Shop All DNA & RNA Microarray Analysis

GeneChip™ Arabidopsis Gene 1.1 ST Array Strip Applied Biosystems™

The Arabidopsis 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 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™ Rhesus Macaque Genome Array Applied Biosystems™

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

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

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

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

* GeneChip Scanner 3000 High-Resolution Update is standard on all instruments shipped starting in September 2003 with serial number series 502. Previous versions, such as serial number series 501, will require the GeneChip Scanner 3000 High-Resolution Update, Catalog Number 00-0110, to be installed.

GeneChip™ Bovine Gene 1.1 ST Array Strip Applied Biosystems™

The Bovine 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.

atSNPtilx520433 Arabidopsis Cartridge Array Applied Biosystems™

The Arabidopsis thaliana is a small flowering plant that is commonly used as a model organism in plant biology and genetics.

The customized GeneChip™ Arabidopsis SNP Genotyping Array can be used for genotyping and whole-transcript gene expression. The array is a 5 µm array with 249,000 SNPs tiled on the array with 4 probes per SNP. The tiling probes are perfect match (PM) only and omit repetitive sequences. The array is used with Whole-Genome Sampling Assay for Agrigenomics Solutions.

Please visit http://www.ncbi.nlm.nih.gov/pubmed/18369451 and http://www.ncbi.nlm.nih.gov/pubmed/17091126 for more detailed information about the array design, assay, and analysis for use in genotyping.

Research article:
Childs L. H., et al. Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana. BMC Genomics 11:188 (2010)

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™ Canine Gene 1.1 ST Array Strip Applied Biosystems™

Canine Gene 1.1 ST Array Strips enable you to:
• Measure expression, across the entire gene, with higher resolution and accuracy than with classical 3'-biased microarray solutions
• Get accurate and reproducible data by using multiple independent measurements for each transcript
• Process four samples on a single array strip with the cost-effective GeneAtlas™ System

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

Key benefits
Highest transcript coverage – get confident expression measurements of well-annotated content with up to 26 probes per transcript
Whole-transcriptome analysis – capture the transcript isoforms you may miss with 3'-biased expression designs
High data correlation – achieve high inter- and intra- array strip signal correlation (R >0.99)
Convenient format – process four samples at the same time with minimal manual array handling
Simple workflow – streamline your work, from target preparation through pathway analysis, and use intuitive software for data interpretation

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

Gene 1.1 ST Array Strips are designed exclusively for the GeneAtlas System – the first personal microarray system to allow four samples to be processed in parallel. It combines affordability, simplified workflow, ease of use, intuitive software, and excellent performance. For more information on the GeneAtlas System, please visit here.

Gene 1.1 ST Array Strips are supported by our easy-to-use and integrated data analysis software pipeline, which includes GeneAtlas Instrument Control Software for instrument processing of array strips, Partek™ Express™ Software for quality control and statistical analysis, and an Ariadne Pathway Studio™ Explore Software for pathway analysis, visualization, and other features that allow you to put your data into a biological context.

Please note that Pathway Studio Explore includes the ResNet™ Mammalian Database, which supports analysis of human, mouse, and rat sequences. The software also offers access to the ResNet Plant Database, which has gene definitions from Entrez for Arabidopsis, rice, and soybean, but other than Arabidopsis, only has relationship data for those species-specific genes. You may contact Ariadne to obtain the ResNet Plant Database on DVD free of charge. For all other organisms, contact Ariadne to explore possibilities for creating a custom database.

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

Axiom™ Genotyping Services, Non-Human Catalog 384 Applied Biosystems™

Axiom™ Genotyping Services, Non-Human Catalog 384
Our service lab has genotyped more than one million samples and called about 650 billion genotypes, enabling our customers to complete their genotyping studies quickly and affordably. Our staff uses expert knowledge of best practices to process and analyze your samples, manage your Axiom Genotyping Services project from start to finish, and meet your crucial deadlines. Descriptions of the variety of Axiom Genotyping Services offered are listed below.

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

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

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

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

Axiom Trout Genotyping Array (384HT 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

Axiom™ Genome-Wide EAS 1 Array Plate Applied Biosystems™

We have got you covered
Axiom World Arrays are designed for genome-wide imputation analysis with a focus in disease-associated genes. The arrays include additional markers that are specific to multiple HapMap populations. These arrays have the industry's highest coverage of rare variants to replicate studies of specific loci and/or genes that have been identified in previous genome-wide association studies. The use of imputation enables a highly cost-effective, budget conscious alternative to other commercially available arrays.

