Shop All DNA & RNA Microarray Analysis

GeneChip™ miRNA 3.1 Array Plate (Applied Biosystems™)

The miRNA 3.1 Array Plates and Trays are powerful tools for studying the role of small non-coding RNA (miRNA, snoRNA, and scaRNA) and their importance in cancer and other diseases. Additionally, we offer the miRNA 4.1 Array Plates and Trays, which offers updated content with the same high performance as the previous generation array.

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

PharmacoScan™ Assay Kit, 24-Format (Applied Biosystems™)

Each PharmacoScan™ Assay Kit includes all necessary array plates, reagents, controls, and consumables to process 88 samples (and 8 controls) with the PharmacoScan Solution workflow.

PharmacoScan Solution is an ideal platform for translational researchers in healthcare, pharma, and research organizations looking to understand how genetic variations affect drug absorption, distribution, metabolism, and excretion (ADME).

By pre-emptively screening for risk factors on a microarray, users in research can precisely and reproducibly analyze 4,627 high- to low-evidence markers* within nearly 1,200 genes* in a single assay. The solution includes copy number variation calling and interrogating predictive markers in complex genes. Unlike solutions that analyze only high-evidence markers, PharmacoScan Solution presents a more comprehensive view for genotyping for pharmacogenomic risk.

Key Features:

• 4,627 markers in 1,191 genes of known pharmacogenomic value
• Comprehensive content of known pharmacogenomic value including Phase I and Phase II enzymes, regulatory/modifier genes, drug target genes, and Phase III/transporter genes
• Comprehensive content of known pharmacogenomic value including Phase I and Phase II enzymes, regulatory/modifier genes, drug target genes, and Phase III/transporter genes
• Genotyping of highly predictive markers in genes including GSTM1, CYP1A2, CYP2D6, CYP2B6, CYP2A6, SULT1A1, CYP2C19, and CYP2C9 that are in highly homologous regions
• Copy number variation (CNV) analysis for copy number states ranging from zero to three-plus for important ADME genes
• Star allele and translation for key genes

Content Description (Figure 1):

• PharmacoScan Solution broadly screens for pharmacogenomic risk factors for research and leverages content carefully selected from top global consortia.
• Core functional pharmacogenomic content including markers from Clinical Pharmacogenomics Implementation Consortium (CPIC) guidelines
• Pharmacogenomics Knowledgebase (PharmGKB) markers in Very Important Pharmacogenes (VIP)
• PharmGKB markers with clinical annotations
• PharmaADME core markers
• Nearly all markers from DMET Plus Solution (1,936 genetic variants across 231 relevant genes)
• Human leukocyte antigen (HLA) markers associated with drug reactions
• Markers for killer cell immunoglobulin-like receptors (KIR), human ancestry identification, and for sample ID and tracking
• Pharmacogenetics/ADME markers in genes targeted for European populations drawn from UK Biobank Axiom Array

Continuity of content for cohort studies and clinical trials

Drug development research and clinical trials are typically conducted over several years. These long-term efforts require a platform that can guarantee multiyear availability of 100% of the specific array content for the entire timeline of initiative. Unlike bead-based technologies that experience batch-to-batch variability and single nucleotide polymorphism (SNP) dropouts with each manufacturing batch, the photolithography manufacturing technology used in PharmacoScan array guarantees 100% fidelity and ensures all markers are present on every manufacturing batch for as long as necessary, addressing a major concern for such long-term efforts.

PharmacoScan Solution utilizes the same chemistry from the Axiom™ assay and GeneTitan™ Multi-Channel (MC) Instrument, a microarray platform preferred worldwide by genetic researchers for the efficient workflow, high throughput, and reproducibility of results critical to multiyear data collection and analysis efforts.

*Disclaimer: Number of variants genotyped by default as well as variant to gene mapping is refined over time.

GeneChip™ Medicago Transcriptome Assay (Applied Biosystems™)

GeneChip™ Medicago Transcriptome Pico Assay, which utilizes 100-2,000 pg of input RNA) is designed for agriculture researchers studying legume genomics and symbiotic relationships between nitrogen-fixing bacteria and plants. Coupled with our free, intuitive Transcriptome Analysis Console (TAC) Software, it is the fastest and most effective whole-transcriptome profiling approach for legume researchers who want results within a crop season.

• In a single experiment, measure expression changes of M. truncatula reference cultivars A17 and R108, and M. sativa (alfalfa).

• With the right results the first time, have confidence in low-level expression data with higher reproducibility than RNA-Seq.

• Within minutes, analyze and visually interpret the expression of genes, exons, and transcript isoforms.

For additional information, see the GeneChip Medicago transcriptome solution data sheet.

