Ingenuity® iReport™
Overview
How Does It Work?
- Easy: Ingenuity iReport reduces data processing bottlenecks by providing a single source for statistical and biological analysis in one accessible step.
- Interactive: Ingenuity iReport provides interactive tools to help you visually organize and filter your results, so you can quickly and effectively narrow in on the biology most relevant to your own experimental data.
- Accurate: Ingenuity iReport leverages the Ingenuity® Knowledge Base, a manually reviewed repository of millions of biological and chemical findings from peer reviewed literature and commonly used databases, so you can quickly relate known biology to your experimental results.
Benefits
PacBio long reads can span an entire RNA molecule and uniquely characterize transcript structure, including splice isoforms and fusion proteins.
Performance Specifications:
| Description | Flexible Performance Range | Example: Read Length Mode (2 x 45 minute movies) |
|---|---|---|
| Read length distribution | ||
| Average | As high as 1,300bp | 1,300bp |
| 95%ile | As high as 3,400bp | 3,300bp |
| Time to Result | ||
| Polymerase rate (average) | > 1 base/second | > 1 base/second |
| Movie Time | 1 min - 45 min | 45 min |
| Time/SMRT Cell (after initial setup) | As fast as 30 min | 2 hrs |
| Template preparation to basecalls | < 1 day | < 1 day |
| Mappable data and headroom | ||
| Total available ZMWs/SMRT Cell | 2 x 75,000 | 2 x 75,000 |
| Reads/SMRT Cell | ≥35,000 | ≥35,000 |
| Mappable data/SMRT Cell | As high as 45MB | 45MB |
| Accuracy | ||
| Consensus* | 99.999% @ 30x | 99.999% @ 30x |
* Based on data from Escherichia coli K12 strain. Performance may very with sample types
Identify and characterize pathogens with strain-level resolution for infectious outbreaks, biodefense, food safety and metagenomics
Performance Specifications:
| Description | Flexible Performance Range | Example: Read Length Mode (2 x 45 minute movies) |
|---|---|---|
| Read length distribution | ||
| Average | As high as 1,300bp | 1,300bp |
| 95%ile | As high as 3,400bp | 3,300bp |
| Time to Result | ||
| Polymerase rate (average) | > 1 base/second | > 1 base/second |
| Movie Time | 1 min - 45 min | 45 min |
| Time/SMRT Cell (after initial setup) | As fast as 30 min | 2 hrs |
| Template preparation to basecalls | < 1 day | < 1 day |
| Mappable data and headroom | ||
| Total available ZMWs/SMRT Cell | 2 x 75,000 | 2 x 75,000 |
| Reads/SMRT Cell | ≥35,000 | ≥35,000 |
| Mappable data/SMRT Cell | As high as 45MB | 45MB |
| Accuracy | ||
| Consensus* | 99.999% @ 30x | 99.999% @ 30x |
* Based on data from Escherichia coli K12 strain. Performance may very with sample types
Faster and more cost-effective DNA sequencing technologies are accelerating investigations of a broad range of genomes – from model organisms to pathogens that may have a direct impact on human health. However, only a limited number of species have been completely sequenced due to the inherent limitations of second-generation sequencing technologies, including GC-bias and the inability to resolve large structural variations. A complete genome is needed to fully understand the biological relevance of an organism.
The complexity of genome assembly is driven by a variety of factors, including the length and number of total fragments and the presence of repeat regions. The PacBio RS single-molecule, real-time sequencing system provides extra-long read lengths that simplify and improve genome assembly. By reducing the number of contigs and producing superior consensus accuracy, researchers can finish genomes at a lower cost and with higher quality data.
PacBio RS benefits:
Complete genome assemblies – long read lengths combine with high accuracy to produce high quality, finished genomes Accurate characterization of large structural variations – long read lengths uniquely provide the ability to sequence large repeat regions and resolve complex structure Unbiased genome coverage– balanced coverage and minimal GC-bias for high-quality assembly of high or low GC organisms or regions Cost-effective and fast– 10x reduction in finishing costs, results in less than a day, and no need for DNA amplificationPublications
Targeted sequencing allows researchers to focus on specific areas of interest within the genome, increasing the cost-effectiveness of studies and the depth of coverage. One common use of targeted sequencing is single nucleotide polymorphism (SNP) detection and validation, where the ability to accurately identify true SNPs and distinguish them from false positives is extremely important.
The PacBio RS directly measures individual molecules, using long reads to fully characterize genetic complexity, including rare SNPs, indels, structural variants, haplotypes and phasing. Single molecule resolution allows comprehensive characterization of heterogeneous samples and identification of variation invisible to multi-molecule sequencing technologies.
PacBio RS benefits:
Reduced false positives – no systematic bias provides confidence in results, higher positive predictive value Observation of structural variants – long read lengths provide characterization of variants Ability to resolve phasing of mutations – observation of haplotypes and correlation to phenotypes or drug response Access to the entire genome – flexibility to sequence through repetitive and GC-rich regionsPublications
Other Bioinformatic Services
XSeq™ Research Screening Panel
RainDance Technologies has collaborated with investigators at Emory University to design the industry’s most comprehensive genetic screening panel for human X-chromosome research. The XSeq™ Research Screening Panel enables scientists to interrogate more than 1,000 genes on the X chromosome simultaneously, and in a single assay, using next-generation sequencing (NGS) technology to detect specific known and novel mutations in a cost-effective manner.
