trait-specific markers selected by United States Department of Agriculture
• 64 parentage markers, including ISAG core markers
• Evenly distributed SNPs across the porcine genome
• Marker annotations aligned to Sscrofa10.2/susScr3 genome and dbSNP 148
• Targeted for commercial breeds including Large White, Landrace, Duroc, and Pietrain

Applications
• Parentage analysis
• Identification of economically important traits
• Genetic improvement of pure lines

Required products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument
Axiom Analysis Suite Software

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

The GeneChip™ Equine 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™ Maize Genome Array (Applied Biosystems™)

The GeneChip™ Maize Genome Array contains probe sets to detect transcripts from Zea mays, one of the most economically important crops in the world. The GeneChip Maize Genome Array, through examination of gene expression patterns of Zea mays, will enable researches to view the global transcription effects of external stimuli, such as fertilizers, pesticides, and growth conditions.

• The GeneChip Maize Genome Array provides comprehensive coverage of over 100 cultivars present in NCBI's UniGene data set, including the most highly represented strains: B73, Ohio43, W22, W23, W64A, and Black Mexican Sweet.
• The Maize Genome Array has 17,555 probe sets to interrogate approximately 14,850 Zea mays transcripts, which represent 13,339 genes (12,113 of which are represented in distinct UniGene clusters).
• Use the Power of the Probe Set and get multiple independent measurements for each transcript that delivers the greatest accuracy and reproducibility of any microarray platform.
• GeneChip System: richer data, sharper insights, better decisions.

Array Profile
The sequence information for this array was selected from NCBI's GenBank™ (up to September 29, 2004) and Zea mays UniGene Build 42 (July 23, 2004) databases. Probe sets on the array include 15 oligonucleotide pairs to detect each transcript, for added robustness and to facilitate detection of polymorphisms.

The Maize Genome Array was created within the GeneChip Consortia Program.

GeneChip™ Drosophila (melanogaster) Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ Drosophila (melanogaster) 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&trade Human Gene 1.1 ST Array Plate (Applied Biosystems™)

The Human Gene 1.1 ST 24-Array Plate and Trays provide the most accurate, sensitive, and comprehensive measurement of protein coding and long intergenic non-coding RNA transcripts.

Comprehensive design
Keeping pace with the research community's understanding of the transcriptome, we have designed whole-transcript arrays that include probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). These whole-transcript array designs provide a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile.

Research over the past 20 years has predominantly focused on protein-coding messenger RNA transcripts and their role in cellular processes, such as disease and development. Recently researchers have identified more that 10,000 transcripts (>200 bases) with little or no protein coding potential. Only a small fraction of these non-coding RNAs has functional annotations to date. However, there is ample evidence that differential expression of lincRNAs plays an important role in the genesis and progression of disease and that aberrant expression of these molecules have also been linked to cancer. Recent advancements in transcriptome profiling provided evidence of the association of lincRNAs in diverse range of cellular functions:

• Regulation of mRNA transcription
• Regulation of mRNA post-transcriptional modifications
• Occlusion/recruitment of transcription factor binding
• Activation and transportation of transcription factors
• Interaction with accessory proteins
• Guide protein complexes to locations in the genome

Key benefits
• Comprehensive coverage provides the best opportunity to discover interesting biology
   - >30,000 coding transcripts
   - 11,000 long intergenic non-coding transcripts
• Measure alternative splicing events/transcript variants with probes designed to maximize exon coverage
• Reproducible: Intra-lot correlation coefficient = 0.99

Content profile
Since the design of the Human Gene 1.1 ST Array Plates, there have been a massive number of new lincRNA that have been identified by the research community. In order to provide the research community with a tool that can measure the differential expression of this exciting class of RNA transcripts, we designed the Human Gene 2.1 ST Array Plates (sold separately). To supplement the lincRNA data contained in RefSeq, we used sequences and transcripts from lncRNA db (www.lncrnadb.com) and Broad Institute, Human Body Map lincRNAs and TUCP (transcripts of uncertain coding potential) catalog (http://www.broadinstitute.org/genome_bio/human_lincrnas/).

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

The GeneChip™ Rabbit 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.

Clariom™ D Assay, mouse (Applied Biosystems™)

Clariom™ D assays, mouse were previously known as GeneChip™ Mouse Transcriptome Array 1.0 (MTA 1.0.)
Accelerate your biomarker discovery from deep within the transcriptome with Clariom D assays, the next-generation of transcriptome-level expression profiling tools. Clariom D assays provide a highly detailed view of the transcriptome and offer the fastest path to actionable results. Available for human, mouse, and rat, Clariom D assays allow translational research scientists to generate high-fidelity biomarker signatures quickly and easily. Based on industry-leading microarray technology, the novel Clariom D assay design provides the most intricate transcriptome-wide gene- and exon-level expression profiles, including the ability to detect alternative splicing events of coding and long non-coding (lnc)RNA, in a single three-day experiment.

Expand your potential to discover novel, informative biomarkers.
The number of known transcribed genes has expanded rapidly in recent years providing more sources for actionable biomarkers, such as transcript variants and lncRNA, that can be used for clinical utility and advancing our understanding of disease mechanisms. Such biomarkers can be missed by lengthy, complex, and costly sequencing and targeted expression approaches, leading to irreproducible signatures and wasted time and money.

With full coverage of the transcribed genome including all known coding and non-coding splice variants, compatibility with clinical sample types, and flexible data analysis software, Clariom D assays are the premier tools for translational researchers performing complex expression biomarker discovery studies and wanting the fastest path to robust, clinically relevant, and actionable results.

