Shop All DNA & RNA Microarray Analysis

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

GeneChip™ PrimeView™ Global Gene Expression Profile Assay (Applied Biosystems™)

The GeneChip PrimeView Global Gene Expression Profile Assay enables expression profiling with an emphasis on established, well-annotated content. More than 36,000 transcripts and variants are measured per sample. Sequences used in the design of the array were selected from RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™.

Features include:
• Cost-effective global confirmation of pluripotency marker expression
• Simple-to-use online analysis tool
• Published method with over 15,000 samples analyzed
• For use with GeneChip Scanner 3000

In addition, the PluriTest™ Assay now accepts PrimeView array data from GeneChip Scanner 3000.

About the PluriTest Assay
The PluriTest Assay is a bioinformatics assay that compares the transcriptional profile of a sample to an extensive reference set of >450 cell/tissue types, including 223 hESC lines, 41 iPSC lines, somatic cells, and tissues. The online analysis tool confirms pluripotency marker expression via two separate scores: Pluripotency and Novelty. The Pluripotency Score informs the user how strongly a model-based pluripotency signature is expressed in the samples analyzed. The Novelty Score indicates the general model fit for a given sample.

More information on the PluriTest Assay ›

Clariom™ S Pico Assay HT, mouse (Applied Biosystems™)

Obtain a gene-level view of the mouse transcriptome with the Clariom S Pico Assays HT for mouse. The Clariom S Pico Assays, mouse serve as a next generation transcriptome-wide gene-level expression profiling tool, which allow for the fastest, simplest, and most scalable path to generating actionable results. Based on industry-leading microarray technology, the novel mouse HT Clariom S Assay design provides extensive coverage of all known well-annotated genes, compatibility with clinical sample types, scalable formats, and flexible data analysis software. Clariom S Pico Assays HT 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. mouse HT 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 HT for mouse 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™ HT 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, mouse HT 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, mouse HT 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 HT for mouse provide you with the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.

GeneChip™ Wheat Genome Array (Applied Biosystems™)

By providing comprehensive coverage of the wheat genome, the GeneChip™ Wheat Genome Array is an important tool for plant genetics. With applications in crop improvement and gene expression studies, the Wheat Genome Array can be used to study nutritional value, crop yield, and effects of environmental stresses on wheat.

• The array contains 61,127 probe sets representing 55,052 transcripts for all 42 chromosomes in the wheat genome
• Use the Power of the Probe Set and get multiple independent measurements for each transcript that deliver the greatest accuracy and reproducibility of any microarray platform
• GeneChip System: richer data, sharper insights, better decisions

Array Profile
The GeneChip Wheat Genome Array offers researchers the most comprehensive and informative content for wheat gene expression research. The design of the array was based on public content from GenBank™ and dbEST. Experts in wheat research provided high-quality sequence data, and the arrays were designed and manufactured with our standard protocols.

Sequence information for the GeneChip Wheat Genome Array includes public content from Triticum aestivum UniGene Build #38 (build date April 24, 2004). Also included are ESTs from the wheat species T. monococcum, T. turgidum, and Aegilops tauschii, and GenBank full-length mRNAs from all species through May 18, 2004.

T. aestivum, the hexaploid bread wheat, contains three genomes; A, B, and D. Triticum turgidum, the tetraploid macaroni wheat species, contains the ancestral A and B genomes, whereas the diploids T. monococcum and A. tauschii contain near relatives of the A and D genomes, respectively. Thus, available content for the modern bread wheat species' three ancestral genomes is included.

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

GeneChip™ Human Gene 2.1 ST Array Plate (Applied Biosystems™)

The Human Gene 2.1 ST 16-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
• 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, the Human Gene 2.1 ST Array Plates was designed. 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™ miRNA 4.1 Array Plate (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 keep pace with the discovery of new and novel miRNA, we are pleased to offer the miRNA 4.1 24-Array Plates and Trays in our catalog of miRNA arrays. This product offers updated content with the same high performance as the previous generation array.

miRNA 4.1 Array Plates and Trays 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 solution – Coupled with Expression Console™ Software and Transcriptome Analysis Console (TAC) Software, researchers have a complete solution from data to decision-making in minutes

Related Links
GeneTitan™ Wash Buffers A and B Module
B2 Control Oligo (3nM)
Genetitan™ miRNA Array Holding Buffer
FlashTag™ Biotin HSR RNA Labeling Kits
FlashTag™ Biotin HSR RNA Labeling Kits
GeneTitan™ Hybridization Module for miRNA Plates
GeneChip™ Hybridization Control Kit

Axiom Canine Genotyping Array Set B (Applied Biosystems™)

Axiom™ Canine Genotyping Array Sets A and B were designed as part of the Expert Array Design program. The arrays offer access to approximately 1.1M markers that were discovered by the National Human Genome Research Institute of the National Institutes of Health. The content, distributed over two arrays, offers dense genotyping for validation and discovery of variants associated with specific phenotypes. All of the new content was discovered through high quality sequencing of over 300 dog genomes. The content on the array was aligned with the CanFam3 reference genome.

Canis Familiaris also serves as a model organism in understanding the human disease drug discovery process. Axiom canine genotyping arrays offer dense genotyping for isolating the variants associated with specific phenotypes. Understanding these genotypes allows breeders to anticipate the phenotypes of potential offspring, maximizing the potential to ensure dogs are mated with minimal inbreeding and to screen for possible genetic disorders.

Features of Axiom Canine Genotyping Array Set B
This array contains over 670,000 variants that are equally distributed across the chromosomes.

Learn more about Canine Array Set A ›

Applications of Axiom Canine Genotyping arrays
• Genome-wide association studies
• Veterinary research
• Direct-to-consumer applications
• As a model organism to help us understand complex human diseases such as cancer and diabetes

Data from the Axiom Canine Genotyping arrays are analyzed with Axiom Analysis Suite and Axiom CNV Summary Tools Software. Automated genotyping analysis with Axiom Analysis Software enables accurate genotyping of samples from various breeds including samples that exhibit in-breeding, a common occurrence in canine species.

Axiom™ Asia Precision Medicine Research Array Kit, 24-format (Applied Biosystems™)

The Axiom Asia Precision Medicine Research Array (PMRA) is a comprehensive imputation-aware genotyping array with more than 750,000 markers. The high-value content on the array is associated with both common and rare diseases for clinical research and disease association studies in East and South Asian populations. This array kit includes the 4x24-format array plate, as well as an Axiom 2.0 Reagent Kit and four Axiom GeneTitan Consumables kits.

The Asia PMRA is ideal for longitudinal cohort studies in precision medicine initiatives, bio-banking, translational research, direct-to-consumer applications, and clinical trials in drug discovery. Markers on the array were selected for the highest genomic coverage from 1000Genomes Project Phase III. Additional gene variants were chosen from broadly referenced public databases, including ClinVar, NHGRI-GWAS catalog, CPIC, PharmaGKB, and PharmaADME. A full description of the array is available in the content flyer.

