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

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.

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 24-array plate containing between 90K and 200K 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.

Clariom™ S Assay HT, human (Applied Biosystems™)

Obtain a gene-level view of the human transcriptome with Clariom S Assays HT 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 HT 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 HT are the tools of choice to find expression biomarkers with known function as quickly, easily, and cost-effectively as possible.

Find answers, move on
Although the number of known transcribed genes has expanded rapidly in recent years, knowledge of the function of each gene is still evolving. Many genes and transcripts found in databases are poorly annotated or unannotated, which can complicate and prolong data analysis and interpretation. Human HT 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 HT 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™ HT Microarray System, offering the flexibility to accommodate both small and large cohort studies. The complete solution comes with reagents and fast, simple Transcriptome Analysis Console (TAC) software to analyze and visualize global expression patterns of genes, pathways, and network interactions in minutes.

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

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

GeneChip™ Mouse Exon 1.0 ST Array (Applied Biosystems™)

GeneChip™ Mouse Exon 1.0 ST Array offers new insight and powerful key information for researchers.

With approximately four probes per exon and roughly 40 probes per gene, the GeneChip™ Mouse Exon 1.0 ST Array enables two complementary levels of analysis-gene expression and alternative splicing.

Multiple probes per exon enable “exon-level” analysis and allow you to distinguish between different isoforms of a gene. This exon-level analysis on a whole-genome scale opens the door to detecting specific alterations in exon usage that may play a central role in disease mechanism and etiology.

The second level is “gene-level” expression analysis, in which multiple probes on different exons are summarized into an expression value of all transcripts from the same gene.

Exon arrays provide the most comprehensive coverage of the genome, including empirically supported and predicted transcribed sequences, enabling the discovery of previously unidentified novel events.

Array Features
•Highest resolution expression analysis, interrogating over 1 million exon clusters within the known and predicted transcribed regions of the entire genome.

Read more

•Tailored GeneChip™ Whole Transcript (WT) Assay and Reagents utilizing a random priming method for generating sense targets along the entire length of the transcripts.

•Flexible data analysis solutions and comprehensive annotation, giving you the opportunity to explore and dissect the data in various user-defined workflows.

Probe Sets: 1.2 million
Exon Clusters: ~ 1 million
Supported by Putative Full-Length mRNA: 266,220 probe sets
Supported by Ensembl Transcripts: 266,791 probe sets
Supported by EST: 554,003 probe sets
Supported by Human or Rat mRNA: 214,763 probe sets
Supported by Gene Prediction: 835,897 probe sets
Probe Selection Region: Along the entire length of the transcripts
Probes/Probe Selection Region: 41
Background Subtraction Strategy: Median intensity of up to 1,000 background probes with the same GC content
Total Features Per Array: >4,500,000
Interrogated Strand: Sense2

1 About 10 percent of the exon probe sets have fewer than four probes due to the probe selection region length and sequence constraints. 2 The probes tiled on the array are designed in the anti-sense orientation, requiring sense-strand labeled targets to be hybridized to the array. By convention, the array is called ST array representing the necessity of using sense targets (the labeled samples to be hybridized to the array).

Starter Pack To ensure optimal results with the GeneChip™ Exon Array system, it is highly recommended that new users begin with the Starter Pack.

*Each Starter Pack contains:

•GeneChip™ Mouse Exon 1.0 ST Array, 30 arrays
•GeneChip™ WT Sense Target Labeling and Control Reagents, 30 reactions
•On-site training including the following arrays and reagents for the training:
•GeneChip™ Mouse Exon 1.0 ST Array, 10 arrays
•GeneChip™ WT cDNA Synthesis and Amplification Kit, 10 reactions
•GeneChip™ WT Terminal Labeling Kit, 10 reactions
•GeneChip™ Sample Cleanup Module, 30 reactions
•GeneChip™ Eukaryotic Poly-A RNA Control Kit, 100 reactions
•GeneChip™ Hybridization Control Kit, 30 reactions

New XRAY demos for exon expression analysis •View a two-minute demo on a typical workflow using Biotique’s XRAY for the analysis of GeneChip™ Exon Arrays
Windows Media Player | Quicktime

•View a two-minute demo on the interpretation of GeneChip™ Exon Array data from Biotique’s XRAY
Windows Media Player | Quicktime


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.

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).


Axiom™ myDesign™ GW Array Plate, 200K-675K (Applied Biosystems™)

With the Axiom™ myDesign™ GW Array Plate, 200K-675K, 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 200K and 675K 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.

Axiom™ Porcine Breeders Array, 384 format (Applied Biosystems™)

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

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

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

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

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

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

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

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

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

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

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

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

GeneChip™ 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.

GeneAtlas™ Hybridization, Wash, and Stain Kit for WT Array Strips (Applied Biosystems™)

The GeneAtlas™ Hybridization, Wash, and Stain Kit for WT Array Strips contains pre-formulated solutions to process whole-transcript (WT) array strips using the GeneAtlas System. The reagents are formulated into the fewest number of individual components possible, reducing preparation and handling steps. With enhanced performance, fewer required reagents, and a simple protocol, target preparation has never been so easy.

The GeneAtlas Hybridization, Wash, and Stain Kit for WT Array Strips includes two boxes. The first box contains sufficient amounts of the hybridization and stain components to process 15 array strips (60 arrays). The hybridization components include the solutions required for preparation of the hybridization cocktail containing the target. The stain components include Stain Cocktail 1 and 3, Stain Cocktail 2, and the Array Holding Buffer. These solutions are used during array processing using the GeneAtlas System.

The second box includes Wash Buffer A and Wash Buffer B, also required for processing arrays. There is sufficient Wash Buffer A and B to process 15 array strips (60 arrays).

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

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

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

The Guinea Pig 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 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™ HT WT PLUS Reagent Kit (Applied Biosystems™)

The GeneChip™ HT WT PLUS Reagent Kit (HT WT PLUS Kit) is designed for automation of the target preparation process for expression analysis on whole-transcriptome (WT) arrays. Designed with reagent chemistries identical to GeneChip WT PLUS Reagent Kit, this high-throughput (HT) solution allows the user to generate hybridization-ready targets from input RNA with minimal hands-on time.

HT WT PLUS 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.

Features and benefits
• A complete target prep kit with proven sensitivity and specificity due to an optimized chemistry for WT arrays
• Automated protocol that enables the processing of up to 96 samples with minimal hands-on time
• Ability to run a variety of sample types, including clinically relevant samples such as whole blood, to enable robust biomarker identification
• Low sample input requirement (50 ng), allowing you to save your precious samples for further downstream studies
• No requirement for ribosomal RNA depletion or a globin reduction step for blood samples

Related Links
HT WT PLUS Consumables for Biomek™ FXP Target Prep Express
GeneChip™ WT PLUS Reagent Kit