Recent studies in human genetics indicate there are more than 800 protein-coding genes on the X chromosome, including many that play key roles in autism and other developmental disorders and intellectual disabilities.1,2 However, current cost and technology constraints make it difficult for researchers to detect many of the important sequence variants associated with these complex disorders. Whole-genome sequencing is expensive and not conducive for routine clinical use; hybridization-based sequence enrichment methods and whole-exome sequencing often lack the required genomic coverage and specificity to target and capture all of the genes and their 5’ promoter and 3’ untranslated regions (UTRs).
The RainDance XSeq panel provides the industry’s leading coverage of the X-chromosome genes associated with the full range of complex X-linked disorders.
The RainDance XSeq™ Research Screening Panel Advantage
• Sequence all of the X Chromosome genes at the same time: Analyze greater than 98% of the genes and their exons fond on the human X chromosome in a single assay.
• Interrogate challenging regions of the genome: Examine all exons and both the 5’ promoter region and 3’ UTR for each gene, as well as repetitive sequences and regions of high sequence homology.
• Discover more disease causing mutations: Gain unprecedented single-base resolution of both common and rare genomic mutations associated with the human X chromosome.
• Eliminate traditional PCR bias: Single-molecule PCR ensures no competition between alleles, which reduces allelic dropout often associated with bulk PCR techniques.
• Optimize sequencer efficiency and increase sample throughput: Reduce amount and cost of downstream NGS required with greater amplification uniformity and enrichment specificity.
• Apply next-generation sequencing technology more routinely: Generate accurate, consistent and reproducible data at a fraction of the overall sample cost compared to existing Sanger sequencing methods.
• Accelerate time to results and simplify workflow: Leverage fully automated instrumentation and intuitive analysis workflow that produces PCR products in less than 1 hour and decreases overall hands-on time to less than 8 hours compared to multi-day hybridization-based sequence enrichment methods.
(after copy add link: http://www.raindancetechnologies.com/documents/product-brief_asdseq.pdf)
ASDSeq™ Research Screening Panel
RainDance Technologies has collaborated with investigators at Emory University and Greenwood Genetic Center to design a comprehensive genetic screening panel for Autism Spectrum Disorder (ASD) research. The ASDSeq™ Research Screening Panel enables researchers to interrogate 62 genes known to affect ASD, in a single assay. Researchers can now cost-effectively apply next-generation sequencing (NGS) more routinely to detect known and novel mutations leading to syndromic forms of this pervasive developmental disorder.
ASD has been a highly active area of research, evidenced by the publication of more than 17,000 peer-reviewed scientific studies over the past ten years1. Despite the growing knowledge base in ASD, life science research has struggled to identify all of the causative mutations implicated in these conditions. Whole-genome sequencing is expensive and not conducive for routine clinical use; hybridization-based sequence enrichment methods and whole-exome sequencing often lack the required genomic coverage and specificity to target and capture all of the genes and their 5’ promoter and 3’ untranslated regions (UTRs).
The RainDance ASDSeq panel delivers the most extensive coverage of the genes associated with this complex disorder.
The RainDance ASDSeq™ Panel Advantage
• Sequence more relevant genes at the same time: Analyze 62 genes associated with ASD in a single test with greater than 92% design coverage of the targeted regions across coding and non-coding exons, splice junctions and 1 kilobase (kb) of both the 5’ promoter and 3’ UTRs.
• Discover more causative mutations: Gain unprecedented single-base resolution of both common and rare genomic mutations associated with ASD.
• Interrogate challenging regions of the genome: Examine exons, repetitive sequences, splice sites, regulatory regions, and areas of high homology.
• Eliminate enrichment bias: Maintain allelic representation of heterozygous alleles with single-molecule PCR.
• Optimize sequencer efficiency and increase sample throughput: Reduce amount and cost of downstream NGS required with greater amplification uniformity and enrichment specificity.
• Apply next-generation sequencing technology more routinely: Generate accurate, consistent and reproducible data at a fraction of the overall sample price compared to Sanger sequencing methods.
• Accelerate time to results and simplify workflow: Leverage fully automated instrumentation and intuitive analysis workflow that produces more than 1 million separate PCR reactions in less than 1 hour. Decrease overall processing time to less than 8 hours compared to multi-day hybridization-based sequence enrichment methods.
(after copy add link: Data Sheet http://www.raindancetechnologies.com/docutments/product-brief_asdseq.pdf
RNA - microRNA
Focused Set
The Dynamic Array Difference
Setup 9,216 gene expression reactions with only 192 pipette steps
Use your existing TaqMan® reagents
Enjoy the same TaqMan data quality
The Dynamic Array Solution
The Fluidigm Dynamic Array enables flexible, easy, and low-cost use of your existing real-time qPCR assays. You can set up 9,216 individual reactions on one dynamic array in a single experiment. Simply dispense 96 gDNA samples and 96 TaqMan assays and the dynamic array will automatically assemble each of the samples and reagents to create individual TaqMan reactions.
Dynamic Arrays
Two versions of dynamic arrays are available: the 96.96 Dynamic Array and the 48.48 Dynamic Array. The 96.96 Dynamic Array allows you to test 96 samples against 96 genes. The 48.48 Dynamic Array enables you to test 48 samples against 48 genes.
96.96 Dynamic Array Data Sheet
48.48 Dynamic Array Data Sheet
192.24 Dynamic Array Data Sheet
RNA - FFPE
Focused Set
The Dynamic Array Difference
Setup 9,216 gene expression reactions with only 192 pipette steps
Use your existing TaqMan® reagents
Enjoy the same TaqMan data quality
The Dynamic Array Solution
The Fluidigm Dynamic Array enables flexible, easy, and low-cost use of your existing real-time qPCR assays. You can set up 9,216 individual reactions on one dynamic array in a single experiment. Simply dispense 96 gDNA samples and 96 TaqMan assays and the dynamic array will automatically assemble each of the samples and reagents to create individual TaqMan reactions.