Highlights:
• Genome-wide association studies (GWAS) imputation module of >540,000 markers from South and East Asian populations
• Broad coverage of common and rare variants associated with human health
• Minimum order size is one kit consisting of one 96-array plate, associated Axiom reagents, and GeneTitan MC consumables sufficient for 96 samples
• The array can be customized with 50,000 markers without affecting the imputation accuracy, or it can be fully customizable as required

Coverage:
• Genome-wide association study (GWAS) variants
• Evidence-based markers of potential clinical relevance (pharmacogenomics, ClinVar, ACMG, exclusive markers)
• Immune-related markers (human leukocyte antigen, killer immunoglobulin-like receptors, autoimmune and inflammatory)
• Functional variants (loss of function, expression quantitative trait loci, nonsynonymous variants, lung phenotypes)
• Disease-related variants (Alzheimer’s disease, cardiometabolic, neurological disorders, diabetes, cancer variants, cardiac variants, other rare variants)
• Tracking-related variants for tracking purposes (fingerprint and sample tracking , mitochondrial, Y chromosome)

GeneChip™ Human Tiling 2.0R Array Set (Applied Biosystems™)

The GeneChip Human Tiling 2.0R Array Set is designed for chromatin immunoprecipitation (ChIP) experiments.

Most comprehensive whole-genome array set for studying protein/DNA interactions in chromatin immunoprecipitation (ChIP) experiments.

•High-density 35 base pair probe spacing offers a more accurate view of protein/DNA interactions
•25-mer probes yield the most specific hybridization results available

Array Profile
The GeneChip™ Human Tiling 2.0R Array Set is designed for chromatin immunoprecipitation (ChIP) experiments. This set of seven arrays contains approximately 45 million oligonucleotide probes to interrogate the human genome. Each array in the set contains over 6.5 million perfect match probes to specifically interrogate genomic regions.

Sequences used in the design of the Human Tiling 2.0R Array Set were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker. The Human Tiling 2.0R Array Set is available either as a whole-genome set of seven arrays (P/N 900772), or individual arrays from the set may be purchased separately. The GeneChip™ Human Promoter 1.0R Array is a subset of the Human Tiling 2.0R Tiling Array Set, and the content was chosen specifically to analyze protein/DNA interactions within promoter regions.

Probes are tiled at an average resolution of 35 base pair, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10bp between probes. Oligonucleotide probes are synthesized in situ complementary to each corresponding sequence.

Instrument and Software Requirements
GeneChip™ Scanner 3000 7G
GeneChip™ Operating Software (GCOS) version 1.3 or higher

Clariom™ GO Screen Assay, human (Applied Biosystems™)

Enable high-throughput testing for gene expression research with the Clariom GO Screen Assay for human samples. The 384-format microarray solution provides a high-throughput, low-cost method to directly measure the expression of ~20,000 genes. The content, developed in collaboration with pharma, includes probes derived from the Gene Ontology gene collection and is ideally suited for secondary compound library screening and hit profiling. The Clariom GO Screen Assay serves as a gene-level expression profiling application that provides a fast, economical path to generate expression data for your research.

Semiconductor-based microarray synthesis technology means stable and reproducible results across large testing efforts. Clariom GO Screen data are compatible with our freely available Transcriptome Analysis Console (TAC) Software, which enables exploratory grouping analysis and identification of gene expression differences between clusters or groupings. The Clariom GO Screen Assay is the tool of choice for large testing efforts across ~20,000 genes.

High volume at low cost
Through close collaboration with leaders in the industry, the Clariom GO Screen Assay was designed to quickly assess changes in key genes and pathways in a high-throughput testing environment. The assay achieves higher throughput at a lower cost by incorporating direct lysis of samples, permitting researchers to bypass RNA purification for cell line applications. With a workflow that is fully enabled by Service Provider partnerships, and complimentary TAC Software, the Clariom GO Screen Assay helps researchers reach conclusions more rapidly.

Reliable gene expression
The Clariom GO Screen Assay targets the most constitutively expressed exons that are least affected by alternative splicing, providing the truest summary of gene expression available. The probes are designed from human genome assembly GRCh38 (hg38) from the Genome Reference Consortium. Each gene is assayed with three unique probes selected for their specificity and uniqueness, as well as their performance across empirical data. By selecting the genes associated with the GO (Gene Ontology) Consortium, the nomenclature and annotation provide a reliable source of material for functional assessment of the gene expression changes that have occurred. Inclusive of these ~20,000 genes are virtually all of the genes found in Wikipedia pathway, commercial panels for literature-associated “biomarker” genes, immunology markers, and inflammation markers. The Clariom GO Screen Assay for human samples provides the coverage you require, the analytical reproducibility you need, and the insights you want to act on your discoveries.

GeneChip™ Bovine Genome Array (Applied Biosystems™)

The GeneChip™ Bovine Genome Array can be used to study gene expression of over 23,000 bovine transcripts. The array is an ideal tool for researchers studying gene expression profiles in cattle. With the broadest representation of publicly available expressed sequence information, bovine researchers will be able to use this array to monitor genetic mechanisms regulating a variety of preferred traits, such as:

• Disease resistance
• Meat and dairy production
• Stress tolerance

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

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

The Mouse Gene 1.1 ST Array Strips enable you to perform low- and medium-throughput expression analysis with minimum hands-on time.

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 2,000 transcripts (>200 bases) in the mouse genome 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
• >28,000 coding transcripts
• >7,000 non-coding (include ˜2,000) 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 Mouse Gene 1.1 ST Array Strip, there has been a substantial increase in the structural and functional understanding of the mouse genome. This increase in knowledge includes the identification of a large number of long intergenic 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 have designed the Mouse Gene 2.1 ST Array Strip (sold separately). To supplement the lincRNA data contained in RefSeq, we use sequence and transcript data from lncRNA db (http://lncrnadb.com/).

GeneChip™ Human Transcriptome Pico Assay 2.0 (Applied Biosystems™)

Designed to empower next-generation expression profiling studies, GeneChip™ Human Transcriptome Pico Assay 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 Clariom™ D Transcriptome Human Transcriptome Pico Assay 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. Clariom™ D Transcriptome Human Transcriptome Pico Assay 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.

Bioinformatics built into the array design; no assembly required
Clariom™ D Transcriptome Human Transcriptome Pico Assay 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 solutionFor the first time ever, Clariom™ D Transcriptome Human Transcriptome Pico Assay 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, Clariom™ D Transcriptome Human Transcriptome Pico Assay 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

GeneChip™ Mouse Gene 1.0 ST Assay (Applied Biosystems™)

The GeneChip™ Mouse Gene 1.0 ST Array and GeneChip WT PLUS Reagent Kit is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile.

Since the design of the GeneChip Mouse Gene 1.0 ST Array, there has been a substantial increase in the structural and functional understanding of the mouse genome. This increase in knowledge includes the identification of a large number of long intergenic 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 GeneChip Mouse Gene 2.0 ST Array (sold separately). To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db (http://lncrnadb.com/).

Comprehensive Design of Gene Arrays
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 2,000 transcripts (>200 bases) in the mouse genome 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 of Gene Arrays
• Comprehensive coverage provides the best opportunity to discover interesting biology
   - >28,000 coding transcripts
   - >7,000 non-coding (include ˜2,000) 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

GeneChip WT PLUS Reagent Kit
The WT PLUS Reagent Kit uses a reverse transcription priming method that primes the entire length of each RNA transcript, including both poly-A and non-poly-A mRNA to provide complete and unbiased coverage of the transcriptome. The kit efficiently generates amplified and biotinylated sense-stranded DNA targets, avoiding loss of specificity due to antisense strand interference.

The WT PLUS Reagent Kit includes the amplification module coupled with GeneChip WT Terminal Labeling and Controls Kit for preparing hybridization-ready targets from 50 ng to 500 ng of total RNA.

