Shop All DNA & RNA Microarray Analysis

GeneChip™ Yeast Genome 2.0 Array (Applied Biosystems™)

The GeneChip™ Yeast Genome 2.0 Array contains probe sets to detect transcripts from both Saccharomyces cerevisiae and Schizosaccharomyces pombe, which are the two most commonly studied species of yeast. Providing comprehensive coverage of both species, the GeneChip Yeast Genome 2.0 Array includes approximately 5,744 probe sets for 5,841 of the 5,845 genes present in S. cerevisiae and 5,021 probe sets for all 5,031 genes present in S. pombe.

The evolutionary divergence between S. cerevisiae and S. pombe over 500 million years ago caused enough sequence divergence between the two species to require selection of separate probe sets for all genes, even the closest cross-species orthologs. Because both species are included on a single array, the GeneChip Yeast Genome 2.0 Array provides a flexible and affordable platform for researchers studying S. cerevisiae, S. pombe, or both species.

The sequence information for this array was selected from public data sources GenBank™ (May 2004) and Sanger Center (June 2004) for the S. cerevisiae and S. pombe genomes, respectively. Probe sets on the array include 11 oligonucleotide pairs to detect each transcript.

GeneChip™ Zebra Finch Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ Zebra Finch 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™ Arabidopsis Genome ATH1 Array (Applied Biosystems™)

The Arabidopsis Genome ATH1 Array, designed in collaboration with TIGR, contains more than 22,500 probe sets representing approximately 24,000 genes.

The array is based on information from the international Arabidopsis sequencing project that was formally completed in December, 2000. In parallel and subsequent to the genome-s completion, TIGR reannotated the entire genome in a project funded by the National Science Foundation and the resulting data was used in the design of this array. Data from the TIGR database (ATH1-121501) is hosted in the NetAffx™ Analysis Center.

For more information, please review the data sheet (pdf, 86 KB).

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, 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 24-array plate containing between 1,000 and 90,000 markers, in a 1x24 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 Gene 1.1 ST Array Strip (Applied Biosystems™)

The Porcine 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™ 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™ Arabidopsis Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ Arabidopsis 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™ HG-U133+ PM Array Strip (Applied Biosystems™)

Proven performance from the industry standard
The Human Genome U133+ PM Array Strip, which enables expression profiling of four samples at a time, is based on the industry-standard GeneChip Human Genome U133 Plus 2.0 Array.*

Key benefits
• Delivers the same industry-leading performance and content as the GeneChip HT HG-U133+ PM Array Plate and Human Genome U133 Plus 2.0 Array in cartridge format
• Strong signal and fold change correlation to previous designs
• Provides multiple independent measurements per transcript for increased confidence in your results
• Interrogates more sequence than a single probe measurement
• Enables increased productivity and efficiency through parallel processing
• Process four samples on a single array strip
• Is conveniently packaged
• Includes all processing trays needed for array strip hybridization, washing, staining, and imaging

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 HG-U133+ PM Array Strip and Array Plate:

• Only perfect match (PM) probes from the cartridge design were retained, while mismatch 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 9 probes
• 6 probe sets were reduced from 11 to 10
• 12,208 probe sets remained unchanged

GeneChip™ Canine Genome 2.0 Array (Applied Biosystems™)

Canis familiaris is an important model organism for biomedical research of human disease conditions. The GeneChip™ Canine Genome 2.0 Array enables researchers to simultaneously interrogate 18,000 C. familiaris mRNA/EST-based transcripts and over 20,000 non-redundant predicted genes.

Sequence information for this array includes content from Canis familiaris UniGene Build #11 (April, 2005), GenBank™ mRNAs up to April 15, 2005, as well as the BROADD1 gene predictions from the boxer dog genome, downloaded from EBI on May 9, 2005. Purchasers of the array will have access to detailed sequence information via CD library files and through the online

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

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

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

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

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

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

More information on the PluriTest Assay ›

GeneChip™ Medicago Genome Array (Applied Biosystems™)

The GeneChip™ Medicago Genome Array is designed specifically to monitor gene expression in Medicago truncatula, Medicago sativa, and the symbiotic organism Sinorhizobium meliloti. The Medicago Genome Array is particularly useful for agriculture researchers studying legume genomics and symbiotic relationships between nitrogen fixing bacteria and plants.

Sequence information for this array was selected from data sources including the TIGR M. truncatula gene index (The Institute for Genomic Research, January 2005), gene predictions from the International Medicago Genome Annotation Group (IMGAG), gene predictions from the S. meliloti genome, and M. sativa EST information made available by TIGR. The array contains over 61,200 probe sets: 32,167 M. truncatula EST/mRNA-based and chloroplast gene-based probe sets; 18,733 M. truncatula IMGAG and phase 2/3 BAC prediction-based probe sets; 1,896 M. sativa EST/mRNA-based probe sets; and 8,305 S. meliloti gene prediction-based probe sets.

Instrument and Software Requirements
GeneChip™ Scanner 3000 7G
GeneChip™ Operating Software (GCOS) v1.3 or higher.

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

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

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

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

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

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

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

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

View the data sheet for details on Clariom™ D Transcriptome Human Transcriptome Pico Assay 2.0 content and coverage.

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

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

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

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

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

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

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

Related Links
GeneChip™ Hybridization, Wash, and Stain Kit