The Axiom Genome-Wide EAS 1 Array Plate is designed for maximum coverage of Admixed population and diseases of East Asian ancestry using intelligent pair-wise and imputation design tools.

Benefits of Axiom World Arrays:
• Saturated coverage in over 5,000 gene regions previously identified as disease-associated: SNPs selected from disease and drug response GWAS databases including the National Human Genome Research Institute (NHGRI) Catalog of Published Associations, the Human Genome Epidemiology Navigator (HuGE), the Pharmacogenetics Knowledge Base (PharmaGKB), and the Pharmacogenetics Membrane Transporter (PMT) database
• Common and rare (MAF ~1%) SNPs and indels from the International HapMap Project and 1000 Genomes Project
• Intelligent, innovative SNP selection maximizes efficient imputation of millions of additional SNPs
• GWAS, replication and fine mapping in one experiment to save time and cost
• Genotype-tested genomic content proven to give informative and reliable results
• High sample pass rate, call rate, and reproducibility
• Compatible with the Axiom 2.0 Reagent Kit, GeneTitan™ MC Instrument, automated or manual workflow, and Axiom Analysis Suite

Other Available Arrays
World Array 1: Axiom Genome-Wide EUR 1 Array Plate – European ancestry
World Array 2: Axiom Genome-Wide AFR 1 Array Plate – Admixed population of West African and European ancestry
World Array 4: Axiom Genome-Wide LAT 1 Array Plate – Admixed population of Native American, European, and West African ancestry

Don't see what you're looking for? Learn how to create an Axiom myDesign™ Array Plate tailored for your study.

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

GeneChip™ Tomato Gene 1.1 ST Array Strip Applied Biosystems™

The Tomato 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™ Human Gene 2.0 ST Assay Applied Biosystems™

The GeneChip™ Human Gene 2.0 ST Array and GeneChip WT PLUS Reagent Kit provide the most accurate, sensitive, and comprehensive measurement of protein coding and long intergenic non-coding RNA transcripts.

Comprehensive design
Keeping pace with the research community's understanding of the transcriptome, we have designed whole-transcript arrays that include probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). These whole-transcript array designs provide a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile.
Research over the past 20 years has predominantly focused on protein coding messenger RNA transcripts and their role in cellular processes, such as disease and development. Recently researchers have identified more that 10,000 transcripts (>200 bases) with little or no protein coding potential. Only a small fraction of these non-coding RNAs has functional annotations to date. However, there is ample evidence that differential expression of lincRNAs plays an important role in the genesis and progression of disease and that aberrant expression of these molecules have also been linked to cancer. Recent advancements in transcriptome profiling provided evidence of the association of lincRNAs in a diverse range of cellular functions:
• Regulation of mRNA transcription
• Regulation of mRNA post-transcriptional modifications
• Occlusion/recruitment of transcription factor binding
• Activation and transportation of transcription factors
• Interaction with accessory proteins
• Guide protein complexes to locations in the genome

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

Content profile
Since the design of the Human Gene 1.0 ST Array, there have been a massive number of new lincRNA that have been identified by the research community. In order to provide the research community with a tool that can measure the differential expression of this exciting class of RNA transcripts, we have designed the Human Gene 2.0 ST Array. To supplement the lincRNA data contained in RefSeq, we used sequences and transcripts from lncRNA db www.lncrnadb.com and Broad Institute, Human Body Map lincRNAs and TUCP (transcripts of uncertain coding potential catalog) lincRNAs

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)

GeneChip™ Wash Buffer A Applied Biosystems™

GeneChip™ Wash Buffer A is a component of the GeneChip Hybridization, Wash, and Stain Kit, but may be purchased separately. The GeneChip Hybridization, Wash, and Stain Kit is used with GeneChip brand arrays in cartridge format, following the target preparation steps described for 3' eukaryotic, prokaryotic, and exon assays.

Functionally tested on GeneChip Brand Arrays, we recommend the Prokaryotic Target Labeling Assay and associated reagents for use in prokaryotic gene expression studies.

Prokaryotic Target Labeling Assay components include:
Control Oligo B2, 3nM
GeneChip DNA Labeling Reagent
GeneChip Poly-A RNA Control Kit

Related Links
GeneChip™ Wash Buffer B

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
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