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

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

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

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

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

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

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

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

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

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

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

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

GeneChip™ HT MG-430 PM Array Plate (Applied Biosystems™)

Proven performance from the industry standard
The GeneChip™HT MG-430 PM 96-Array Plate enables high-throughput expression profiling of multiple samples using the same industry-standard content as the GeneChip Mouse Genome 430 2.0 Array.*

The HT MG-430 PM Array Plate enables you to:
• Measure gene expression of more than 39,000 transcripts on a single array
• Get accurate and reproducible data by using multiple independent measurements for each transcript

Key Benefits
• Enables increased productivity and efficiency through parallel processing
   - Process 16, 24, or 96 samples on a single array plate
• Same industry-leading performance and content as the Mouse Genome 430 2.0 Array in cartridge format
   - Strong signal and fold change correlation to previous designs
• Multiple independent measurements per transcript for increased confidence in your results
   - Interrogates more sequence than a single probe measurement
• Conveniently packaged
   - Individual 16-, 24-, and 96-array plates available
   - All processing trays included

Content 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 107, June 2002) and refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute Center for Genome Research (MGSC, April 2002).

*The HT MG-430 PM Array Plate only retains perfect match (PM) probes from the cartridge design. Mismatch (MM) probes were removed.

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™ Mouse Genome 430A 2.0 Array (Applied Biosystems™)

The GeneChip™ Mouse Genome 430A 2.0 Array is a single array representing approximately 14,000 well-characterized mouse genes.

The GeneChip™ Mouse Genome 430A 2.0 Array is a single array representing approximately 14,000 well-characterized mouse genes that can be used to explore biology and disease processes. New, reduced feature size means that you can use smaller sample volumes than the previous Mouse Expression Array 430A without compromising performance.

•Provides coverage of well-substantiated genes in the transcribed mouse genome on a single array
•Analyzes the expression level of approximately 14,000 well-characterized mouse genes
•The Power of the Probe Set - offering multiple independent measurements for each transcript delivering the greatest accuracy and reproducibility of any microarray platform
•All probe sets represented on the GeneChip™ Mouse Expression Array 430A are included on the GeneChip Mouse Genome 430A 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 107, June 2002) and then refined by analysis and comparison with the publicly available draft assembly of the mouse genome from the Whitehead Institute for Genome Research (MGSC, April 2002).

Specificity: Connexin 26, 32, 43

Reactivity: Human, Mouse, Rat

Applications: See product data sheet for recommended Usage for each antibody.

Mouse Diversity Genotyping Array (Applied Biosystems™)

The Mouse Diversity Genotyping Array enables researchers to accurately characterize a broad range of mouse strains and their crosses and uncover genetic changes in mouse models of disease.

With more than 120 times the number of SNPs of competing products, and an average of 4.3 kilobases (kb) between SNPs, the Mouse Diversity Genotyping Array has greater density and distribution than any other publicly available mouse SNP array.

Mouse Diversity Genotyping Array offers:
• More than 120 times the genotyping power of competing products
   - Interrogate more than 623,000 single nucleotide polymorphisms (SNPs)
• More than 100 times the linkage mapping power
   - Map to a resolution of 4.3 kb
• The only array with copy number probes
   - Explore more than 916,000 non-polymorphic regions targeted to functional elements and regions known to harbor segmental duplications
• High performance metrics for 12 classical inbred laboratory strains and their F1 crosses
   - 98.6% call rate
   - 99.9% reproducibility
   - 99.5% concordance
   - < 0.5% error rate
• The broadest coverage of laboratory mouse strains
   - Probes represent SNPs derived from 12 classical inbred strains and 7 wild-derived and wild strains
• The most flexible approach
   - One array for both classical inbred and wild-derived strains for any mouse genetics application
• The lowest cost per genotype
   - Just fractions of a penny per SNP

For more information on the design of the array, please see Yang H., et al. A customized and versatile high-density genotyping array for the mouse. Nature Methods 6(9):663-666 (2009).

GeneChip™ Human Transcriptome Assay 2.0 (Applied Biosystems™)

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

View the data sheet for details on HTA 2.0 content and coverage.

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

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

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

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

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

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

Related Links
GeneChip™ Hybridization, Wash, and Stain Kit

Axiom™ Precision Medicine Diversity Research Array Plus Kit, 96-format (Applied Biosystems™)

The Axiom Precision Medicine Diversity Research Array (PMD Research Array) is a comprehensive imputation-aware genotyping resource designed to drive deeper scientific insights into complex disease susceptibility, pharmacogenomics (PGx), and genetic factors underlying wellness and lifestyle in diverse populations to advance population genomics studies. It offers >850,000 markers selected for high genomic coverage from the 1000Genomes Project Phase III. Additional gene variants were chosen from broadly referenced public databases, including ClinVar, NHGRI-GWAS catalog, CPIC, PharmaGKB, and PharmaADME.

The PMD Research Array is ideal for bio-banking, longitudinal cohort studies in precision medicine initiatives, clinical and translational research, and clinical trials in drug discovery.