Features and benefits:
• A complete target prep kit with proven sensitivity and specificity resulting from an optimized design for WT arrays
• A low sample input requirement of 50 ng. The kit works with a variety of sample types, including fresh-frozen tissues, cell lines, and whole blood
• StreamLined workflow with no ribosomal RNA depletion requirement or a globin reduction step for blood samples
• Opportunities to bundle WT arrays with WT reagents, offering exceptional cost savings
• Convenient single source for ordering and support

Axiom™ Precision Medicine Diversity Research Array Plus Kit, 96-format (Applied Biosystems™)

The Axiom Precision Medicine Diversity Research Array (PMD Research Array) is a comprehensive imputation-aware genotyping resource designed to drive deeper scientific insights into complex disease susceptibility, pharmacogenomics (PGx), and genetic factors underlying wellness and lifestyle in diverse populations to advance population genomics studies. It offers >850,000 markers selected for high genomic coverage from the 1000Genomes Project Phase III. Additional gene variants were chosen from broadly referenced public databases, including ClinVar, NHGRI-GWAS catalog, CPIC, PharmaGKB, and PharmaADME.

The PMD Research Array is ideal for bio-banking, longitudinal cohort studies in precision medicine initiatives, clinical and translational research, and clinical trials in drug discovery.

This array kit includes the 1x96-format array plate, Axiom 2.0 Plus reagents, and Axiom GeneTitan Consumables Kit. The Axiom 2.0 Plus reagents include primers for the gene-specific amplification step which enables access to alleles with known relevance to drug metabolism. For PMD Research Array offered with Axiom 2.0 reagents, please see Cat. No. 951962.

Highlights:
• Clinically relevant variants with emphasis on variants in ACMG59 genes
• Over 5,000 variants in over 1,100 genes of known PGx value including CPIC Level A variants
• Accurate genotyping of highly predictive markers in genes including CYP2D6, CYP1A2, CYP2B6, CYP2A6, SULT1A1, CYP2C19, and CYP2C8 that are in highly homologous regions with known relevance to drug metabolism. The array offers haplotypes and diplotypes for PGx variants in translation tables and includes Star Allele Nomenclature as part of the standard deliverables.
• Blood phenotyping variants for blood typing and bleeding disorders
• Customizable—the array can be customized with up to 50,000 markers without affecting the imputation accuracy, or it can be fully customized as required

Coverage:
• Genome-wide association study (GWAS) imputation module with ~800,000 markers across all ancestral populations
• Evidence-based markers for relevant variants including ClinVar variants for comprehensive coverage of ACMG59 genes
• PGx variants per Clinical Pharmacogenomics Implementation Consortium (CPIC) guidelines and Pharmacogenomics Knowledge Base (PharmGKB), variants in Very Important Pharmacogenes (VIP), and PharmaADME core variants. The ADME category includes alleles with known relevance to drug metabolism.
• Blood typing variants that can be used to genotype and identify rare blood donors, bleeding disorders, and blood conditions such as sickle cell
• Disease-related variants (Alzheimer’s, cancer, cardiac, cardiometabolic, diabetes, neurological disorder, and other rare variants)
• Immune-related markers (human leukocyte antigen, killer immunoglobulin-like receptors, autoimmune, and inflammatory)
• Functional variants (loss of function, expression quantitative trait loci, nonsynonymous variants, lung phenotypes)
• Ancestry, wellness, and traits-related variants—includes environment and lifestyle variants such as those associated with skin and eye pigmentation, caffeine consumption, cholesterol levels, weight and obesity; variants used for tracking (fingerprint and sample tracking, mitochondrial, Y chromosome)

Clariom™ S Assay, mouse (Applied Biosystems™)

Obtain a gene-level view of the mouse transcriptome with the Clariom S Assays for mouse. The Clariom S Assays, mouse serve as a next generation transcriptome-wide gene-level expression profiling tool, which allow for the fastest, simplest, and most scalable path to generating actionable results. Based on industry-leading microarray technology, the novel mouse Clariom S Assay design provides extensive coverage of all known well-annotated genes, compatibility with clinical sample types, scalable formats, and flexible data analysis software. Clariom S 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. mouse Clariom S 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 Assays for mouse 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, mouse 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, mouse 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 Assays for mouse provide you with the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.

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

The GeneChip™ Rice (Jp) 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™ Poplar Genome Array (Applied Biosystems™)

The GeneChip™ Poplar Genome Array is designed specifically to monitor gene expression in Poplar (Populus sp.). In total, the Poplar Genome Array contains more than 61,000 probe sets representing over 56,000 transcripts and gene predictions.

This array was created in collaboration with leading poplar researchers through the GeneChip Consortia Program and was designed based on content from UniGene Build #6 (March 16, 2005) and from GenBank™ mRNAs and ESTs for all Populus species up to April 26, 2005. Additional array design content was derived from the predicted gene set v1.1 from the Populus genome project (P. trichocarpa), led by the U.S. Department of Energy and based at the Joint Genome Institute (JGI), Walnut Creek, CA (download date May 4, 2005).

Instrument and Software Requirements
• GeneChip Scanner 3000, enabled for High-Resolution Scanning* or GeneChip Scanner 3000 7G
• GeneChip Operating Software (GCOS) v1.1.1, which contains the High-Resolution Scanning Update

* GeneChip Scanner 3000 High-Resolution Update is standard on all instruments shipped starting in September 2003 with serial number series 502. Previous versions, such as serial number series 501, will require the GeneChip Scanner 3000 High-Resolution Update, Catalog Number 00-0110, to be installed.

Genome-Wide Human SNP Array 6.0 (Applied Biosystems™)

With more than 1.8 million markers, including 946,000 probes for the detection of copy number variants and 906,600 SNPs, the Affymetrix™ Genome-Wide Human SNP Array 6.0 is a powerful tool for a variety of cytogenetic applications.

Pure Power and Performance

The new Affymetrix Genome-Wide Human SNP Array 6.0 features 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. The SNP Array 6.0 is the only platform with analysis tools to truly bridge copy number and association, including a new, high-resolution reference map and a copy number polymorphism (CNP) calling algorithm developed by the Broad Institute. The SNP Array 6.0 demonstrates industry-leading performance and represents more genetic variation on a single array than any other product, providing maximum panel power and the highest physical coverage of the genome.

The high price-performance value of the SNP Array 6.0 enables researchers to design association studies with larger sample sizes in the initial scan and replication phases, thereby significantly increasing the overall genetic power of their studies.

Affymetrix Cytogenetics Research Products

Affymetrix Copy Number Solution

Copy Number and LOH analysis tools in Genotyping Console

More than 906,600 SNPs:
•Unbiased selection of 482,000 SNPs; historical SNPs from the SNP Array 5.0
•Selection of additional 424,000 SNPs
           -Tag SNPs
           -SNPs from chromosomes X and Y
           -Mitochondrial SNPs
           -New SNPs added to the dbSNP database
           -SNPs in recombination hotspots

More than 946,000 copy number probes:
•202,000 probes targeting 5,677 CNV regions from the Toronto Database of Genomic Variants
•744,000 probes, evenly spaced along the genome
•Detected 10 times more copy number changes than other SNP/CN platforms
•Three times more coverage of CNPs; only platform with non-polymorphic probes
•GTC 3.0 leverages new, high-resolution reference map and CNP calling algorithm developed by the Broad Institute

More Information:
New Software Tools for Copy Number and LOH Analysis


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

The GeneChip™ Human Gene 1.0 ST Array provides the most accurate, sensitive, and comprehensive measurement of protein coding and long intergenic non-coding RNA transcripts. We also offer the GeneChip Human Gene 2.0 ST Array, which can measure differential expression of long intergenic non-coding RNA transcripts.

