Shop All DNA & RNA Microarray Analysis

GeneChip™ Human Genome U133 Plus 2.0 Array (Applied Biosystems™)

GeneChip™ Human Genome U133 Plus 2.0 Array

Benefits of the first and most comprehensive whole human genome expression array
• Convenient one-array view.
• Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts.
• 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
All probe sets represented on the GeneChip Human Genome U133 Set are identically replicated on the GeneChip Human Genome U133 Plus 2.0 Array. The sequences from which these probe sets were derived were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then 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).

In addition, there are 9,921 probe sets representing approximately 6,500 genes. These gene sequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from the UniGene database (Build 159, 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).

GeneChip™ Mouse Gene 2.0 ST Array (Applied Biosystems™)

The GeneChip™ Mouse Gene 2.0 ST Array is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile.

Since the design of the GeneChip Mouse Gene 1.0 ST Array, there has been a substantial increase in the structural and functional understanding of the mouse genome. This increase in knowledge includes the identification of a large number of long intergenic lincRNA that have been identified by the research community. In order to provide the research community with a tool that can measure the differential expression of this exciting class of RNA transcripts, we designed the GeneChip Mouse Gene 2.0 ST Array. To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db (http://lncrnadb.com/).

Comprehensive design
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

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

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

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

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

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

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

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

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

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

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

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

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

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

Comprehensive design
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 1.1 ST Array Strips offer 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 Strip 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 Strip, there has 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 have designed the Rat Gene 2.1 ST Array Strip.

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

With the Axiom™ myDesign™ TG Array Plate, 90K-200K, you can create fully customizable genotyping array panels for genome-wide association, replication, fine mapping, and candidate gene studies. Based on the universal workflow of the Genotyping Solution, myDesign Arrays offer unprecedented scale and flexibility to design the most optimal array for your species of interest.

The Array Plate contains one 96-array plate containing between 90K and 200K markers, in a 1x96 configuration (Minimum order size of 480 samples). An example template showing SNP submission can be found here.

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

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

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

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

Axiom™ Cotton Genotyping Array (Applied Biosystems™)

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

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

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

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

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

GeneChip™ miRNA 4.1 Array Plate (Applied Biosystems™)

Many diseases, including cancer, are frequently described as diseases of disordered gene expression. It is estimated that more than 30% of protein translation of coding genes is regulated by miRNA. There is also a large amount of growing evidence suggesting miRNA interacts with long non-coding RNA in the signaling networks that regulate alternative splicing events, which impacts cellular processes such as apoptosis, proliferation, and differentiation. All of which have shown to be causative elements in diseases such as cancer.

Measuring the changes in these critical nodes of regulation is extremely important for deciphering the biological context of differentially expressed genes. This array design is a powerful tool for studying the role of small non-coding RNAs and their involvement in a broad spectrum of developmental and physiological mechanisms.

To keep pace with the discovery of new and novel miRNA, we are pleased to offer the miRNA 4.1 24-Array Plates and Trays in our catalog of miRNA arrays. This product offers updated content with the same high performance as the previous generation array.

miRNA 4.1 Array Plates and Trays help bring you closer to biology with:
Comprehensive coverage – Designed to interrogate all mature miRNA sequences in miRBase Release 20
Easily correlate miRNA results – Analysis files contain host gene ID, predicted and validated miRNA target genes, and clustered miRNA information
Easy analysis – Analyze human, mouse, rat, or every miRNA for all species using the same array
Low sample input – Requires as little as 130 ng total RNA
Simple, fast, and free analysis solution – Coupled with Expression Console™ Software and Transcriptome Analysis Console (TAC) Software, researchers have a complete solution from data to decision-making in minutes

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

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

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

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

Research over the past 20 years has predominantly focused on protein coding messenger RNA transcripts and their role in cellular processes, such as disease and development. Recently researchers have identified more that 2,000 transcripts (>200 bases) in the mouse genome with little or no protein coding potential. Only a small fraction of these non-coding RNAs has functional annotations to date. However, there is ample evidence that differential expression of lincRNAs plays an important role in the genesis and progression of disease and that aberrant expression of these molecules have also been linked to cancer. Recent advancements in transcriptome profiling provided evidence of the association of lincRNAs in diverse range of cellular functions:

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

Key benefits
• Comprehensive coverage provides the best opportunity to discover interesting biology
• >28,000 coding transcripts
• >7,000 non-coding (include ˜2,000) long intergenic non-coding transcripts
• Measure alternative splicing events/transcript variants with probes designed to maximize exon coverage
• Reproducible: Intra-lot correlation coefficient =0.99

Content profile
Since the design of the Mouse Gene 1.1 ST Array Strip, there has been a substantial increase in the structural and functional understanding of the mouse genome. This increase in knowledge includes the identification of a large number of long intergenic lincRNA that have been identified by the research community. In order to provide the research community with a tool that can measure the differential expression of this exciting class of RNA transcripts, we have designed the Mouse Gene 2.1 ST Array Strip (sold separately). To supplement the lincRNA data contained in RefSeq, we use sequence and transcript data from lncRNA db (http://lncrnadb.com/).

Pepper (Capsicum) SNP Genotyping Array (B520549) (Applied Biosystems™)

This pepper array is a 6.4M feature GeneChip™ Array that has applications in massively parallel genotyping. The array design was supported by seven companies and the UC Discovery grant. This design is based on the public pepper ESTs and genetic information from GeneBank™ and the EST information of 21 libraries from Seoul National University (S. Korea). The genotyping array uses single feature polymorphism (SFP) markers with applications in quantitative trait loci (QTL) analysis, where whole-genome coverage is desired. The high-density GeneChip microarray is used to detect SFPs in more than 30,000 pepper genes.

Please visit https://pepchip.genomecenter.ucdavis.edu for more detailed information about the array design, assay, and analysis for use in genotyping.

Research articles:
Ashrafi H., et al. Genome-Wide SNP Discovery from de novo Assemblies of pepper (Capsicum annuum) Transcriptomes. International Conference on the Status of Plant and Animal Genome Research Poster presentation (Poster P0480) January 14-18, 2012, San Diego, CA.

Borevitz, J. O., et al. Large-scale identification of single-feature polymorphisms in complex genomes. Genome Research 13(3):513-523 (2003)

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

With the Axiom™ myDesign™ TG Array Plate, 1K-90K, you can create fully customizable genotyping array panels for genome-wide association, replication, fine mapping, and candidate gene studies. Based on the universal workflow of the Genotyping Solution, myDesign Arrays offer unprecedented scale and flexibility to design the most optimal array for your species of interest.

The Array Plate contains one 96-array plate containing between 1,000 and 90,000 markers, in a 1x96 configuration (Minimum order size of 480 samples). An example template showing SNP submission can be found here.

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

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

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

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

Axiom™ Trout Genotyping Array (384 format) (Applied Biosystems™)

Axiom Trout Genotyping Array (384 format) was designed under the Affymetrix Expert Design Program in collaboration with the National Center for Cool and Cold Water Aquaculture, USDA-ARS, USA, and AquaGen, Trondheim, Norway. The array includes 57,501 markers and is available in both 96 format and 384 format.

Axiom Trout Genotyping Array offers a standard high-throughput, cost-effective, and robust genotyping technology to conduct genome-wide association studies (GWAS), to study genetic architecture, perform marker-trait association, and to increase accuracy of breeding programs. The high marker density on the array ensures a broad coverage of the trout genome to provide representation of all regions in the genome.

Features of Axiom Trout Genotyping Array
Comprehensive content: The array includes 57,501 markers spaced across the genome as follows:
    - 17,000 markers that are unique to SNPs discovered in a previous USDA study1
    - 20,000 markers unique to an outbred Norwegian commercial population
    - Amino acid shifting SNPs
    - SNPs preferentially located within a gene and with minor allele frequency (MAF) >0.2
    - Y chromosome-specific SNPs near the sdY gene (male-specific in rainbow trout)2

Applications of Axiom Trout Genotyping Array
Complex trait research and molecular breeding
    - GWAS and quantitative trait locus (QTL) mapping
    - Identification of economically important traits
    - Improved accuracy in aquaculture breeding programs through genomic selection

Population and evolutionary genetics
    - Development of new breeding populations
    - Differentiation between fish of different origins
    - Gender determination via sdY chromosome-specific probes
    - Differentiation of farmed and wild populations

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

GeneChip™ Human Genome U133A 2.0 Array (Applied Biosystems™)

The Human Genome U133A 2.0 Array is a single array representing 14,500 well-characterized human genes that can be used to explore human biology and disease processes. Newer design and reduced feature size mean that you can use smaller sample volumes than the previous HG-U133 Array without compromising performance.

• Provides coverage of well-substantiated genes in the transcribed human genome on a single array
• Analyzes the expression level of 18,400 transcripts and variants, including 14,500 well-characterized human genes
• Comprised of more than 22,000 probe sets and 500,000 distinct oligonucleotide features
• 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
• All probe sets represented on the Human Genome U133A Array are identically replicated on the Human Genome U133A 2.0 Array

Array Profile
Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database (Build 133, April 20, 2001) and then were 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).

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

For more information, please review the data sheet (pdf, 169 KB)

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

The Mouse Gene 2.1 ST Array Strips enable you to perform low- and medium-throughput expression analysis with minimum hands-on time.

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

Research over the past 20 years has predominantly focused on protein coding messenger RNA transcripts and their role in cellular processes, such as disease and development. Recently researchers have identified more that 2,000 transcripts (>200 bases) in the mouse genome with little or no protein coding potential. Only a small fraction of these non-coding RNAs has functional annotations to date. However, there is ample evidence that differential expression of lincRNAs plays an important role in the genesis and progression of disease and that aberrant expression of these molecules have also been linked to cancer. Recent advancements in transcriptome profiling provided evidence of the association of lincRNAs in diverse range of cellular functions:• Regulation of mRNA transcription
• Regulation of mRNA post-transcriptional modifications
• Occlusion/recruitment of transcription factor binding
• Activation and transportation of transcription factors
• Interaction with accessory proteins
• Guide protein complexes to locations in the genome

Key benefits
• Comprehensive coverage provides the best opportunity to discover interesting biology
• >28,000 coding transcripts
• >7,000 non-coding (include ˜2,000) long intergenic non-coding transcripts
• Measure alternative splicing events/transcript variants with probes designed to maximize exon coverage
• Reproducible: Intra-lot correlation coefficient =0.99

Content profile
Since the design of the Mouse Gene 1.1 ST Array Strip (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 have designed the Mouse Gene 2.1 ST Array Strip. To supplement the lincRNA data contained in RefSeq, we use sequence and transcript data from lncRNA db (http://lncrnadb.com/).

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

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

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

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

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

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

Clariom™ S Assay, mouse (Applied Biosystems™)

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

Find answers, move on
Although the number of known transcribed genes has expanded rapidly in recent years, knowledge of the function of each gene is still evolving. Many genes and transcripts found in databases are poorly annotated or unannotated, which can complicate and prolong data analysis and interpretation. mouse Clariom S Assays focus on well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies and to quickly assess changes in key genes and pathways. With less time required for data analysis, Clariom S Assays for mouse help researchers reach conclusions more rapidly.

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

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

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

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

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