Dynamic Arrays
Two versions of dynamic arrays are available: the 96.96 Dynamic Array and the 48.48 Dynamic Array. The 96.96 Dynamic Array allows you to test 96 samples against 96 genes. The 48.48 Dynamic Array enables you to test 48 samples against 48 genes.
96.96 Dynamic Array Data Sheet
48.48 Dynamic Array Data Sheet
192.24 Dynamic Array Data Sheet
DNA - Focused Set
SNP
The Dynamic Array Difference
Setup 9,216 SNP Genoptyping reaction with 192 pipette steps
Use your existing TaqMan® reagents
Enjoy 99% conversion rates and 99% call rates
The Dynamic Array Solution
The Fluidigm Dynamic Arrays allow you to use your existing TaqMan SNP Genotyping assays in a flexible, easy-to-use and cost effective fashion. Each dynamic array allows you to setup up to 9,216 individual TaqMan reactions in a single experiment. Simply dispense 96 gDNA samples and 96 TaqMan assays and the dynamic array will then do the work of assembling the samples and reagents to create individual TaqMan reactions.
Dynamic Arrays
There are currently two versions of dynamic arrays available; the 96.96 Dynamic Array allows you to test 96 samples against 96 SNP’s. The 48.48 Dynamic Array allows you to test 48 samples against 48 SNP’s.
96.96 Dynamic Array Data Sheet
48.48 Dynamic Array Data Sheet
192.24 Dynamic Array Data Sheet
DNA - Focused Set
qPCR(CNV)
The Digital Array Difference
Ability to distinguish the difference between four and five copies
Simple, fast, and reliable workflow
The convenience of standard TaqMan® assays and reagents
The Power of Digital PCR
The digital array enables a new level of sensitivity and flexibility in detecting copy number variations by employing the power of digital PCR. The Fluidigm Digital Array is the first commercially available digital PCR platform with a completely optimized workflow, ready-to-use software and high density resolution.
Copy Number Variation Application
The digital array allows simultaneous quantification of both the gene of interest and a reference gene by using a different fluorescent dye for each assay. The ratio of the signal is the relative copy number of the gene of interest in the sample.
48.770 Digital Array Data Sheet
12.765 Digital Array Data Sheet
192.24 Dynamic Array Data Sheet
RNA - microRNA
Whole Genome
The Dynamic Array Difference
Setup 9,216 gene expression reactions with only 192 pipette steps
Use your existing TaqMan® reagents
Enjoy the same TaqMan data quality
The Dynamic Array Solution
The Fluidigm Dynamic Array enables flexible, easy, and low-cost use of your existing real-time qPCR assays. You can set up 9,216 individual reactions on one dynamic array in a single experiment. Simply dispense 96 gDNA samples and 96 TaqMan assays and the dynamic array will automatically assemble each of the samples and reagents to create individual TaqMan reactions.
Dynamic Arrays
Two versions of dynamic arrays are available: the 96.96 Dynamic Array and the 48.48 Dynamic Array. The 96.96 Dynamic Array allows you to test 96 samples against 96 genes. The 48.48 Dynamic Array enables you to test 48 samples against 48 genes.
96.96 Dynamic Array Data Sheet
48.48 Dynamic Array Data Sheet
192.24 Dynamic Array Data Sheet
RNA - Total
Focused Set
The Dynamic Array Difference
Setup 9,216 gene expression reactions with only 192 pipette steps
Use your existing TaqMan® reagents
Enjoy the same TaqMan data quality
The Dynamic Array Solution
The Fluidigm Dynamic Array enables flexible, easy, and low-cost use of your existing real-time qPCR assays. You can set up 9,216 individual reactions on one dynamic array in a single experiment. Simply dispense 96 gDNA samples and 96 TaqMan assays and the dynamic array will automatically assemble each of the samples and reagents to create individual TaqMan reactions.
Dynamic Arrays
Two versions of dynamic arrays are available: the 96.96 Dynamic Array and the 48.48 Dynamic Array. The 96.96 Dynamic Array allows you to test 96 samples against 96 genes. The 48.48 Dynamic Array enables you to test 48 samples against 48 genes.
96.96 Dynamic Array Data Sheet
48.48 Dynamic Array Data Sheet
192.24 Dynamic Array Data Sheet
Other Bioinformatic Services
Experimental Design and Consultations
A successful microarray research project starts with a well-designed experiment. Expression Analysis frequently provides consultations with our PhD statisticians and/or scientists to discuss experimental design. After data transfer, each investigator can request a completion call from one of our PhD scientists to review interesting results or ask about the potential for follow-on studies.
When we consider your experiment, important issues include:
Specification of goals: Is the primary interest in gene discovery, class discovery or class prediction?
Breadth of objectives: What situations or factors should the experiment include to be representative?
Sources of variability: What are the possible causes and how do we control unwanted variation?
Sources of bias: What are the possible causes and how do we control unwanted bias?