GeneChip™ Drosophila Genome 2.0 Array (Applied Biosystems™)

The GeneChip™ Drosophila Genome 2.0 Array is a microarray tool for studying expression of Drosophila melanogaster transcripts.

• Provides comprehensive coverage of the transcribed Drosophila genome on a single array
• Comprised of 18,880 probe sets, analyzing over 18,500 transcripts
• Sophisticated bioinformatics tools available through the NetAffx™ Analysis Center to rapidly obtain biologically meaningful results

Array Profile
Sequences used in the design of the GeneChip Drosophila Genome 2.0 Array were selected from Flybase version 3.1. Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Fourteen pairs of oligonucleotide probes are used to measure the level of transcription of each sequence.

Instrument Software Requirements
• GeneChip Scanner 3000, enabled for High-Resolution Scanning*
• GeneChip Operating Software (GCOS) v1.1.1, which contains the High-Resolution Scanning Update
*GeneChip Scanner 3000 High-Resolution Update is standard on all instruments shipped starting in September 2003 with serial number series 502. Previous versions, such as serial number series 501, will require the GeneChip Scanner 3000 High-Resolution Update, Catalog Number 00-0110, to be installed.

For more information, please review the data sheet (pdf, 700 KB).

Axiom™ Asia Precision Medicine Research Array Kit, 96-format (Applied Biosystems™)

The Axiom Asia Precision Medicine Research Array (PMRA) is a comprehensive imputation-aware genotyping array with more than 750,000 markers. The high-value content on the array is associated with both common and rare diseases for clinical research and disease association studies in East and South Asian populations. This array kit includes the 1x96-format array plate, as well as an Axiom 2.0 Reagent Kit and Axiom GeneTitan Consumables Kit.

The Asia PMRA is ideal for longitudinal cohort studies in precision medicine initiatives, bio-banking, translational research, direct-to-consumer applications, and clinical trials in drug discovery. Markers on the array were selected for the highest genomic coverage from 1000Genomes Project Phase III. Additional gene variants were chosen from broadly referenced public databases, including ClinVar, NHGRI-GWAS catalog, CPIC, PharmaGKB, and PharmaADME. A full description of the array is available in the content flyer.

Highlights:
• Genome-wide association studies (GWAS) imputation module of >540,000 markers from South and East Asian populations
• Broad coverage of common and rare variants associated with human health
• Minimum order size is one kit consisting of one 96-array plate, associated Axiom reagents, and GeneTitan MC consumables sufficient for 96 samples
• The array can be customized with 50,000 markers without affecting the imputation accuracy, or it can be fully customizable as required

Coverage:
• Genome-wide association study (GWAS) variants
• Evidence-based markers of potential clinical relevance (pharmacogenomics, ClinVar, ACMG, exclusive markers)
• Immune-related markers (human leukocyte antigen, killer immunoglobulin-like receptors, autoimmune and inflammatory)
• Functional variants (loss of function, expression quantitative trait loci, nonsynonymous variants, lung phenotypes)
• Disease-related variants (Alzheimer’s disease, cardiometabolic, neurological disorders, diabetes, cancer variants, cardiac variants, other rare variants)
• Tracking-related variants for tracking purposes (fingerprint and sample tracking , mitochondrial, Y chromosome)

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 HT, rat (Applied Biosystems™)

Obtain a gene-level view of the rat transcriptome with the Clariom S Pico Assays HT for rat. The Clariom S Pico Assays, rat serve as a next generation transcriptome-wide gene-level expression profiling tool, which allow for the fastest, simplest, and most scalable path to generating actionable results. Based on industry-leading microarray technology, the novel rat HT Clariom S Assay design provides extensive coverage of all known well-annotated genes, compatibility with clinical sample types, scalable formats, and flexible data analysis software. Clariom S Pico Assays HT 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. rat HT 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 HT for rat 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™ HT 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, rat HT 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, rat HT 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 HT for rat provide you with the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.

GeneChip™ miRNA 4.0 Assay (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 keep pace with the discovery of new and novel miRNA, we are pleased to offer the GeneChip™ miRNA 4.0 Array and Flashtag™ Bundle to our growing catalog of miRNA arrays. This array offers updated content with the same high performance as the previous-generation array.

GeneChip miRNA 4.0 Arrays 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 solution – Coupled with Expression Console™ Software and Transcriptome Analysis Console (TAC) Software, researchers have a complete solution from data to decision-making in minutes

GeneChip™ Porcine Genome Array (Applied Biosystems™)

The GeneChip™ Porcine Genome Array is an important tool for studying gene expression in the porcine animal model. Domestic pigs are an important food source and, because of the many anatomical and physiological similarities to humans, are also used extensively for medical research. In particular, the pig makes an excellent research model for wound repair, reproductive diseases, cancer, cardiovascular disease, and diabetes.

• The Porcine Genome Array contains 23,937 probe sets to interrogate 23,256 transcripts in pig, which represents 20,201 genes.
• 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 GeneChip Porcine Genome Array provides comprehensive coverage of the Sus scrofa transcriptome. The array contains 23,937 probe sets that interrogate approximately 23,256 transcripts from 20,201 S. scrofa genes.

The sequence information for this array was selected from public data sources including UniGene Build 28 (August 2004), GenBank™ mRNAs up to August 24, 2004, and GenBank porcine mitochondrial and rRNA sequences. Probe sets consist of up to eleven probe pairs. The array format consists of eleven micron features synthesized on the 100 format.

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

Instrument and Software Requirements
• GeneChip Scanner 3000, enabled for High-Resolution Scanning*
• GeneChip Operating Software (GCOS) v1.1.1 or higher, which includes the GeneChip Scanner 3000 High-Resolution Scanning Patch

*GeneChip Scanner 3000 High-Resolution Update is standard on all instruments shipped starting in September 2003 with serial number series 502. Previous versions, such as serial number series 501, will require the GeneChip Scanner 3000 High-Resolution Update, Catalog Number 00-0110, to be installed.

GeneChip™ Human Promoter 1.0R Array (Applied Biosystems™)

The GeneChip™ Human Promoter 1.0R Array is designed for chromatin immunoprecipitation (ChIP) experiments. The Human Promoter Array is a single array comprised of over 4.6 million probes tiled through over 25,500 human promoter regions. Sequences used in the design of the Human Promoter array were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker. Promoter regions were selected using sequence information from:

• 35,685 ENSEMBL genes (version 21_34d, May 14, 2004)
• 25,172 RefSeq mRNAs (NCBI GenBank™, February 7, 2004)
• 47,062 complete-CDS mRNA (NCBI GenBank, December 15, 2003)

Features and Benefits
• Single array to study protein/DNA interactions in over 25,500 human promoters
• High-density 35 bp probe spacing offers more probes per promoter for the most accurate view of protein/DNA interactions
• Extensive 10 kb coverage for each promoter region ensures the most comprehensive promoter analysis
• 25-mer probes yield the most specific hybridization results available
• Economical single array design you can use in your own lab

Probes are tiled at an average resolution of 35 bp, as measured from the central position of adjacent 25-mer oligos, leaving a gap of approximately 10 bp between probes. Each promoter region covers approximately 7.5 kb upstream through 2.45 kb downstream of 5' transcription start sites. For over 1,300 cancer-associated genes, coverage of promoter regions was expanded to include additional genomic content. This more extensive coverage spans from 10 kb upstream through 2.45 kb downstream of transcriptional start sites.

