Shop All DNA & RNA Microarray Analysis

GeneChip™ Rice Genome Array (Applied Biosystems™)

The GeneChip™ Rice Genome Array offers researchers comprehensive transcriptome coverage for rice gene expression research. This array contains probes to query 51,279 transcripts representing two rice cultivars, with approximately 48,564 japonica transcripts and 1,260 transcripts representing the indica cultivar. This unique design was created within the GeneChip Consortia Program and provides scientists with a single array that can be used for the study of rice. High-quality sequence data were derived from GenBank™ mRNAs, TIGR gene predictions, and the International Rice Genome sequencing project. The arrays were designed using NCBI UniGene Build #52, (May 7, 2004) incorporating predicted genes from GenBank and the TIGR Os1 v2 data set. (ftp.tigr.org FASTA, 89.3 MB).

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™ Rat Gene 2.0 ST Assay (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 Arrays and GeneChip WT PLUS Reagent Kit 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 of Rat Gene 2.0 ST Arrays
• 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 of Rat Gene 2.0 ST Arrays
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 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

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™ Maize Genome Array (Applied Biosystems™)

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

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

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

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

GeneChip™ Rhesus Macaque Genome Array (Applied Biosystems™)

The rhesus macaque, Macaca mulatta, is an important model organism for human disease research. The GeneChip™ Rhesus Macaque Genome Array enables researcher to study gene expression in the rhesus animal model by simultaneously interrogating over 47,000 M. mulatta transcripts. Additionally, the Rhesus Genome Array contains several relevant viral organisms for studying host-disease immune response.

The sequence information for this array was selected from public data sources including data from the University of Nebraska, the Baylor School of Medicine - Rhesus Macaque Whole Genome Shotgun Assembly (October 1, 2004), and GenBank™ STSs, ESTs, and mRNAs up to March 30, 2005. Additionally, probe sets were designed to interrogate rhesus transcripts orthologous to the 3' end of human transcripts (GeneChip Human Genome U133 Plus 2.0 Array and RefSeq sequences up to March 2005).

Acknowledgements: We would like to acknowledge Dr. Rob Norgren from the University of Nebraska for his invaluable input into the design of the Rhesus Genome Array.

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.

GeneChip™ Rat Gene 1.0 ST Assay (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 1.0 ST Arrays and GeneChip WT PLUS Reagent Kit 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 of Rat Gene 1.0 ST Arrays
• 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 of Rat Gene 1.0 ST Arrays
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 (sold separately).

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

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

The GeneChip™ Chicken 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 96-Array Plate and Trays enables high-throughput expression profiling of 96 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/).

Axiom™ Genotyping Services, Non-Human Catalog 96 (Applied Biosystems™)

Axiom™ Services non-Human Catalog 96
Our service lab has genotyped more than one million samples and called about 650 billion genotypes, enabling our customers to complete their genotyping studies quickly and affordably. Our staff uses expert knowledge of best practices to process and analyze your samples, manage your Axiom Genotyping Services project from start to finish, and meet your crucial deadlines. Descriptions of the variety of Axiom Genotyping Services offered are listed below.

Axiom Catalog Array Genotyping Services
Our Axiom Catalog Array Genotyping Services offer hassle-free, high quality data for any existing Axiom Genome-Wide Array Plates or pre-designed arrays. This includes genotyping services using arrays for a variety of organisms and for a range in number of SNPs from 675,000 to two million.

myDesign™ Array Genotyping Services
myDesign Array Genotyping Services enable you to create fully or semi-customized genotyping arrays containing 1,500 to 2.6 million markers and then have them processed by our Research Services Laboratory with the same high-quality and fast turnaround time we provide for our catalog arrays.

For any of the above services, Please inquire for more information.

Clariom™ D Assay, mouse (Applied Biosystems™)

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

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

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

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

When you have precious samples, get it right the first time.
• 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™ 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™ 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.

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

The Rat 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™ 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 (sold separately), 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.

Clariom™ S Assay, human (Applied Biosystems™)

Obtain a gene-level view of the human transcriptome with the Clariom S Assays for human. The Clariom S Assays, human 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 Human 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. 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™ Tomato Genome Array (Applied Biosystems™)

Tomato is an important food crop worldwide, and the GeneChip™ Tomato Genome Array is designed specifically to monitor gene expression in tomato (Lycopersicon esculentum). The comprehensive array consists of over 10,000 L. esculentum probe sets to interrogate over 9,200 L. esculentum transcripts. The Tomato Genome Array is particularly useful for agriculture researchers studying tomato genetics.

This array was created in collaboration with leading tomato researchers through the GeneChip Consortia Program. Sequence information for this array was selected from public data sources including Lycopersicon esculentum UniGene Build #20 (October 3, 2004) and GenBank™ mRNAs up to November 5, 2004.

Instrument 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.