We commonly advise clients regarding many types of studies, including:
Two-group comparisons: Baseline vs. Experimental groups
Multi-group comparisons: Baseline vs. Treatment Group A vs. Treatment Group B
Time-course experiments with repeated measures of the same subject
Complex multi-way experiments involving two or more factors that have individual or synergistic effects Predictive marker experiments that associate expression values to complex of continuous phenotypes
Replication within Experiments
Many clients request advice on the number of samples to be included in microarray studies. Expression Analysis recommends that for statistical inferences, at least three biological replicates are needed for any study, but five or more replicates are preferred. As population variances increase, so do the number of replicates required to adequately query the population. For example, human studies usually require at least twice as many samples as animal studies. Blood samples typically require more replicates than other tissue types. In contrast, studies with cell lines require only a few replicates to ensure assay reproducibility. Expression Analysis recommends the inclusion of biological replicates, rather than technical replicates. We find that the high quality of chip manufacturing and sample processing obviates the need, in general, for purely technical replicates. Biological variability is typically much greater than technical variability. Precious resources are much better leveraged by including more biological replicates in the study, if available.
Novel Analysis Methods
Expression Analysis has developed novel analysis methods for identifying more differentially expressed genes and for predicting “No Call” genotypes in population studies. These methods are a result of our extensive expertise with the Affymetrix platform and reflect our commitment to provide a higher level of service to our clients.
Custom Bioinformatics
- Pathway analysis and GO Classification Analysis
- Text mining and association
- Mappings of Affymetrix probes to transcript sequences and reference sequences
- Sample size/power analysis
- Cross-platform gene expression comparisons
- Protocol evaluation
GWAS
The digenysis™ Approach: The genetic analysis of both allele variation and copy number
Diagenesis (root word) – a recombination of the constituents resulting in a new product. The basic methodology of digenysis is a rigorous statistical approach that begins with the primary constituents of the study: the array measurements of the two alleles of each SNP. However, with digenysis, these measurements are not used to call genotypes. Instead, digenysis recombines and transforms these allele measurements into values that contrast as well as summarize the allelic intensities. It then performs statistical tests for allelic and copy number association directly while simultaneously accounting for latent factors such as subpopulation and processing biases. This figure provides an overview of the standard analysis process flow and the alternative flow of digenysis:
Gene Expression
Data Deliverables for Expression Assays
QC Results - This report contains the QC results collected for each sample during target preparation and hybridization, such as spectrophotometer readings and hybridization metrics.
Raw Data Files - Expression Analysis returns the primary, platform-specific data files and text files that can be incorporated into analysis software.
Data Summaries and Comparisons – This file assimilates expression data, such as signal intensities and detection calls for every sample in a common study, and includes substantial gene annotation information. We also provide basic comparisons between control and treated samples.
Custom Analysis Services • Expression Analysis is equipped to provide custom analysis services, including:
- Alternative Measures of Expression (e.g., PLIER and PLIER variants, RMA, GCRMA, PDNN, or dCHIP)
- Alternative Chip Normalization Techniques (e.g., quantile, invariant set, median scaling, z-scaling)
- Principal Components Analysis and related graphs to detect outliers and hidden factors in samples
- Hierarchical Clustering with Heat Maps
- ANOVA/Linear Model Analysis including repeated measures analysis
- Analysis of differential gene list related to potential enrichment of GO terms or pathways
- Biomarker prediction and validation
- Predictive signature model robustness and sensitivity analysis
- Advanced Statistical Graphics
Two-Group Comparison with Permutation Analysis for Differential Expression (PADE)
Expression Analysis provides a two-group comparison analysis to detect and estimate changes in expression between two experimental groups that are each represented by multiple specimens per group. The comparison incorporates a permutation analysis for differential expression (PADE™). This analysis helps to mitigate false positives, a very important consideration when analyzing whole genome chips where potentially tens of thousands of statistical tests are examined in parallel. Expression Analysis also provides a two-group comparison analysis for repeated measures designs (RM-PADE) to account for those experiments or clinical trials when the subjects are used as their own matched control.
Reduction of Invariant Probes (REDI)
Most Affymetrix GeneChips contain multiple oligonucleotide probes for interrogating the same transcript. Through an examination of thousands of hybridization experiments, Expression Analysis has established that certain Perfect Match probes fail to respond adequately to the amount of target transcript in a sample. Our research shows that roughly 30% of the PM probes are poorly performing, affecting 80% of the probe sets. Probe sets that contain these invariant probe sequences are compromised in their ability to discern variations in transcript levels, thereby reducing sensitivity and the magnitude of differential expression values. Expression Analysis developed REDI analysis to remove these invariant probes from data analysis, resulting in the detection of more differentially expressed transcripts. This method is available for the HG-U133 family, the Rat230 family, and the Mouse430 family of GeneChips.
Genotyping Copy Number
Data Deliverables for Genotyping Assays
QC Results - This report contains the QC results collected for each sample during target preparation and hybridization, such as spectrophotometer readings and hybridization metrics.
Raw Data Files - Expression Analysis returns the primary, platform-specific data files and text files that can be incorporated into analysis software.
Data Summaries – Data summaries are also available summarizing calls for SNP IDs along with assessments of Hardy-Weinberg equilibrium, estimates of Copy Number and/or LOH, or other factors based on the analysis method and study design.
SNP Imputation Expression Analysis developed and tested a novel and robust computational strategy, referred to as SNP Imputation, for estimating the genotype at the “No Call” SNPs based on other data in the experiment. We have found that the imputed genotypes are up to 99% accurate, depending on the population diversity of the test specimens.
Copy Number Analysis Expression Analysis provides a variety of analysis options for estimating chromosomal copy number changes from SNP chip data. We can provide the information and results in tabular and/or graphical form including an aligned chromosomal view.
LOH Analysis Expression Analysis also performs analysis related to Loss of Heterozygosity (LOH), especially when matching normal populations are provided. Similar to Copy Number Analysis, the LOH analysis results can be provided in tabular and/or graphical form including an aligned chromosomal view.
Bioinformatic Services
Expression Analysis provides statistical and bioinformatic data analysis services that help explain the large amounts of data commonly generated by gene expression genotyping and sequencing experiments. The analysis often begins with an experimental design consultation to discuss important aspects of population variation, genomic coverage, and expected results. Expression Analysis has developed useful standard methods to facilitate projects. When necessary, Expression Analysis can develop and deliver custom solutions. Our bioinformatic staff consists of all PhD-level scientists trained in bioinformatics, biology and statistics. The software infrastructure for arrays is a combination of custom-built and open-source software layered onto SAS and R/Bioconductor and includes specialized application software. Also available; automated data analysis pipelines for array gene expression and linux cluster systems for sequencing applications. EA bioinformatic services cover a wide range of genomic applications.
RNA - FFPE
Whole Genome
RNA samples from FFPE specimens are amplified and labeled using the NuGen FFPE kit. Depending on the tissue procurement, fixation method and length of FFPE storage, a high percentage of transcripts, up to 50%, can be detected.
RNA - microRNA
Whole Genome
The GeneChip® miRNA Array is a powerful tool for studying the role of microRNAs (miRNAs) and their importance in cancer and other diseases. In addition, miRNA studies facilitate the discovery of biomarkers and disease signatures.
Non-coding RNAs are emerging as a major component of the regulatory circuitry that underlies the development and physiology of complex organisms. miRNAs are small, single-stranded RNAs that regulate gene expression by partial complementary base pairing to specific mRNAs. This annealing inhibits protein translation and in some cases facilitates the degradation of mRNA.
RNA - FFPE
Focused Set
For focused panels of up to 1,536 genes, the DASL Assay is deployed on multi-sample Universal Arrays3. The DASL Human Cancer Panel is a pool of selected probe groups that targets 502 genes collected from 10 publicly-available cancer gene lists. Genes were chosen based on their frequency of appearance on these lists and the frequency of literature citations of these genes in association with cancer. Each gene in the Cancer Panel is targeted in three locations with three probe groups per gene.
DASL Gene Expression: DASL Human Cancer Panel
Maximal sample throughput with low- to mid-multiplex expression profiling is achieved by using the DASL assay with VeraCode® technology on the BeadXpress® platform. Customizable VeraCode DASL kits allow for the simultaneous profiling of 32-384 transcripts of choice.
RNA - FFPE
Whole Genome
The DASL Assay (cDNA-mediated annealing, selection, extension, and ligation) is highly robust for gene expression profiling of traditionally difficult to assay samples, such as those having very low RNA input amounts or abundance, or with RNA degradation, particularly with formalin-fixed, paraffin-embedded (FFPE) specimens. This assay generates highly reproducible results with as little as 10–100 ng total RNA from fresh-frozen tissue or 50–200 ng total RNA from FFPE samples. The array assays more than 24,000 transcripts and uses the HumanHT-12 BeadChip.
RNA - FFPE
Sequencing
Small RNA Discovery and Analysis is an Illumina Genome Analyzer application that enables the discovery and profiling of all forms of small non-coding RNA from any organism without prior sequence information. With the ability to analyze up to four million small RNAs simultaneously in one sample, DGE: Small RNA Discovery and Analysis offers researchers the broadest and deepest profiling solution for small RNA currently available. Unlike the relative expression profiles microarray hybridization technology generates, DGE records the numerical frequency of a sequence in the library population.
Small RNA Discovery and AnalysisRequest a Quote | Specimen/Shipping Requirements
RNA - microRNA
Focused Set
These recently discovered short RNA transcripts (21–22 nucleotides long) have been identified in diverse organisms, and are thought to be post-transcriptional modulators of gene expression. Current estimates are that as many as 30% of mammalian genes are regulated by miRNA. Regulation by miRNA has been shown to be an essential mechanism contributing to normal cell physiology and cellular developmental. There have been many descriptions of miRNA dysregulation implicated in the etiology and progression of disease of including cancer. Illumina has created two fixed panels of miRNA assays, one for human and one for mouse. Both panels assay a complete and broad spectrum of miRNA. The Human and Mouse MicroRNA panels quantitate the levels of 1146 or 656 miRNA, respectively and represent approximately 97% of known miRNAs (described in the Sanger Institute’s miRBase Release 12.05), plus additional novel content derived using Illumina sequencing technology.
Human v2 MicroRNA Expression Profiling
DNA - Focused Set
Resequencing
Resequencing genes or genomic areas of interest is increasingly recognized as extremely valuable in the identification of mutations involved in certain congenital diseases. We offer resequencing services using custom Affymetrix CustomSeq® Resequencing GeneChips® which deliver 300,000 bases of double-stranded sequence per microarray. Sequences may cover a single contiguous region or multiple dispersed fragments, facilitating the analysis of whole genomes, multiple genes, and/or multiple organisms on a single array.
RNA - microRNA
Whole Genome
Small RNA Discovery and Analysis is an Illumina Genome Analyzer application that enables the discovery and profiling of all forms of small non-coding RNA from any organism without prior sequence information. With the ability to analyze up to four million small RNAs simultaneously in one sample, DGE: Small RNA Discovery and Analysis offers researchers the broadest and deepest profiling solution for small RNA currently available. Unlike the relative expression profiles microarray hybridization technology generates, DGE records the numerical frequency of a sequence in the library population.