Get all the data you need.
• Rapidly identify complex disease signatures using >214,000 transcripts sourced from the largest number of public databases, the most comprehensive coverage of the mouse transcriptome.
• Confidently detect genes, exons, and alternative splicing events that give rise to coding RNA and lncRNA isoforms.
• Detect rare and low-expressing transcripts otherwise not detected by common sequencing approaches.
• Go from data to insight in minutes with intuitive, highly visual, free analysis software.

When you have precious samples, get it right the first time.
• Utilize RNA from various sample types including blood, cells, and fresh/fresh-frozen tissues.
• Preserve sample integrity and reduce data variability with an assay that does not require a globin or rRNA removal step.

Clariom D solutions are available in a single sample (cartridge array) format for use on the GeneChip™ 3000 instrument system and include reagents and fast, simple Transcriptome Analysis Console (TAC) software to analyze and visualize global expression patterns of genes, exons, pathways, and alternative splicing events.

Get the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.

GeneChip™ Zebrafish Genome Array (Applied Biosystems™)

The GeneChip™ Zebrafish Genome Array can be used to study gene expression of over 14,900 Danio rerio transcripts. Sequence information for this array was selected from the following public data sources: RefSeq (July 2003), GenBank™ (release 36.0, June 2003), dbEST (July 2003), and UniGene (Build 54, June 2003). Probe sets on the array were designed with 6 oligonucleotide pairs to detect each transcript.

This array was designed in collaboration with representative members of the Zebrafish community and the National Institutes of Health.

Note: The DsRed probe set is provided with permission from BD Biosciences, and BD Biosciences grants users a limited license to utilize this probe set only on this array. Other uses of the probe set, or other DsRed sequence or sequences requires a license from BD Biosciences.

GeneChip™ Human Transcriptome Array 2.0 (Applied Biosystems™)

Designed to empower next-generation expression profiling studies, GeneChip™ Human Transcriptome Array 2.0 provides the ability to go beyond gene-level expression profiling by providing the coverage and accuracy required to accurately detect all known transcript isoforms produced by a gene.

View the data sheet for details on HTA 2.0 content and coverage.

Comprehensive exploration of the transcriptome
Research has shown that the tens of thousands of human genes contain hundreds of thousands of exons, which produce hundreds of thousands of different transcript isoforms. These transcript isoforms are produced when the exons of a gene may be included within, or excluded from, the final, processed messenger RNA produced from that gene. Until now, measuring and analyzing these transcript isoforms has been nearly impossible due to technology limitations, sample input requirements, and lack of analysis capabilities/tools.

Comprehensive transcriptome analysis requires combining transcript diversity from multiple data sources
Most genes produce multiple transcript isoforms, and measuring changes in the relative abundance of each isoform provides new insights into disease and biology. HTA 2.0 has combined multiple data sources to ensure you are able to independently analyze the broadest collection of transcript isoforms available.

Data sources used to design and annotate the array
RefSeq                                    Vertebrate Genome Annotation (Vega) database
Ensembl                                   MGC Mammalian Gene Collection (v10)
UCSC Known Genes               www.noncode.org
UCSC lincRNA transcripts        lncRNA db
Broad Institute, Human Body Map lincRNAs, and TUCP (transcripts of uncertain coding potential) catalog

Better data than 2 full lanes of sequencing
See the HTA 2.0 Flyer in the Documents Section below for additional information. HTA 2.0 provides superior accuracy and precision coupled with the most comprehensive view of the transcriptome.

Bioinformatics built into the array design; no assembly required
HTA 2.0 maximizes the amount of unique and valuable information possible by minimizing the conserved sequence synthesized on the array. This high-resolution array design contains an unprecedented >6.0 million probes covering coding transcripts and non-coding transcripts. 70% of the probes on this array cover exons for coding transcripts, and the remaining 30% of probes on the array cover exon-exon splice junctions and non-coding transcripts. The unparalleled coverage of this array provides the deepest insight into all coding and non-coding transcripts available.

Simple, fast, and free analysis solution
For the first time ever, HTA 2.0 coupled with Expression Console™ Software and TAC Software offers researchers a complete solution from data to decision making in minutes. This complete analysis solution is provided to all researchers using our expression arrays at no additional cost. In addition, HTA 2.0 data analysis is supported by the same analysis solutions and service providers being used for other expression array data.

Related Links
GeneChip™ Hybridization, Wash, and Stain Kit

Axiom™ Bovine-Ovine-Caprine Genotyping Array (Applied Biosystems™)

Axiom Bovine-Ovine-Caprine Genotyping Array (Axiom Ovicap Array) for animal genotyping was designed through the Affymetrix Expert Design Program. The array includes single nucleotide polymorphisms (SNPs) that were identified by the United States Department of Agriculture Agricultural Research Service (USDA ARS), International Sheep Genomics Consortium (ISGC), and the International Goat Genome Consortium for each of the three different species (bovine, ovine, and caprine, respectively. The content for caprine includes SNPs located within the four casein genes implicated in milk production.The array also includes markers for ovine and bovine parentage analysis.

Highlights
• Expert design: developed by key opinion leaders in the community
• Informative, including parentage markers from existing in-market arrays, allowing compatibility with previous studies
• A singe array for three species:
   - Bovine: 54,560 markers.
   - Ovine: 54,236 markers.
   - Caprine: 60,034 markers.

Applications
• Construction of high-resolution genetic maps
• Genetic improvement of pure lines
• Fine mapping of quantitative trait loci (QTL)
• Calculating breeding values
• Parentage analysis

Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument