Shop All DNA & RNA Microarray Analysis

GeneChip™ miRNA 4.0 Array (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 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™ Plasmodium/Anopheles Genome Array (Applied Biosystems™)

The GeneChip™ Plasmodium/Anopheles Genome Array includes probe sets to over 4,300 Plasmodium falciparum transcripts and approximately 14,900 Anopheles gambiae transcripts. The Plasmodium/Anopheles Genome Array was developed in collaboration with the Malaria Research Institute at the Johns Hopkins Bloomberg School of Public Health.

P. falciparum sequence information for this array was collected primarily from PlasmodB (version 4.1, June 2003) and augmented with sequence information from GenBank™ and dbEST. Sequence information for A. gambiae was drawn primarily from Ensembl (Build 2, 2003) and augmented with sequence information from GenBank and dbEST.

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

Axiom™ myDesign™ GW Array Plate, 1.3M-2.0M (Applied Biosystems™)

With the Axiom™ myDesign™ GW Array Plate, 1.3M-2.0M, 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 1.3 million and 2 million markers, in a 3x32 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.

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™ Canine Gene 1.1 ST Array Plate (Applied Biosystems™)

The GeneChip™ Canine Gene 1.1 ST 24-Array Plate enables you to:
• Measure expression, across the entire gene, with higher resolution and accuracy than with classical 3'-biased microarray solutions
• Get accurate and reproducible data by using multiple independent measurements for each transcript
• Process up to 96 samples on a single array plate with the GeneTitan™ Instrument

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

Key benefits
Highest transcript coverage — get confident expression measurements of well-annotated content with up to 26 probes per transcript
Whole-transcriptome analysis — capture the transcript isoforms you may miss with 3'-biased expression designs
High data correlation — achieve high inter- and intra-array strip signal correlation (R >0.99)
Convenient format — process up to 96 samples at the same time with minimal manual array handling

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

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

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

The Mouse Gene 2.1 ST 24-Array Plate and Trays enables high-throughput expression profiling of 24 samples at a time using the same content as the industry-standard GeneChip™ Mouse Gene 1.0 ST Array

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 Plates (sold separately), 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 Mouse Gene 2.1 ST Array Plates. To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db (http://lncrnadb.com/).

GeneChip™ S. aureus Genome Array (Applied Biosystems™)

This GeneChip™ array is available through our Made-to-Order Program, which enables you to purchase selected custom array designs and previous-generation GeneChip arrays no longer available as catalog products. Learn more about ordering and support of GeneChip Custom Arrays.

For comprehensive monitoring of the relative mRNA abundance of S. aureus sequences.
The GeneChip S. aureus Genome Array is useful for studying the expression of sequences in the following four strains of Staphylococcus aureus: N315 (National Institute of Technology and Evaluation, Japan), Mu50 (National Institute of Technology and Evaluation, Japan), NCTC 8325 (University of Oklahoma), and COL (TIGR).

The array contains probe sets to over 3,300 S. aureus open reading frames. Additionally, the array also contains probes to study both forward and reverse orientation of over 4,800 intergenic regions throughout the S. aureus genome.

For more information, please review the data sheet (pdf, 114 KB).

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.

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

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

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

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

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

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

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

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

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

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

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

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

Axiom™ myDesign™ TG Array, 90K-200K (Applied Biosystems™)

With the Axiom™ myDesign™ TG Array Plate, 90K-200K, 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 90K and 200K markers, in a 1x96 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.

Clariom™ S Assay, human (Applied Biosystems™)

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

Find answers, move on
Although the number of known transcribed genes has expanded rapidly in recent years, knowledge of the function of each gene is still evolving. Many genes and transcripts found in databases are poorly annotated or unannotated, which can complicate and prolong data analysis and interpretation. Human Clariom S 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 human help researchers reach conclusions more rapidly.

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

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

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

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

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

GeneChip™ Medicago Transcriptome Assay (Applied Biosystems™)

GeneChip™ Medicago Transcriptome Pico Assay, which utilizes 100-2,000 pg of input RNA) is designed for agriculture researchers studying legume genomics and symbiotic relationships between nitrogen-fixing bacteria and plants. Coupled with our free, intuitive Transcriptome Analysis Console (TAC) Software, it is the fastest and most effective whole-transcriptome profiling approach for legume researchers who want results within a crop season.

• In a single experiment, measure expression changes of M. truncatula reference cultivars A17 and R108, and M. sativa (alfalfa).

• With the right results the first time, have confidence in low-level expression data with higher reproducibility than RNA-Seq.

• Within minutes, analyze and visually interpret the expression of genes, exons, and transcript isoforms.

For additional information, see the GeneChip Medicago transcriptome solution data sheet.

GeneChip™ Guinea Pig Gene 1.0 ST Array (Applied Biosystems™)

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

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

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

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

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

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

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

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

Workflow
Researchers can also use IGB to visualize results in a genomic context. Genomic annotations including RefSeq sequences, SNPs and genomic locations from various sources can be viewed alongside microarray gene expression signal data.
The Gene 1.0 ST Array data analysis workflow is similar to the workflow for 3' gene expression analysis, utilizing Expression Console 1.1, third-party GeneChip-compatible software and annotation tools in the NetAffx Analysis Center and IGB.

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

Axiom™ 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™ Canine Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ Canine 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™ HT HG-U133+PM Array Plate (Applied Biosystems™)

Description: Proven performance from the industry standard
The GeneChip™ HT HG-U133+ PM 24-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

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™ Barley Genome Array (Applied Biosystems™)

The GeneChip Barley Genome Array was designed and funded by the USDA-IFAFS Triticeae Improvement group (R. Wise, T. Close, G. Muehlbauer, R. Wing, and A. Kleinhofs) in collaboration with Affymetrix and the international barley community.

Contact us about ordering and support of GeneChip Made-to-Order arrays.

The GeneChip Barley Genome Array was designed and funded by the USDA-IFAFS Triticeae Improvement group (R. Wise, T. Close, G. Muehlbauer, R. Wing, and A. Kleinhofs) in collaboration with Affymetrix and the international barley community. A community effort resulted in a significant improvement to sequence quality through better clustering and derived annotations.

Sequences used for the Barley Genome Array design were collected from consortia labs submitting EST sequences and by collecting sequences from the NCBI/GenBank non-redundant database. Approximately 400,000 raw barley ESTs were submitted from 84 libraries, and about 350,000 survived quality pruning.

Stringent CAP3 clustering (-p95 -d60 -f100 -h50) was performed and resulted in 53,030 “unigenes” (26,634 contigs and 26,396 singletons). 25,500 contigs and singletons had complete 3’ ends suitable for array design (see HarvEST Triticeae v0.95 and higher). This included all 1,145 known barley genes (including alleles) from the NCBI non-redundant database. The nonredundant cloned gene set was integrated with the EST clusters to aid in scaffolding the ESTs and also to retrieve any rare interesting genes (e.g., Mla, Rar1, Sgt1, Rpg1) for inclusion on the GeneChip microarray. After pruning against an enhanced Triticeae repeat element database (TREP), the exemplar set of 25,500 contigs and singletons was submitted to Affymetrix for initial computation. Annotation is available in NetAffix Data Analysis Center and from HarvEST.

Potential applications for the barley array include analysis of malting properties, pest and disease control, abiotic stress tolerance, nutritional characteristics, and reproductive development. The GeneChip Barley Genome Array was released in June, 2003.

Visit BarleyBase, a USDA-funded public repository for plant microarray data.

GeneChip™ Cotton Genome Array (Applied Biosystems™)

The GeneChip Cotton Genome Array is a single GeneChip brand array comprised of 239,777 probe sets representing 21,854 cotton transcripts.

The GeneChip™ Cotton Genome Array is a single GeneChip brand array comprised of 239,777 probe sets representing 21,854 cotton transcripts. Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq, and were created from the Gossypium hirsutum UniGene database (Build 2, August 2006) and the Gossypium raimondii UniGene database (Build 2, September 2005). These sequences derive from the many contributors from the Cotton Community. Some select sequences were generously made publicly available prior to publication by a group within the Cotton Community specifically to enhance the design of the GeneChip Cotton Genome Array.

The GeneChip™ Cotton Genome Array is based on EST sequences from four species of Cotton: Gossypium hirsutum, Gossypium raimondii, Gossypium arboretum, and Gossypium barbadense. The Array was designed in close collaboration with the Cotton Research Community as part of the GeneChip Consortia Program.

For more information, please review the Package Insert (pdf, 209 KB).


GeneChip™ C. elegans Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ C. elegans 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™ Chicken Gene 1.0 ST Array (Applied Biosystems™)

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

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

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

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

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

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

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

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

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

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

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

Axiom™ myDesign™ TG Array, 1K-90K (Applied Biosystems™)

With the Axiom™ myDesign™ TG Array Plate, 1K-90K, 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 1,000 and 90,000 markers, in a 1x96 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.

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.

Eureka™ Bovine Parentage Panel (Applied Biosystems™)

Eureka™ Bovine Parentage Panel was developed in collaboration with key scientists from Agricultural Research Services-U.S. Meat Animal Research Center (ARS-USMARC). The panel includes 122 SNPs, one hundred of which overlap with the International Society of Animal Genetics (ISAG) core markers. Eureka Bovine Parentage Panel offers an affordable, high-throughput, and robust targeted genotyping by sequencing (GBS) technology to parentage studies to increase accuracy of bovine breeding programs. The low marker density panel ensures accurate interrogation of all the bovine parentage markers in all regions of the genome.

Features of Eureka Bovine Parentage Panel
Content: The panel consists of 100 core SNPs and an additional set of 22 markers that can be used internationally to make results comparable between laboratories.

Applications of Eureka Bovine Parentage Panel
• Molecular breeding
    -Identification of economically important traits
    -Improved accuracy in bovine breeding programs through genomic selection

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™ Rat Gene 2.0 ST Array (Applied Biosystems™)

Comprehensive design
We understand that rats are an important model organism commonly used for studying human disease. In order to keep your experiments relevant to the understanding of the transcriptome, we have designed an array based on the most recent genome content for generating genome-wide expression profiles.

The GeneChip™ Rat Gene 2.0 ST Array offers a unique feature not available in other microarrays. Unlike traditional array designs that rely on a probe(s) designed to the first exon of the gene's 3' end, the hundreds of thousands of probes in this array are designed to every exon of every transcript represented on the array.

The high transcript coverage (median of 22 probes per gene) yields accurate detection for genome-wide transcript expression changes. These arrays provide higher resolution and accuracy than many of the classical 3'-biased microarray solutions available. The whole-transcript analysis approach enables researchers to detect multiple transcript isoforms from a given gene, including those that could be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.

Key benefits
• Whole-transcript analysis enables the capture of transcript isoforms you may miss with 3'-biased expression designs
• Comprehensive transcriptome coverage provides the best opportunity to discover interesting biology:
   - >27,000 protein coding transcripts
   - >24,000 Entrez genes
• Measure alternative splicing events/transcript variants with probes designed to maximize coverage of exons
• Reproducible: Signal correlation coefficient ≥ 0.99

Content profile
Since the design of the GeneChip Rat Gene 1.0 ST Array, there has been a substantial increase in the structural and functional understanding of the rat genome. 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 Rat Gene 2.0 ST Array.

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

Canine 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&trade Human Gene 1.1 ST Array Plate (Applied Biosystems™)

The Human Gene 1.1 ST 96-Array Plate and Trays provide the most accurate, sensitive, and comprehensive measurement of protein coding and long intergenic non-coding RNA transcripts.

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

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

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

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

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

GeneChip™ 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).

Specificity: Connexin 26, 32, 43

Reactivity: Human, Mouse, Rat

Applications: See product data sheet for recommended Usage for each antibody.

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

The Rat Gene 1.1 ST 24-Array Plate and Trays enables high-throughput expression profiling of 24 samples at a time using the same content as the industry-standard GeneChip™ Rat Gene 1.0 ST Array.

Comprehensive design
We understand that rats are an important model organism commonly used for studying human disease. In order to keep your experiments relevant to the understanding of the transcriptome, we have designed an array based on the most recent genome content for generating genome-wide expression profiles.

The GeneChip Gene ST family of arrays offers a unique feature not available in other microarrays. Unlike traditional array designs that rely on a probe(s) designed to the first exon of the gene's 3' end, the hundreds of thousands of probes on each Gene ST Array Plate are designed to every exon of every transcript represented on the array.

The high transcript coverage (median of 22 probes per gene) yields accurate detection for genome-wide transcript expression changes. These arrays provide higher resolution and accuracy than many of the classical 3'-biased microarray solutions available. The whole-transcript analysis approach enables researchers to detect multiple transcript isoforms from a given gene, including those that could be missed using a 3'-biased expression design, such as splice variants, non-polyadenylated transcripts, transcripts with alternative polyadenylation sites, and truncated transcripts.

Key benefits
• Whole-transcript analysis enables the capture of transcript isoforms you may miss with 3'-biased expression designs
• Comprehensive transcriptome coverage provides the best opportunity to discover interesting biology:
   - >27,000 protein coding transcripts
   - >24,000 Entrez genes
• Measure alternative splicing events/transcript variants with probes designed to maximize coverage of exons
• Reproducible: Signal correlation coefficient ≥0.99

Content profile
Since the design of Rat Gene 1.1 ST Array Plates, there has been a substantial increase in the structural and functional understanding of the rat 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 Rat Gene 2.1 ST Array Plates (sold separately).