RNA - Total
Whole Genome
3’ Gene Express Analysis Arrays
Human Genome Arrays
Human Genome U133 Plus 2.0 Array
Human Genome U133 Set
Human Genome U133A 2.0 Array
Human Genome U95 Set
Mouse Genome Arrays
Mouse Expression Set 430
Mouse Genome 430 2.0 Array
Mouse Genome 430A 2.0 Array
Murine Genome U74v2 Set
Rat Genome Arrays
Rat Expression Set 230
Rat Genome 230 2.0 Array
Rat Genome U34 Set
Drosophila Genome Arrays
Drosophila Genome 2.0 Array
Drosophila Genome Array
Xenopus laevis Genome Arrays
Xenopus laevis Genome Array
Xenopus laevis Genome 2.0 Array
Yeast Genome Arrays
Yeast Genome 2.0 Array
Yeast Genome S98 Array
Misc.
Arabidopsis ATH1 Genome Array
Barley Genome Array
Bovine Genome Array
C. elegans Genome Array
Canine Genome 2.0 Array
Chicken Genome Array
Citrus Genome Array
Cotton Genome Array
Maize Genome Array
Medicago Genome Array
Plasmodium/Anopheles Genome Array
Poplar Genome Array
Porcine Genome Array
Rhesus Macaque Genome Array
Rice Genome Array
Soybean Genome Array
Sugar Cane Genome Array
Tomato Genome Array
Vitis vinifera (Grape) Genome Array
Wheat Genome Array
Xenopus tropicalis Genome Array
Zebrafish Genome Array
Tiling Arrays
Human Genome Arrays
ENCODE 2.0R ArrayHuman Promoter 1.0R Array
Human Tiling 1.0R Array Set
Human Tiling 2.0R Array Set
Mouse Genome Arrays
Mouse Promoter 1.0R Array
Mouse Tiling 1.1R Array Set
Mouse Tiling 2.0R Array Set
E. coli Genome Arrays
E. coli Antisense Genome Array
E. coli Genome 2.0 Array
Chromosome 21/22 Genome Arrays
Chromosome 21/22 1.0 Array Set
Chromosome 21/22 2.0R Array
Drosophila Genome Arrays
Drosophila Tiling 1.0R Array
Drosophila Tiling 2.0R Array
Misc.
Arabidopsis Tiling 1.0R Array
C. elegans Tiling 1.0R Array
S. cerevisiae Tiling 1.0R Array
S. pombe Tiling 1.0FR Array
P. aeruginosa Genome Array
S. aureus Genome Array
Exon & Gene Level Arrays
Human Genome Arrays
Human Exon 1.0 ST Array
Human Gene 1.0 ST Array
Mouse Genome Arrays
Mouse Exon 1.0 ST Array
Mouse Gene 1.0 ST Array
Rat Genome Arrays
RNA - microRNA
Sequencing
Small RNA Discovery and Analysis is an Illumina Genome Analyzer application that enables the discovery and profiling of all forms of small non-coding RNA from any organism without prior sequence information. With the ability to analyze up to four million small RNAs simultaneously in one sample, DGE: Small RNA Discovery and Analysis offers researchers the broadest and deepest profiling solution for small RNA currently available. Unlike the relative expression profiles microarray hybridization technology generates, DGE records the numerical frequency of a sequence in the library population.
Small RNA Discovery and Analysis
RNA - Total
Focused Set
Using either the Universal-16 or the Universal-96 choice Array Matrix format for sample processing, the DASL Assay offers researchers the opportunity to analyze hundreds to thousands of RNA transcripts derived from previously collected, preserved samples. The DASL Assay leverages the proven GoldenGate Assay protocol to provide high-quality data for an RNA-based application. Because the probe groups span only about 50 bases, partially degraded RNA can be used in the assay. The availability of additional, unique probe sequences per gene increases the sensitivity of the assay, allowing the quantitation of low-abundance transcripts, even in partially degraded samples.
DNA - Focused Set
SNP
The Affymetrix Targeted Genotyping System screens approximately 3,000 to 20,000 SNPs on application-specific or custom microarrays. These assays incorporate Molecular Inversion Probe technology, which generates allele-specific targets labeled with one of four unique fluorescent dyes.
Universal 70K Tag Array
Universal 25K Tag Array
Universal 10K Tag Array
Universal 5K Tag Array
Universal 3K Tag Array
RNA - Total
Whole Genome
Whole genome hybridization-based arrays offer an economical method to quickly perform expression profiling of a few or a large set of specimens. Illumina expression arrays feature up-to-date content largely derived from a recent release of the NCBI RefSeq database. The Direct Hybridization format offers the highest multiplexing for whole-genome expression profiling of up to 48,000 transcripts. Data quality and reproducibility are supported in part by the high level of bead type redundancy (up to an average of 30 beads per probe) on every array. Array probes consist of a single 50-mer gene-specific probe for each transcript from the 3’ end of the transcript. A minimal amount of total RNA (50-100 ng) is required for the single-cycle in vitro transcription (IVT) reaction.
HumanHT-12 Expression BeadChip
MouseWG-6 Expression BeadChip
Performance Specs
MouseRef-8 Expression BeadChip
Performance Specs
Digital Gene Expression (DGE): Tag Profiling
Illumina offers a whole genome expression platform that can generate expression profiles for any transcript from any gene in any organism. DGE creates genome wide expression profiles through sequencing, not hybridization. This allows for the ability to identify, quantify, and annotate expressed transcripts on the level of the whole genome in the absence of existing microarrays or prior sequence knowledge. This assay offers unlimited dynamic range, a tunable depth of coverage for rare transcript discovery and quantification. DGE records the numerical frequency of a sequence in the library population, thereby eliminating background signals.
