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Nanostring nCounter System
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nanoString nCounter Analysis System

One Powerful, Fully Automated System for Translation Research

NanoString’s nCounter platform is complete solution for digitally detection and counting large sets of molecules in a single tube.
For translational researchers studying pathways or hypotheses generated on discovery platforms, the nCounter analysis system is ideal solution.
 
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Feature

1. More Genes
: Analyze multiple pathways for up to 800 genes

2. High Sensitivity : Eliminate sample splitting, minimize amplification - get better data from every cell

3. Digital Counting : Determine fractional fold changes - eliminate the variability of analog data

4. High Throughput : Analyze hundreds of samples per day

5. Sample compatible
: Study even difficult sample types, including FFPE samples


The Chemistry and Technology
  
The nCounter Analysis System utilizes a novel digital color-coded barcode technology that is based on direct multiplexed measurement of gene expression and offers high levels of precision and sensitivity (>1 copy per cell). The technology uses molecular "barcodes" and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.
Each color-coded barcode represents a single target molecule. Barcodes hybridize directly to your target molecules and can be individually counted without the need for amplification– providing very sensitive digital data.

1. Hybridization
NanoString’s Technology employs two ~50 base probes per mRNA that hybridize in solution. The Reporter Probe carries the signal; the Capture Probe allows the complex to be immobilized for data collection스크린샷 2013-05-24 오후 3.42.20.png

2. Purify and Immobilize (Sample Processing)
After hybridization, the excess probes are removed and the probe/target complexes aligned and immobilized in the nCounter Cartridge.
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3. Count (Digital Data Acquisition)
Sample Cartridges are placed in the Digital Analyzer for data collection. Color codes on the surface of the cartridge are counted and tabulated for each target molecule.



nCounter Analysis System

Fully Automated, Multi-application System
The nCounter® Analysis System delivers a complete and cost-effective solution for detecting and counting large sets of target molecules in a high-performance, user-friendly workflow.

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nCounter® Prep Station and nCounter® Digital Analyzer


Feature
Delivers 10,000s of precise data points every day
- Digital detection of target molecules and high levels of multiplexing means no compromise between data quality and data quantity.
Straightforward, high-quality data with rapid results
-Data output files include the target identifier and count number along with a comprehensive set of internal controls that enables each assay to be highly quantitative and reproducible.
Sample type flexibility
Ready-to-use reagents
Intuitive, easy-to-use touchscreen user-interface
Manufactured under GMP/ISO 13485

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Simplified, User-friendly Workflow

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nCounter® Custom CodeSet Design Process

The nCounter Custom CodeSet design process is completed in 4 easy steps .

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1. nCounter® Gene Expression CodeSets

nCounter® Gene Expression CodeSets offer a cost-effective way to analyze the expression levels of up to 800 genes simultaneously, with high precision and accuracy. The system can directly assay tissue and blood lysates as well as Formalin-Fixed Paraffin-Embedded (FFPE) extracts in a simple workflow that requires only 15 minutes of total hands-on time per reaction.

Feature

Gene Expression Panels                
Many off-the-shelf Panel Kits are currently available which include CodeSets targeting genes associated with inflammation, immunology, and cancer as well as a reference gene CodeSet  for aiding in reference gene selection. Each Panel Kit arrives in your lab QC’d and ready-to-use with all the reagents and consumables you need to perform the assay.

1. nCounter® GX Human Kinase Kit
: Gene Expression CodeSet profiling of 519 human kinase genes and 8 internal reference genes. CodeSets are available in quantities to run 12, 24, 48 or 96 assays
2. nCounter® GX Human Immunology Kit
: Gene Expression CodeSet profiling 511 immunology-related human genes and 15 internal reference genes. CodeSets are available in quantities to run 12, 24, 48 or 96 assays
3. nCounter® Human Cancer Reference Kit
: Gene Expression CodeSet profiling 230 cancer-related human genes and 6 internal reference genes. CodeSets are available in quantities to run 12, 24, 48 or 96 assays.
4. nCounter® Human Inflammation Kit
: Gene Expression CodeSet profiling 184 inflammation-related human genes and 6 internal reference genes. CodeSets are available in quantities to run 12, 24, 48 or 96 assays
5. nCounter® Mouse Inflammation Kit
: Gene Expression CodeSet profiling 179 inflammation-related mouse genes and 6 internal reference genes. CodeSets are available in quantities to run 12, 24, 48 or 96 assays.
6. nCounter® Human Reference GX Kit
: Gene Expression CodeSet profiling 18 human reference genes expressed at different levels across a wide variety of tissues. This kit is designed to provide a fast and easy way to select reference genes for your experiments. CodeSets are available in quantities to run 12, 24, 48 or 96 assays
7. nCounter® Customer Assay Evaluation (CAE) Kit
: Gene Expression CodeSet profiling 48 human genes from the Microarray Quality Control Study (MAQC). This kit is designed for core labs to train additional operators of the nCounter Analysis System. CodeSets are available in quantities to run 12, 24, 48 or 96 assays
8. nCounter® Virtual Gene Sets


9. Oncology Panel

       PanCancer Pathways Panel

       Perform multiplex gene expression analysis with 770 genes from 13 cancer-associated canonical pathways including:

       MAPK, STAT, PI3K, RAS, Cell Cycle, Apoptosis, Hedgehog, Wnt, DNA Damage Control, Transcriptional Regulation,

       Chromatin Modification, and TGF-ẞ.

