Human Expression Profiling Arrays & Assays

Clariom™ S Assay, human (Applied Biosystems™)

Obtain a gene-level view of the human transcriptome with the Clariom S Assays for human. The Clariom S Assays, human 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 Human 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. Human 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 human help researchers reach conclusions more rapidly.

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

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

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

Get the truest level of gene-level expression
To generate robust gene-level expression, Human Clariom S Assays detect only the exons present in all known transcript isoforms expressed from a single gene locus-constitutive exons. This differs from other gene-level array technologies and shallow RNA-Seq, which provide either a biased view of gene expression or data that are complicated by variation in expression of transcript variants. By detecting only constitutive exons throughout the length of each known gene, Human 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 human provide you with the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.

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™ Human Genome U133 Plus 2.0 Assay (Applied Biosystems™)

The GeneChip™ Human Genome U133 Plus 2.0 Assay is used with the GeneChip Human Genome U133 Plus 2.0 Array.

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™ Human Gene 1.0 ST Array (Applied Biosystems™)

The GeneChip™ Human Gene 1.0 ST Array provides the most accurate, sensitive, and comprehensive measurement of protein coding and long intergenic non-coding RNA transcripts. We also offer the GeneChip Human Gene 2.0 ST Array, which can measure differential expression of long intergenic non-coding RNA transcripts.

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

Obtain a gene-level view of the human transcriptome with the Clariom S Pico Assays for human. The Clariom S Pico Assays, human 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 Human 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 Pico 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. Human Clariom S Pico 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 Pico Assays for human help researchers reach conclusions more rapidly.

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

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

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

Get the truest level of gene-level expression
To generate robust gene-level expression, Human Clariom S Assays detect only the exons present in all known transcript isoforms expressed from a single gene locus-constitutive exons. This differs from other gene-level array technologies and shallow RNA-Seq, which provide either a biased view of gene expression or data that are complicated by variation in expression of transcript variants. By detecting only constitutive exons throughout the length of each known gene, Human 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 Pico Assays for human provide you with the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.

GeneChip&trade Human Gene 1.1 ST Array Plate (Applied Biosystems™)

The Human Gene 1.1 ST 96-Array Plate and Trays 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 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 1.1 ST Array Plates, 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 designed the Human Gene 2.1 ST Array Plates (sold separately). 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 (http://www.broadinstitute.org/genome_bio/human_lincrnas/).

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

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
In order to provide the research community with a tool that can evaluate a growing class of lincRNAs, we have designed theHuman Gene 2.1 ST Array Strip. To supplement the lincRNA data contained in RefSeq, we use sequence sand transcripts from lncRNA db (www.lncrnadb.com) and Broad Institute, Human Body Map lincRNAs, and TUCP (transcripts of uncertain coding potential) catalog (http://www.broadinstitute.org/genome_bio/human_lincrnas/).

PrimeView Human Gene Expression Assay (Applied Biosystems™)

The PrimeView Human Gene Expression Assay enables you to:
• Measure gene expression of more than 36,000 transcripts and variants per sample
• Get accurate and reproducible gene expression data by using multiple independent measurements for each transcript

Proven performance from the industry standard
The PrimeView Human Gene Expression Assay enables expression profiling using probe sets with an emphasis on established, well annotated content. Sequences used in the design of the assay were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™.

Key benefits
• Offers excellent gene expression specificity and reproducibility
• Produces reliable results with multiple independent measurements per transcript
• Provides complete coverage of the annotated genome
• Highest transcript coverage in the industry with the most recent annotation

Content profile
• The PrimeView Human Gene Expression Assay is comprised of more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation.
• The EST and mRNA sequences used in the design were clustered and assembled to create consensus sequences that represent alternative splice forms. Each assembly was then analyzed for orientation and alternative 3' end evidence.
• Content was chosen to cover all well-annotated genes and transcripts from RefSeq v36 and by leveraging all available EST and mRNA evidence that fall into the same clusters, to rigorously detect alternate 3' ends of those well-annotated genes.

• More than 1,000 probe sets represent transcripts that have no official gene symbol in UniGene, but are based on predicted RefSeq sequences and UniGene clusters with good evidence of actual transcription.

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

PrimeView Human Gene Expression Array (Applied Biosystems™)

The PrimeView Human Gene Expression Array enables you to:
• Measure gene expression of more than 36,000 transcripts and variants per sample
• Get accurate and reproducible gene expression data by using multiple independent measurements for each transcript

Proven performance from the industry standard
The GeneChip PrimeView Human Gene Expression Array cartridge enables expression profiling using probe sets with an emphasis on established, well annotated content. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™.

Key benefits
• Offers excellent gene expression specificity and reproducibility
• Produces reliable results with multiple independent measurements per transcript — 11 probes per set for well-annotated sequences, 9 probes per set for the remainder
• Provides complete coverage of the annotated genome
• Highest transcript coverage in the industry with the most recent annotation — covers all well- annotated genes and transcripts from RefSeq

Content profile
• The PrimeView Human Gene Expression Array is comprised of more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation.
• The EST and mRNA sequences used in the design were clustered and assembled to create consensus sequences that represent alternative splice forms. Each assembly was then analyzed for orientation and alternative 3' end evidence.
• Content was chosen to cover all well-annotated genes and transcripts from RefSeq v36 and by leveraging all available EST and mRNA evidence that fall into the same clusters, to rigorously detect alternate 3' ends of those well-annotated genes.
• More than 1,000 probe sets represent transcripts that have no official gene symbol in UniGene, but are based on predicted RefSeq sequences and UniGene clusters with good evidence of actual transcription.

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

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

Obtain a gene-level view of the human transcriptome with the Clariom S Pico Assays HT for human. The Clariom S Pico Assays, human 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 Human HT Clariom S Assay design provides extensive coverage of all known well-annotated genes, compatibility with clinical sample types, scalable formats, and flexible data analysis software. Clariom S Pico Assays HT are the tools of choice to find expression biomarkers with known function as quickly, easily, and cost-effectively as possible.

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

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

When you have precious samples, get it right the first time
• Generate robust expression profiles from as little as 100 pg of total RNA–as few as 10 cells.
• Utilize RNA from various sample types including blood, cells, and fresh/fresh-frozen or FFPE tissues.
• Preserve sample integrity and reduce data variability with an assay that does not require a globin or rRNA removal step.
• Save time and money with fully automated sample preparation options.
Clariom S solutions are available formats for single-sample (cartridge array) processing on the GeneChip™ 3000 instrument system and high-throughput automated processing (plate array) on the GeneTitan™ HT Microarray System, offering the flexibility to accommodate both small and large cohort studies. The complete solution comes with reagents and fast, simple Transcriptome Analysis Console (TAC) software to analyze and visualize global expression patterns of genes, pathways, and network interactions in minutes.

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

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

GeneChip™ Human Transcriptome Array 2.0 (Applied Biosystems™)

Designed to empower next-generation expression profiling studies, GeneChip™ Human Transcriptome Array 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 array
RefSeq                                    Vertebrate Genome Annotation (Vega) database
Ensembl                                   MGC Mammalian Gene Collection (v10)
UCSC Known Genes               www.noncode.org
UCSC lincRNA transcripts        lncRNA db
Broad Institute, Human Body Map lincRNAs, and TUCP (transcripts of uncertain coding potential) catalog

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

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

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

GeneChip™ Human Gene 2.1 ST Array Plate (Applied Biosystems™)

The Human Gene 2.1 ST 16-Array Plate and Trays 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 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 1.1 ST Array Plates, 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, the Human Gene 2.1 ST Array Plates was designed. 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 (http://www.broadinstitute.org/genome_bio/human_lincrnas/).

Clariom™ D Assay, human (Applied Biosystems™)

Accelerate your biomarker discovery from deep within the transcriptome with Clariom D Assays for human, the next generation of transcriptome-level expression profiling tools. Clariom D Assays provide a highly detailed view of the transcriptome and offer the fastest path to actionable results.Clariom D Assays allow translational research scientists to generate high-fidelity biomarker signatures quickly and easily. Based on industry-leading microarray technology, the novel design of these assays provides the most intricate transcriptome-wide gene- and exon-level expression profiles, including the ability to detect alternative splicing events of coding and long non-coding (lnc)RNA, in a single three-day experiment.

Expand your potential to discover novel, informative biomarkers
The number of known transcribed genes has expanded rapidly in recent years, providing more sources for actionable biomarkers, such as transcript variants and lncRNA, that can be used for clinical utility and advancing our understanding of disease mechanisms. Such biomarkers can be missed by lengthy, complex, and costly sequencing and targeted expression approaches, leading to irreproducible signatures and wasted time and money.

With full coverage of the transcribed genome including all known coding and non-coding splice variants, compatibility with clinical sample types, and flexible data analysis software, Clariom D assays are the premier tools for translational researchers performing complex expression biomarker discovery studies and wanting the fastest path to robust, clinically relevant, and actionable results.

Get all the data you need
• Rapidly identify complex disease signatures from >540,000 transcripts sourced from the largest number of public databases, the most comprehensive coverage of the human transcriptome available, to ensure biomarkers are not missed.
• Confidently detect genes, exons, and alternative splicing events that give rise to coding RNA and lncRNA isoforms.
• Detect rare and low-expressing transcripts otherwise not detected by common sequencing approaches.
• Go from data to insight in minutes with intuitive, highly visual, free analysis software.
When you have precious samples, get it right the first time.

• Utilize RNA from various sample types including blood, cells, and fresh/fresh-frozen tissues.
• Preserve sample integrity and reduce data variability with an assay that does not require a globin or rRNA removal step.

Clariom D solutions are available in a single sample (cartridge array) format for use on the GeneChip™ 3000 instrument system and include reagents and fast, simple Transcriptome Analysis Console (TAC) software to analyze and visualize global expression patterns of genes, exons, pathways, and alternative splicing events.

Get the coverage you require, the reproducibility you need, and the insights you want to act on your discoveries.