Digital Gene Expression: Tag Profiling
mRNA-Seq
Whole transcriptome mRNA-Seq supports both genome-wide expression discovery and profiling, enabling the discovery and measurement of transcript abundance over five orders of magnitude, and accurately quantify tissue-specific isoforms. This enables the generation of full sequence date from any poly-A tailed RNA to analyze novel transcripts, novel isoforms, alternative splice sites, rare transcripts, and cSNPs in one experiment.
Transcriptome Analysis: mRNA-Seq
Data Sheet
RNA - Total
Sequencing
Whole transcriptome RNA-Seq supports both genome-wide expression discovery and profiling, enabling the discovery and measurement of transcript abundance over five orders of magnitude, and accurately quantify tissue-specific isoforms. This enables the generation of full sequence date from any poly-A tailed RNA to analyze novel transcripts, novel isoforms, alternative splice sites, rare transcripts, and cSNPs in one experiment.
DNA - Focused Set
DMET
Expression Analysis provides comprehensive analysis of patient genotypes for predicting drug response and metabolic profiling. DMET is the only product available that covers over 90% of ADME Core drug metabolism biomarkers defined by the PharmaADME group (1936 known drug metabolism markers in 225 genes), including common and rare variations, insertions, deletions, copy number, triallelic SNPs and pseudogenes. DMET arrays are useful for discovering new biomarkers, determining drug responders, identifying populations or drug response outliers, selective patient recruitment, differentiating new drugs, optimizing reactivity and for mechanism of action (MOA) studies.
DNA - Focused Set
ChIP Sequencing
Gene Regulation and Epigenetic Analysis / DNA-Protein Interaction Analysis (ChIP-Seq)
Accurately survey interactions between protein, DNA, and RNA to interpret regulation events central to many biological processes and disease states. Quantify in vivo protein-DNA interactions using the combination of chromatin immunoprecipitation with Illumina’s sequencing technology (ChIP-Seq) on a genome-wide scale. Identify a broad range of interactions with confidence, and use millions of counts to differentiate real events from noise.
Illumina sequencing enables cost-effective and precise analysis of protein/nucleic acid interactions and gives you the freedom to interpret binding events without being confined to set number of array features or candidate sequences.
- Open Platform: Study any immunoprecipitate from any organism with a sequenced genome without any prior assumptions
- Comprehensive Access: Map in vivo binding sites across the entire genome
- Cost-Effective Analysis: 1/10-1/30th cost of whole-genome ChIP-chip
- Robust and Precise Detection: Obtain higher signal-to-noise ratios than array platforms, and map binding sites less than 50 bp
- Optimized Kits: Accelerate whole-genome protein-nucleic acid interaction analysis with Illumina’s easy-to-use protocols and analysis tools.
DNA - Focused Set
Resequencing
Illumina’s Genome Analyzer system’s powerful combination of read-length and paired-end flexibility enables the broadest range of genomic sequencing applications. Illumina’s robust sequencing chemistry supports a wide range of read lengths, allowing researchers to tailor each run to meet their needs. The industry-leading raw read accuracy at 75+ bp single-reads, short-insert paired-end reads and long-insert mate pairs enable targeted resequencing utilizing upfront DNA sequence enrichment technologies such as RainDance’s.
RainStorm™ microdroplet-based technology, Agilent’s SureSelect Target Enrichment System, or long range PCR is offered by EA.
DNA - Focused Set
SNP
Illumina offers a broad range of products on both Infinium and GoldenGate based assays for focused content panels that support a variety of applications such as candidate-gene studies in cancer, cardiovascular disease, admixture mapping, and genome-wide genotyping in non-human species.
Currently several Infinium focused content BeadChips are available along with the option to design custom high-density focused content panel. All of these products use 12-sample BeadChips designed with 6,000-60,800 SNPs of your choice; HD Custom BeadChips support 60,0001-200,000 SNP assays.
HumanCVD BeadChip
Performance Specs
CanineSNP20 BeadChip
EquineSNP50 BeadChip
Performance Specs
A variety of standard GoldenGate focused content panels are available, again with the option to design custom assay panels for a wide range of genomes and experimental strategies. These assays can be designed for 32-, 16-, and 12-sample Universal BeadChips or the 96-sample Universal Array Matrix.
African American Admixture Panel
DNA - Whole Genome
Resequencing
Analysis of mitochondrial mutations is informative for a variety of applications from disease genetics to forensic identification. The GeneChip® Human Mitochondrial Resequencing Array 2.0 provides the most efficient and cost-effective method for detecting germ line and heteroplasmic mutations by delivering the complete mitochondrial genome with minimal PCR.
Human Mito Resequencing Array 2.0
Performance Specs
The GeneChip® SARS Array provides a standard assay for complete sequence analysis of the Severe Acute Respiratory Syndrome (SARS). This product is for research purposes only and not intended for use in the diagnosis of disease. The SARS resequencing array is supported on existing Affymetrix instrumentation.
DNA - Focused Set
ADME
The Human1M-Duo DNA assay supports analysis of genes involved in drug absorption, distribution, metabolism, and excretion, with greater than 20,000 markers in more than 300 important gene regions related to drug metabolism.