This array kit includes the 1x96-format array plate, Axiom 2.0 Plus reagents, and Axiom GeneTitan Consumables Kit. The Axiom 2.0 Plus reagents include primers for the gene-specific amplification step which enables access to alleles with known relevance to drug metabolism. For PMD Research Array offered with Axiom 2.0 reagents, please see Cat. No. 951962.

Highlights:
• Clinically relevant variants with emphasis on variants in ACMG59 genes
• Over 5,000 variants in over 1,100 genes of known PGx value including CPIC Level A variants
• Accurate genotyping of highly predictive markers in genes including CYP2D6, CYP1A2, CYP2B6, CYP2A6, SULT1A1, CYP2C19, and CYP2C8 that are in highly homologous regions with known relevance to drug metabolism. The array offers haplotypes and diplotypes for PGx variants in translation tables and includes Star Allele Nomenclature as part of the standard deliverables.
• Blood phenotyping variants for blood typing and bleeding disorders
• Customizable—the array can be customized with up to 50,000 markers without affecting the imputation accuracy, or it can be fully customized as required

Coverage:
• Genome-wide association study (GWAS) imputation module with ~800,000 markers across all ancestral populations
• Evidence-based markers for relevant variants including ClinVar variants for comprehensive coverage of ACMG59 genes
• PGx variants per Clinical Pharmacogenomics Implementation Consortium (CPIC) guidelines and Pharmacogenomics Knowledge Base (PharmGKB), variants in Very Important Pharmacogenes (VIP), and PharmaADME core variants. The ADME category includes alleles with known relevance to drug metabolism.
• Blood typing variants that can be used to genotype and identify rare blood donors, bleeding disorders, and blood conditions such as sickle cell
• Disease-related variants (Alzheimer’s, cancer, cardiac, cardiometabolic, diabetes, neurological disorder, and other rare variants)
• Immune-related markers (human leukocyte antigen, killer immunoglobulin-like receptors, autoimmune, and inflammatory)
• Functional variants (loss of function, expression quantitative trait loci, nonsynonymous variants, lung phenotypes)
• Ancestry, wellness, and traits-related variants—includes environment and lifestyle variants such as those associated with skin and eye pigmentation, caffeine consumption, cholesterol levels, weight and obesity; variants used for tracking (fingerprint and sample tracking, mitochondrial, Y chromosome)

GeneChip™ Tomato Genome Array (Applied Biosystems™)

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

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

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

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

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™ RG-230 PM Array Strip (Applied Biosystems™)

Proven performance from the industry standard
The RG-230 PM Array Strip enables expression profiling of four samples at a time using the same industry-standard content as the GeneChip™ Rat Genome 230 2.0 Array*.

The RG-230 PM Array Strip enables you to:
• Measure gene expression of more than 30,000 transcripts and variants from more than 28,000 well-substantiated rat genes on a single array
• Get accurate and reproducible data by using multiple independent measurements for each transcript

Key Benefits
• Enables increased productivity and efficiency through parallel processing—Process four samples on a single array strip
• Same industry-leading performance and content as the Rat Genome 230 2.0 Array in cartridge format—Strong signal and correlation to previous designs
• Multiple independent measurements per transcript for increased confidence in your results—Interrogates more sequence than a single probe measurement
• Conveniently packaged—All processing trays included

Content 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 107) and refined by analysis and comparison with the publicly available draft assembly of the rat genome from the Whitehead Institute Center for Genome Research.

*The RG-230 PM Array Strip only retains perfect match (PM) probes from the cartridge design. Mismatch (MM) probes were removed.

Axiom™ Rice Genotyping Array (Applied Biosystems™)

Axiom Rice Genotyping Array offers comprehensive genomic coverage, which allows researchers to easily assay the natural variation of rice varieties worldwide to identify genes underlying important phenotypic traits (e.g., high yields), to understand genetic sources of variation, and to differentiate cultivars for fingerprinting and classification purposes.

Axiom Rice Genotyping Array includes 42,961 markers from GeneChip™ Rice 44K Genotyping Arrayand 5,499 markers from a whole-genome SNP array (RICE6K) for genomic breeding in rice.

Highlights:
Content
   - Backwards compatibility with older data based on 44,000 makers from GeneChip Rice 44K SNP Genotyping Array
   - Detection of common genetic variants within and between the major subpopulations of rice, including indica, aus, tropical japonica, temperate japonica, and group V ("aromatic")
   - Efficient progeny screening in rice breeding with markers identified by Yu et al.

Applications:
Complex-trait research
   - Flexible and fast identification and classification of germplasm
   - Identification of high-yield variants
   - Genome-wide association mapping and tracking of disease genes
Molecular breeding
   - Allows for fingerprinting rice germplasm, genotyping bulked segregating pools, checking seed authenticity, and selecting genetic background
   - Enables genetic variation analysis of any O. sativa strain
   - Offers information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonica groups

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

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

The GeneChip™ Human Gene 2.0 ST Array provides 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
• 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