The array interrogates regions proximal to transcription start sites and contains probes for approximately 59 percent of CpG islands annotated by UCSC in NCBI human genome assembly (Build 34). The probes selected for the Human Promoter 1.0R Array are a subset of the probes used in the whole-genome ChIP array set, the GeneChip Human Tiling 2.0R Array Set (P/N 900772).

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

The GeneChip™ Rat Genome 230 2.0 Array 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

Array Profile
All probe sets represented on the GeneChip Rat Expression Set 230 are included on the GeneChip Rat Genome 230 2.0 Array. Sequences used in the design of the GeneChip Rat Genome 230 2.0 Array 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 Array 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 Array.

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

Axiom Genome-Wide Population-Optimized Human Arrays are genotyping panels that offer the best genetic coverage of rare and common variants for genome-wide disease association studies.

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

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

Other Maximum Genome-Wide Coverage Arrays
These array plates are designed to maximize whole-genome coverage of common and rare alleles, including SNPs within 10 kb of genes.
Axiom Genome-Wide CEU 1 Array Plate - The first cost-effective array to maximize coverage of rare variants (MAF >1%) for European populations
The Axiom Genome-Wide CHB 1 and CHB 2 Array Set Bundle - This set bundle contains the Axiom Genome-Wide CHB 1 Array Plate and the Axiom Genome-Wide CHB 2 Array Plate. The Axiom Genome-Wide CHB 1 Array Plate maximizes genomic coverage of common alleles (MAF >5%) of the Han Chinese genome. The Axiom 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 Axiom Genome-Wide CHB 2 Array Plate - This array is designed to target rare variants (MAF 2-5%) as a complement to Axiom Genome-Wide CHB 1 Array Plate. The Axiom Genome-Wide CHB 1 and CHB 2 Array Set Bundle enables the most comprehensive commercially available genome-wide coverage in CHB populations.

• The 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.

Please visit our NetAffx Analysis Center for more information on microarray analysis

Don't see what you're looking for? Learn how to create an Axiom myDesign™ Array Plate tailored for your study.

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

Clariom™ D Pico 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.
• 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.

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™ 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™ Feline Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ Feline 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™ Rice Gene 1.1 ST Array Strip, China (Applied Biosystems™)

The Rice (Cn) 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 HG-U133+PM Array Plate (Applied Biosystems™)

Description: Proven performance from the industry standard
The GeneChip™ HT HG-U133+ PM 96-Array Plate enables high-throughput expression profiling of multiple samples at a time using the same content as the industry-standard GeneChip Human Genome U133 Plus 2.0 Array*.

The HT HG-U133+ PM Array Plate enables you to:
• Measure gene expression of more than 47,000 transcripts and variants, including more than 33,000 well-characterized genes and UniGene clusters per sample
• Get accurate and reproducible data by using multiple independent measurements for each transcript

Scatter plots represent median MAQC B - MAQC A signals for each array type. The high correlation coefficients indicate similar biology is being observed (Fig. 1 and Fig. 2).

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 Human Genome U133 Plus 2.0 Array in cartridge format
   - Strong signal and fold change correlation to previous plate and cartridge 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 arrays were selected from GenBank™, dbEST and RefSeq. The majority of sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the University of California, Santa Cruz Golden-Path human genome database (April 2001 release).

An additional set of sequence clusters were created from Build 159 of UniGene (January 25, 2003) and refined by analysis and comparison with a number of other publicly available databases, including the Washington University EST trace repository and the NCBI human genome assembly (Build 31). Sequences were further analyzed for correct orientation, false priming, false clustering, alternative splicing and alternative polyadenylation.

*Two design changes were introduced with the GeneChip HT HG-U133+ PM Array Plate:
• Only perfect match (PM) probes from the cartridge design were retained while mismatch (MM) probes were removed.
• Empirical data was used to select the best-performing probes resulting in reducing the number of PM probes
   - 42,461 probe sets were reduced from 11 to nine probes
   - Six probe sets were reduced from 11 to 10

Axiom™ Cotton Genotyping Array (Applied Biosystems™)

Axiom Cotton Genotyping Array was designed through Affymetrix- Expert Design Program, and the markers on the array were selected from public databases in collaboration with the National Botanical Research Institute, India. The array includes 35,550 markers that were discovered in G. hirsutum and G. barbadense.

Axiom Cotton Genotyping Array can be used to analyze samples from different populations by adding up to 380,000 custom markers or by transferring polymorphic markers with 100%; fidelity on to the Axiom 384HT myDesign™ breeders array. The Axiom GT1 algorithm can automatically cluster, assign genotypes, and classify the markers into six different categories for easy visualization.

Features of Axiom Cotton Genotyping Array
Comprehensive content:
The Axiom Cotton genotyping array includes a total of 35,550 markers:
• 28,158 intra-specific markers identified using gene-enriched genomic sequences of G. hirsutum.
• 7,392 markers discovered using genome reduction methodology that is based on restriction site conservation (GR-RSC).
   - 5,286 markers were discovered in an inter-specific assembly of G. hirsutum and G. barbadense.
   - 2,106 markers are intra-specific to G. hirsutum.

Applications of Axiom Cotton Genotyping Array
Complex trait research and molecular breeding:
• GWAS and QTL mapping
• Identification of economically-important traits
• Improved accuracy marker-assisted selection programs through genomic selection

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Precision Medicine Diversity Research Array Kit, 96-format (Applied Biosystems™)

The Axiom Precision Medicine Diversity Research Array (PMD Research Array) is a comprehensive imputation-aware genotyping resource designed to drive deeper scientific insights into complex disease susceptibility, pharmacogenomics (PGx), and genetic factors underlying wellness and lifestyle in diverse populations to advance population genomics studies. It offers >850,000 markers selected for high genomic coverage from the 1000Genomes Project Phase III. Additional gene variants were chosen from broadly referenced public databases, including ClinVar, NHGRI-GWAS catalog, CPIC, PharmaGKB, and PharmaADME.

The PMD Research Array is ideal for bio-banking, longitudinal cohort studies in precision medicine initiatives, clinical and translational research, and clinical trials in drug discovery.

This array kit includes the 1x96-format array plate, Axiom 2.0 Reagents, and Axiom GeneTitan Consumables Kit. For PMD Research Array with Axiom 2.0 Plus reagents, please see Cat. No. 951961.

Highlights:
• Clinically relevant variants with emphasis on variants in ACMG59 genes
• Over 5,000 variants in over 1,100 genes of known PGx value including CPIC Level A variants
• Blood phenotyping variants for blood typing and bleeding disorders
• Customizable—the array can be customized with up to 50,000 markers without affecting the imputation accuracy, or it can be fully customized as required

Coverage:
• Genome-wide association study (GWAS) imputation module with ~800,000 markers across all ancestral populations
• Evidence-based markers for relevant variants including ClinVar variants for comprehensive coverage of ACMG59 genes
• PGx variants per Clinical Pharmacogenomics Implementation Consortium (CPIC) guidelines and Pharmacogenomics Knowledge Base (PharmGKB), variants in Very Important Pharmacogenes (VIP), and PharmaADME core variants. The ADME category includes alleles with known relevance to drug metabolism.
• Blood typing variants that can be used to genotype and identify rare blood donors, bleeding disorders, and blood conditions such as sickle cell
• Disease-related variants (Alzheimer’s, cancer, cardiac, cardiometabolic, diabetes, neurological disorder, and other rare variants)
• Immune-related markers (human leukocyte antigen, killer immunoglobulin-like receptors, autoimmune, and inflammatory)
• Functional variants (loss of function, expression quantitative trait loci, nonsynonymous variants, lung phenotypes)
• Ancestry, wellness, and traits-related variants—includes environment and lifestyle variants such as those associated with skin and eye pigmentation, caffeine consumption, cholesterol levels, weight and obesity; variants used for tracking (fingerprint and sample tracking, mitochondrial, Y chromosome)

GeneChip™ Chicken Genome Array (Applied Biosystems™)

The GeneChip™ Chicken Genome Array is a key research tool for the study of chicken genomics and chicken viral pathogens.

• This array contains comprehensive coverage of 32,773 transcripts corresponding to over 28,000 chicken genes. The Chicken Genome Array also contains 689 probe sets for detecting 684 transcripts from 17 avian viruses.
• Use the Power of the Probe Set and get multiple independent measurements for each transcript that deliver the greatest accuracy and reproducibility of any microarray platform.
• GeneChip System: richer data, sharper insights, better decisions.

Array Profile
Sequence information for the GeneChip Chicken Genome Array can be used to study gene expression of 33,457 chicken and viral transcripts. Species covered include Gallus gallus (chicken) and 17 avian viruses. Sequence information for this array includes public content from GenBank™, UniGene (Build 18; 15 May 2004), and Ensembl (version 1, released May 2004). Probe sets on the array were designed with 11 oligonucleotide pairs to detect each transcript.

Instrument and Software Requirements
• GeneChip Scanner 3000, enabled for High-Resolution Scanning*
• GeneChip Operating Software (GCOS) and the GeneChip Scanner 3000 High-Resolution Scanning Patch (provided separately)
*GeneChip Scanner 3000 High-Resolution Update is standard on all instruments shipped starting in September 2003 with serial number series 502. Previous versions, such as serial number series 501, will require the GeneChip Scanner 3000 High-Resolution Update, Catalog Number 00-0110, to be installed.

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

FFPE DNA Extraction Services (Applied Biosystems™)

Maximize cancer discoveries from FFPE samples with FFPE Express 2.0 Services. The FFPE Express Service offers high-quality copy number and genotype data with whole-genome coverage and high resolution in cancer genes for use with challenging FFPE samples.

This robust solution offers:

High-resolution, cancer-relevant, whole-genome coverage
    • Enhanced coverage developed in collaboration with world-renowned cancer scientists
    • Reveals the genomic complexity of cancer with:
       • Integrated analysis of whole-genome copy number changes and copy-neutral loss of heterozygosity (LOH)
       • Linear dynamic range: 0-60 copies
    • Interrogates the entire genome
    • More than 335,000 markers

High-quality data from 75 ng of input DNA
    • More than 6,000 samples processed by our Research Services Laboratory
    • Average pass rate of 92 percent
    • Successful on samples as old as 28 years

Advanced data analysis
    • We have partnered with BioDiscovery, an industry-leading software provider, to enable a more comprehensive data analysis solution.

Convenience and quality
Experience the convenience of our Research Services Laboratory—just send in your DNA to FFPE Express Services and visualize the results. Our Research Services Laboratory has processed thousands of the most challenging FFPE samples with a pass rate of greater than 92 percent, and our lab has the quality systems in place to handle your project with the highest standard of care and excellence. Take advantage of our expertise and receive data of the highest quality with the FFPE Express 2.0 Service.

Learn how scientists are using MIP technology and FFPE Express 2.0 Services
Molecular inversion probes: a novel microarray technology and its application in cancer research
View a list of publications using FFPE Express technology
Scientist spotlight, MIP technology reveals important copy number changes in pediatric cancers

PrimeView Human Gene Expression Array (Applied Biosystems™)

The PrimeView Human Gene Expression 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

Proven performance from the industry standard
The GeneChip PrimeView Human Gene Expression Array cartridge enables expression profiling using probe sets with an emphasis on established, well annotated content. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™.

Key benefits
• Offers excellent gene expression specificity and reproducibility
• Produces reliable results with multiple independent measurements per transcript — 11 probes per set for well-annotated sequences, 9 probes per set for the remainder
• Provides complete coverage of the annotated genome
• Highest transcript coverage in the industry with the most recent annotation — covers all well- annotated genes and transcripts from RefSeq

Content profile
• The PrimeView Human Gene Expression 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 RefSeq or via UniGene 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.

OncoScan™ CNV Assay (Applied Biosystems™)

The OncoScan CNV Assay is a whole-genome copy number microarray-based assay that enables the detection of relevant copy number variations (CNVs) such as copy number gain and loss, loss of heterozygosity (LOH), copy neutral loss of heterozygosity (cnLOH), ploidy, allele specific changes, break point determination, mosaicism, clonal heterogeneity, and chromothripsis. The assay has the same copy number coverage as the OncoScan CNV Plus Assay but does not include somatic mutation coverage. It provides the reagents for sample preparation from formalin-fixed paraffin-embedded (FFPE) tumor samples and microarray hybridization and staining. Designed to cover the entire genome as well as known cancer drivers, this assay is part of a comprehensive workflow that enables the generation of in-depth copy number data from as little as 80 ng of DNA per sample.

Key features of the OncoScan CNV Assay include:
Whole-genome copy number analysis—detect structural variants such as deletions, duplications, LOH, cnLOH, break point determination, ploidy, mosaicism and unbalanced translocations that are not well characterized by short read sequencing or targeted sequencing
Comprehensive coverage—whole-genome analysis of genes with established significance and importance in cancer and tumor progression as well as those with emerging evidence, helping to "future-proof" the technology investment and minimize revalidation burden
Complete flexibility—detect chromosomal arm aberrations, focal changes, LOH, and cnLOH in a single assay, helping reduce costs and processing times
Robust performance—obtain standardized results from lot to lot and operator to operator
Low sample input and fast results—get results in 72 hours from only 80 ng of FFPE-derived DNA
Rapid analysis—free software provides intuitive data visualizations for hundreds of samples in minutes
High-resolution copy number detection in priority cancer genes—accurate identification of very small (50–125 kb) to large (Mb) copy number variations

Coverage and performance
• 50–100 kb copy number resolution in ˜900 cancer genes
• 300 kb genome-wide copy number resolution outside of the cancer genes
• Genome-wide LOH detection including copy-neutral LOH detection
• High dynamic range of 10+ copies
• Demonstrated concordance with FISH-confirmed amplifications in key cancer genes including ERBB2 (Her2), EGFR, MDM2, MYC, and FGFR1

Analysis software
Data analysis is free of charge and easy using one of the three available softwares:
Chromosome Analysis Suite (ChAS), for copy number calls for a few samples
Nexus Express Software, for copy number and somatic mutation calls for tens to hundreds of samples

PharmacoScan™ Assay Kit, 24-Format (Applied Biosystems™)

Each PharmacoScan™ Assay Kit includes all necessary array plates, reagents, controls, and consumables to process 88 samples (and 8 controls) with the PharmacoScan Solution workflow.

PharmacoScan Solution is an ideal platform for translational researchers in healthcare, pharma, and research organizations looking to understand how genetic variations affect drug absorption, distribution, metabolism, and excretion (ADME).

By pre-emptively screening for risk factors on a microarray, users in research can precisely and reproducibly analyze 4,627 high- to low-evidence markers* within nearly 1,200 genes* in a single assay. The solution includes copy number variation calling and interrogating predictive markers in complex genes. Unlike solutions that analyze only high-evidence markers, PharmacoScan Solution presents a more comprehensive view for genotyping for pharmacogenomic risk.

Key Features:

• 4,627 markers in 1,191 genes of known pharmacogenomic value
• Comprehensive content of known pharmacogenomic value including Phase I and Phase II enzymes, regulatory/modifier genes, drug target genes, and Phase III/transporter genes
• Comprehensive content of known pharmacogenomic value including Phase I and Phase II enzymes, regulatory/modifier genes, drug target genes, and Phase III/transporter genes
• Genotyping of highly predictive markers in genes including GSTM1, CYP1A2, CYP2D6, CYP2B6, CYP2A6, SULT1A1, CYP2C19, and CYP2C9 that are in highly homologous regions
• Copy number variation (CNV) analysis for copy number states ranging from zero to three-plus for important ADME genes
• Star allele and translation for key genes

Content Description (Figure 1):

• PharmacoScan Solution broadly screens for pharmacogenomic risk factors for research and leverages content carefully selected from top global consortia.
• Core functional pharmacogenomic content including markers from Clinical Pharmacogenomics Implementation Consortium (CPIC) guidelines
• Pharmacogenomics Knowledgebase (PharmGKB) markers in Very Important Pharmacogenes (VIP)
• PharmGKB markers with clinical annotations
• PharmaADME core markers
• Nearly all markers from DMET Plus Solution (1,936 genetic variants across 231 relevant genes)
• Human leukocyte antigen (HLA) markers associated with drug reactions
• Markers for killer cell immunoglobulin-like receptors (KIR), human ancestry identification, and for sample ID and tracking
• Pharmacogenetics/ADME markers in genes targeted for European populations drawn from UK Biobank Axiom Array

Continuity of content for cohort studies and clinical trials

Drug development research and clinical trials are typically conducted over several years. These long-term efforts require a platform that can guarantee multiyear availability of 100% of the specific array content for the entire timeline of initiative. Unlike bead-based technologies that experience batch-to-batch variability and single nucleotide polymorphism (SNP) dropouts with each manufacturing batch, the photolithography manufacturing technology used in PharmacoScan array guarantees 100% fidelity and ensures all markers are present on every manufacturing batch for as long as necessary, addressing a major concern for such long-term efforts.

PharmacoScan Solution utilizes the same chemistry from the Axiom™ assay and GeneTitan™ Multi-Channel (MC) Instrument, a microarray platform preferred worldwide by genetic researchers for the efficient workflow, high throughput, and reproducibility of results critical to multiyear data collection and analysis efforts.

*Disclaimer: Number of variants genotyped by default as well as variant to gene mapping is refined over time.

GeneChip™ Guinea Pig Gene 1.1 ST Array Plate (Applied Biosystems™)

The GeneChip™ Guinea Pig Gene 1.1 ST 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.

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

Obtain a gene-level view of the mouse transcriptome with the Clariom S Pico Assays for mouse. The Clariom S Pico Assays, mouse serve as a next generation transcriptome-wide gene-level expression profiling tool, which allow for the fastest, simplest, and most scalable path to generating actionable results. Based on industry-leading microarray technology, the novel mouse Clariom S Assay design provides extensive coverage of all known well-annotated genes, compatibility with clinical 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. mouse 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 mouse 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, mouse 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, mouse 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 mouse provide you with the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.

GeneChip™ Soybean Gene 1.1 ST Array Plate (Applied Biosystems™)

The GeneChip™ Soybean 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™ 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™ Precision Medicine Research Array Kit (Applied Biosystems™)

The Axiom Precision Medicine Research Array (PMRA) is a broad and powerful genotyping resource for researchers driving deeper scientific insights into a variety of important health questions related to common and rare inherited diseases, genetic risk profiling, immune response, pharmacogenomics research, and many other areas associated with precision medicine. This array kit includes the 1x96-format array plate, as well as an Axiom 2.0 Reagent Kit and Axiom GeneTitan Consumables Kit.

Highlights:
• Genome-wide association study (GWAS) variants
• Clinically actionable variants
• Variants to cover immune function, autoimmune diseases, and inflammatory diseases and response
• Pharmacogenomic variants
• Functional variants
• Cancer common variants
• Blood phenotype variants
• Fingerprint/sample tracking variants

The PMRA may be customized with de novo markers or markers selected from the Axiom Genomic Database of genotype-tested markers.

GWAS variants
The array includes a genome-wide imputation grid with about 800,000 markers. The GWAS module has been designed to cover the five ancestral population groups [African (AFR), admixed American (AMR), East Asian (EAS), European (EUR), and South Asian (SAS) ancestry] with the highest mean r2 genomic coverage across all ancestral populations.

Clinically actionable variants
This module includes clinically relevant variants from ClinVAR and enables assessment of actionable genetic risk across a wide range of populations.

Blood phenotype variants
These include variants selected for evidence of association with various red blood cells and platelets, regulation of blood homeostasis, and red blood cell group phenotypes

Pharmacogenomic variants
The array prioritizes inclusion of pharmacogenomics variants per CPIC guidelines and variants contributing to star allelles.

Cancer common markers
Chosen from the list of published common variants associated with cancer phenotypes identified via GWAS, as per NHGRI-EBI GWAS catalog as well as some recently published and unpublished cancer-associated SNPs.

Immune-related markers
Markers were chosen to cover immune function as well as autoimmune diseases and inflammatory diseases and response. This includes human leukocyte antigen (HLA) and killer immunoglobulin-like receptor (KIR) markers and variants were included that show evidence for association with specific autoimmune and inflammatory disorders.

Functional variants
Includes loss of function markers selected from biobank arrays as well as human disease mutation and exome databases. Markers were included to support mapping functional non-coding variations to identify genetic markers associated with gene transcription variability and differential gene expression.

Fingerprint/sample tracking variants
Axiom PMRA includes over 300 variants for sample tracking and fingerprinting to eliminate any sample contamination during analysis. These variants have been successfully used in large biobank studies to ensure sample integrity during analysis.

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.

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

Axiom Genome-Wide Population-Optimized Human Arrays are genotyping panels that offer the best genetic coverage of rare and common variants for genome-wide disease association studies.

The Axiom Genome-Wide CHB 1 Array Plate maximizes genomic coverage of common alleles (MAF >5%) of the Han Chinese genome.

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

Other Maximum Genome-Wide Coverage Arrays
These array plates are designed to maximize whole-genome coverage of common and rare alleles, including SNPs within 10 kb of genes.
Axiom Genome-Wide CEU 1 Array Plate - The first cost-effective array to maximize coverage of rare variants (MAF >1%) for European populations
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
The Axiom Genome-Wide CHB 1 and CHB 2 Array Set Bundle - This set bundle contains the Axiom Genome-Wide CHB 1 Array Plate and the Axiom Genome-Wide CHB 2 Array Plate. The Axiom Genome-Wide CHB 1 Array Plate maximizes genomic coverage of common alleles (MAF >5%) of the Han Chinese genome. The Axiom 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 Axiom Genome-Wide CHB 2 Array Plate - This array is designed to target rare variants (MAF 2-5%) as a complement to Axiom Genome-Wide CHB 1 Array Plate. The Axiom Genome-Wide CHB 1 and CHB 2 Array Set Bundle enables the most comprehensive commercially available genome-wide coverage in CHB populations.The Axiom Genome-Wide CHB 2 Array Plate designed to target rare variants (MAF 2%-5%) can be accessed at 901842.
The 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.

Please visit our
NetAffx Analysis Center for more information on microarray analysis

Don't see what you're looking for? Learn how to create an Axiom myDesign™ Array Plate tailored for your study.