DNA - Whole Genome
CNV
Copy number variants (CNV) make up more than 10% of the human genome. Altered CNV can lead to gene dosage imbalances and change responses to drugs and susceptibility to disease, including Parkinson’s and Alzheimer’s. In addition, researching the mechanisms that lead to CNV formation may provide valuable insight on human genome evolution. EA offers a variety of analysis options for estimating chromosomal copy number changes. These analyses rely on data from the polymorphic and nonpolymorphic markers on the Affymetrix whole-genome microarrays. Results are returned in tabular and/or graphical displays, including an aligned chromosomal view.
Genome-Wide Human SNP Array 6.0
Performance Specs
GeneChip Human Mapping 250k Sty Array Performance Specs
DNA - Whole Genome
De Novo Sequencing
The unique combination of read length, read depth, and flexible paired-end insert sizes makes Genome Analyzer data ideal for de novo sequencing. The system’s unparalleled raw read accuracy enables confident and efficient production of high quality, long contig assemblies. With the ability to generate up to 18 Gb of 75+ bp paired-end data per run, any lab can rapidly and cost-effectively de novo sequence any sized genome.
Numerous novel algorithmic approaches have been developed that make optimal use of the benefits of Illumina sequencing technology for de novo assembly. Using these tools, researchers are demonstrating the utility of Genome Analyzer data to assemble small and large, complex genomes.
- Paired Reads - Generate long scaffolds and highly accurate contigs using multiple insert lengths with high library diversity.
- Read Length - Use paired-end reads in excess of 2 x 100 bases for mammalian-scale de novo assembly.
- Raw-Read Accuracy - Access the highest yield of perfect reads and Q35 data to generate long, error-free contigs.
- Assembly Tools - Leverage a rapidly growing number of assemblers optimized for Genome Analyzer reads, such as Velvet, EULER-SR, and SSAKE.
DNA - Whole Genome
Methylation
DNA methylation plays a critical role in the regulation of gene expression and is known to be an essential mechanism for guiding normal cellular development. Additionally, numerous studies have implicated aberrant methylation in the etiology of many human diseases including cancer. For the investigation of genome-wide methylation patterns Illumina employs its Infinium based chemistry that quantitatively interrogates 27,578 CpG loci covering more than 14,000 genes. This assays requires 500 ng of input genomic DNA, and profiles 12 samples in parallel.
Illumina Human Methylation27 BeadChip
Illumina Human Methylation 450 BeadChip
Request a Quote | Specimen/Shipping Requirements
DNA - Whole Genome
Resequencing
Illumina’s Genome Analyzer system’s powerful combination of read-length and paired-end flexibility enables the broadest range of genomic sequencing applications. Illumina’s robust sequencing chemistry supports a wide range of read lengths, allowing researchers to tailor each run to meet their needs. This platform supports de novo whole-genome sequencing and resequencing, SNP discovery, the identification of copy number variations and chromosomal rearrangements including deletions, insertions, and translocations.
Genome Analyzer Applications: DNA Sequencing
DNA - Whole Genome
Genotyping
EA offers both discovery and clinical services using the Affymetrix genotyping platform to identify SNPs. With the Affymetrix genome-wide GeneChip arrays, we screen up to approximately one million human SNPs per microarray. Each SNP is interrogated by a set of different allele-specific probes resulting in the generation of a robust data set. The primary data files, and data files that can be incorporated into analysis software, are returned to you. In addition, we prepare a QC report that contains the QC results collected for each sample during target preparation and hybridization, such as spectrophotometer readings and hybridization metrics.
The Human SNP assay kit amplifies known polymorphic regions in genomic DNA after enzyme digestion.
Genome-Wide Human SNP Array 6.0
Performance Specs
Genome-Wide Human SNP Array 5.0
Performance Specs
Mapping 500k Array Set
Performance Specs
Mapping 100k Array Set
Performance Specs
DNA - Whole Genome
CNV
Copy number variants (CNV) account for a substantial portion of the variation within the human genome. Altered CNV can lead to gene dosage imbalances and change responses to drugs and susceptibility to disease, including Parkinson’s and Alzheimer’s. Expression Analysis is pleased to offer Illumina’s DNA Analysis BeadChips targeting this new CNV content.
DNA - Whole Genome
Genotyping
Expression Analysis offers Illumina’s Infinium HD whole genome DNA analysis BeadChips for SNP genotyping and analysis of structural variants. Assay panels contain from 300,000 to 1,200,000 markers per specimen and accommodate 2 to 12 samples per chip and require only 200 ng to 400 ng of genomic DNA per sample. Custom content can also be added to these chips. The Infinium HD Assay procedure employs whole-genome amplification without PCR or ligation with two-step allele detection providing high call rates and accuracy.
HumanOmni5-Quad
HumanOmni2.5S
HumanOmni2.5-8
The HumanOmni1-Quad BeadChip provides an unparalleled, extensive view of the genome, in a high-throughput format.
Intelligently selected SNPs from all three HapMap phases capture more genomic variation and provide the best combination of power, price and throughput available for genome wide association studies.
Illumina HumanOmni1-Quad BeadChip
The HumanOmni2.5-Quad is the most comprehensive set of common and unexplored rare SNP content for diverse world populations.
Variation down to 2.5% minor allele frequency (MAF) - that’s 50% greater coverage of common and rare variants than any other previous array.
Illumina HumanOmni2.5-Quad BeadChip
The HumanOmni1S is a supplemental microarry, adding novel data from the first releases of the 1000 Genomes Project (1kGP) with a minor allele frequency to ~2.5%
The Human OmniExpress allows comprehensive coverage of common variants with the industry’s highest output.
Illumina The HumanOmniExpress BeadChip