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

Axiom™ myDesign™ GW Array Plate, 675K-1.3M (Applied Biosystems™)

With the Axiom™ myDesign™ GW Array Plate, 675K-1.3M, you can create fully customizable genotyping array panels for genome-wide association, replication, fine mapping, and candidate gene studies. Based on the universal workflow of the Genotyping Solution, myDesign Arrays offer unprecedented scale and flexibility to design the most optimal array for your species of interest.

The Array Plate contains one 96-array plate containing between 675,000 and 1.3 million markers, in a 2x48 configuration (Minimum order size of 480 samples).An example template showing SNP submission can be found here.

The Expert Design Program enables a consortium of researchers to design genotyping arrays for their species of interest with de novo SNPs or SNPs from the Axiom™ Genomic Database. Consortia members interested in developing a new array can
contact us for design consultation.

myDesign Custom Arrays feature:
Low minimums – Custom arrays for as few as 480 samples; small repeat orders at attractive prices
Flexible content – Fully customizable panels focused on your SNPs of interest; multiple species on one array supported
Consistent supply – Get 100% identical SNP content at any time and for as long as your research necessitates
High precision – Every SNP is manufactured with a high degree of precision using photolithographic templates
More marker selection freedom – Interfering SNPs can be as close as 10 bases from candidate SNPs
Cost effective – High return on investment; attractive pricing without requiring large consortium volumes

myDesign Arrays are available in formats suitable for the appropriate number of markers:
384HT myDesign Custom Arrays – 1,500 to 50,000 markers per array. 384 arrays per plate
myDesign Targeted Genotyping (TG) Arrays – 1,500 to 200,000 markers per array for targeted genotyping in applications in genotype-trait association, genomic selection, and screening; 96 or 24 arrays per plate
myDesign Genome-Wide (GW) Arrays – 200,000 to 2.6 million SNPs for validation and genome-wide association studies; 96 or 24 arrays per plate; multiple array designs can be used for large studies

myDesign Genotyping Arrays include:
Axiom 2.0 Reagent Kit for automated or manual processing of up to 96 samples or Axiom 2.0 384HT Reagent Kit for processing 384 samples
• A fully automated workflow with validated robotics methods for target preparation and array processing based on the Beckman Biomek™ FXP Target Prep Express System and a GeneTitan MC Instrument

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

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

Clariom™ S Assay, rat (Applied Biosystems™)

Obtain a gene-level view of the rat transcriptome with the Clariom S Assays for rat. The Clariom S Assays, rat serve as a next generation transcriptome-wide gene-level expression profiling tool, which allow for the fastest, simplest, and most scalable path to generating actionable results. Based on industry-leading microarray technology, the novel rat Clariom S Assay design provides extensive coverage of all known well-annotated genes, compatibility with clinical sample types, scalable formats, and flexible data analysis software. Clariom S 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. rat Clariom S 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 Assays for rat 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, rat 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, rat 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 Assays for rat provide you with the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.

CytoScan™ Dx Assay Training Kits

CytoScan™ Dx Training Kit includes arrays, reagents, and control samples necessary to perform the CytoScan™ Dx Assay Training. For more information on CytoScan™ Dx Assay, please go here.

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

The GeneChip™ Marmoset 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™ 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

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).

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™ Medicago Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ Medicago 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™ C. elegans Genome Array (Applied Biosystems™)

This whole genome array represents 22,500 transcripts from Caenorhabditis elegans, a model organism for developmental biology and functional genomics.

Sequence information used to select these probe sets came from the December 05, 2000 Sanger Center database release and GenBank™ release 121. All sequences were functionally re-annotated by us for improved descriptions.

For more information, please review the package insert.

GeneChip™ Vitis vinifera (Grape) Genome Array (Applied Biosystems™)

The GeneChip™ Vitis vinifera Genome Array is the first array to provide comprehensive coverage of the V. vinifera genome.

Convenient one-array view
• 14,000 V. vinifera transcripts and 1,700 transcripts from other Vitis species can be interrogated
• Use the Power of the Probe Set and get multiple independent measurements for each transcript that deliver the greatest accuracy and reproducibility of any microarray platform
• GeneChip System: Richer data, sharper insights, better decisions

Array Profile
Oligonucleotide probes complementary to each corresponding sequence are synthesized in situ on the arrays. Sixteen pairs of oligonucleotide probes are used to measure the level of transcription of each sequence represented on the GeneChip Vitis vinifera (Grape) Genome Array. Sequences used in the design of the V. vinifera Genome Array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 7, Oct 2003).

Axiom™ Wheat HD Genotyping Arrays (Applied Biosystems™)

Axiom Wheat HD Genotyping Arrays were designed through Affymetrix Expert Design Program in a collaboration led by Dr. Keith Edwards, project leader and professor of Cereal Functional Genomics at the School of Biological Sciences and member of the Cabot Institute, University of Bristol.*

This product is part of a two array set. Array Plate B can be accessed at 550491 Axiom™ Wheat HD Genotyping Arrays.

The arrays were designed through a public sector pre-breeding program dedicated to accelerating the genetic improvement of modern wheat varieties. Select from one of two formats:
• Axiom; Wheat HD Genotyping Array, a high-density research tool with 817,000 SNPs in a two-array set in the 96-array plate format
• Axiom; Wheat Breeder's Genotyping Array, which includes 35,000 SNPs for worldwide elite wheat lines in the 384-array plate format

Markers on these arrays can be queried on the CerealsDB website (http://www.cerealsdb.uk.net/). This is a searchable database that was created by the Functional Genomics group at the University of Bristol, UK for the purpose of making SNP information available to the worldwide wheat community. It is updated regularly and contains:

• SNP statistics: Map location or contig code, 120 bp flanking sequences. MAF and PIC score are provided for SNPs on Axiom Wheat Breeder's Genotyping Array
• Variety comparison: Select two or more varieties of wheat to see the SNPs in common or SNPs that are different between them

*Expert Design Arrays are designed by key opinion leaders in the plant and animal genomics community and made available to the public for the purpose of advancing research and breeding programs. These arrays contain genetic markers and annotations that are provided by the original customer who designed the array and are therefore not updated by Affymetrix in the same manner as other catalog products. Through the program, Affymetrix continually provides agrigenomics researchers access to genotyping arrays that have been utilized by their peers in the research community.

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

GeneAtlas™ Hybridization, Wash, and Stain Kit for 3' IVT Arrays (Applied Biosystems™)

The GeneAtlas™ Hybridization, Wash, and Stain Kit contains pre-formulated solutions to process 3' IVT 4-Array Strips on the GeneAtlas System. The reagents are formulated into the fewest number of individual components possible, reducing preparation and handling steps. With enhanced performance, fewer required reagents, and a simple protocol, target preparation has never been so easy.

The GeneAtlas Hybridization, Wash, and Stain Kit includes two boxes. The first box contains sufficient amounts of the hybridization and stain components to process 15 four-array strips. The hybridization components include the solutions required for preparation of the hybridization cocktail containing the target. The stain components include Stain Cocktail 1 and 3, Stain Cocktail 2, and the Array Holding Buffer. These solutions are used during the processing of the arrays in the GeneAtlas System.

The second box includes Wash Buffer A and Wash Buffer B, also required for the processing of the arrays. There is sufficient Wash Buffer A and B to process 15 four-array strips.

The Stain Cocktail 1 and 3, Stain Cocktail 2, Array Holding Buffer, and Wash Buffers A and B are ready-to-use solutions. The hybridization cocktail is prepared by combining the 1.3X Hybridization Mix and nuclease-free water with the target prepared during the specific GeneAtlas 3' IVT Express target labeling assay.

The GeneAtlas Hybridization, Wash, and Stain Kit should always be stored at 2 to 8° C.