       PanCancer Immune Profiling Panel

       Perform multiplex gene expression analysis with 770 genes from 24 different immune cell types, common checkpoint

       inhibitors, CT antigens, and genes covering both the adaptive and innate immune response.

       PanCancer Progression Panel

       Perform multiplex gene expression analysis with 770 genes from each step in the cancer progression process

       including: angiogenesis, extracellular matrix remodeling (ECM), epithelial-to-mesenchymal transition (EMT) and

       metastasis.

       Breast Cancer 360Panel

       The nCounter Breast Cancer 360 panel and data analysis service provides a unique 360 degree view of gene

       expression for the breast tumor microenvironment and immune response. Now researchers can more quickly decode

       the complexities of breast cancer biology, develop novel breast cancer gene signatures, and categorize disease

       heterogeneity using 32 biological signatures including signatures based upon the validated PAM50 and Tumor

       Inflammation Signature* (TIS) assays

       PanCancer IO 360Panel

       The PanCancer IO 360 Gene Expression Panel is a unique 770 gene expression panel for research use only (RUO) that

       combines vital components involved in the complex interplay between the tumor, microenvironment and immune

       response in cancer allowing for a multifaceted characterization of disease biology and interrogation of mechanisms of

       immune evasion.

       Developed specifically for translational research, this powerful new panel incorporates 47 potentially predictive

       Research Use Only (RUO) biological signatures including the 18-gene Tumor Inflammation Signature as recently

       described in JCI


10. Neuroscience Panel

        ① Neuropathology Panels

       Perform comprehensive multiplex gene expression analysis with 770 genes included in six fundamental themes of       

       neurodegeneration: neurotransmission, neuron-glia interaction, neuroplasticity, cell structure integrity,

       neuroinflammation and metabolism.

       Neuroinflammation Panels

       Perform comprehensive multiplex gene expression analysis with 770 genes included for research of immunity and

       inflammation, neurobiology and neuropathology, and metabolism and stress


Custom CodeSets
NanoString also offers the ultimate in flexibility by designing CodeSets to your specifications for any organism and gene set that you wish to analyze. Each customer receives a free consultation with our CodeSet design team.

Sensitivity and Reproducibility

Sensitivity, Reproductibility and Dynamic Range
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Gene counts from two technical replicates plotted against one another demonstrate the assay reproducibility over a wide dynamic range (10–50,000 counts). 
One total RNA sample was split into two separate hybridization reactions and processed independently on the nCounter Analysis System. In this experiment, 75 counts is equal to a concentration of approximately 1 copy per cell. This data illustrates the high level of sensitivity and precision of the assay even at very low levels of expression.

Cell Lysate with Matched Total RNA
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Raw cell lysate was input directly into the nCounter Analysis System hybridization reaction using approximately 2,500, 5,000 and 10,000 cells in lysis buffer and compared to 100ng of purified total RNA as plotted on the x-axis. Results were highly correlated with one another and demonstrate that comparable data can be achieved with either protocol.

Sample Flexibility


Matched Whole Blood Lysate and Total RNA


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PAXgene™ lysed whole blood replicates were input directly into the hybridization reaction and compared to a matched purified total RNA sample as plotted on the x-axis. Results demonstrate that high quality data can be obtained by using PAXgene lysed whole blood.

FFPE Samples
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FFPE-derived purified total RNA was input directly into the hybridization reaction and compared to a matched purified total RNA from fresh tissue on the x-axis. Results
demonstrate that high quality data can be achieved from FFPE samples.



2. nCounter® Single Cell Gene Expression Assay

The nCounter® Single Cell Gene Expression Assay greatly expands the types of studies that can be analyzed on the nCounter Analysis System. Entire biological pathways and custom gene signatures can now be studied for single cells and the flexibility of the single tube assay allows interrogation of the exact gene number of interest.

Feature

More Genes
Analyze multiple pathways for up to 800 genes flexible format allows interrogation of exact gene number of interest; same workflow when analyzing anywhere from 20 to 800 genes
Single Cell Sensitivity
Obtain single cell sensitivity while minimizing amplification single tube assay provides a simple workflow & utilizes the entire sample
Digital Counting
Single molecule counting minimizes data noise determine fractional fold changes
High Throughput
Obtain 10,000s of single cell expression values every day

Up to 800 Targets from a Single Cell
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nCounter Single Cell Expression Assays enables detection of up to 800 genes. Fold changes observed between Human Reference and Brain Reference total RNA with 800
probes. Values from standard nCounter Gene Expression assays with 100ng total RNA as input (x-axis) are shown vs. fold changes observed with 100pg total RNA input material prepared according to the nCounter Single Cell Gene Expression Protocol (y-axis).

High Correlation of Fold Changes
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nCounter Single Cell Expression Assays enable sensitive detection of fold changes at the single cell level. Fold changes observed with probes using standard GX assay input of 100ng on the x-axis and 10pg, an amount of RNA equivalent to a single cell, prepared according to the nCounter Single Cell Gene Expression Protocol on the y-axis.

Make Every Cell Count
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 Counts observed after amplification with the input amount indicated for individual probes in a 150-plex CodeSet are shown with robust expression (>250 counts) in red, moderate expression (50–250 counts) in yellow and minimal expression (<50 counts) in green. nCounter Single Cell Expression Assays identify distinct gene expression profiles in single cells. Data is shown for 90 single cells, the average of 90 individual cells, and a triplicate average of a 100-cell pool.


3. nCounter® miRNA Expression Assays

nCounter® miRNA Expression Assays provide a cost-effective profiling solution capable of accurately discriminating between miRNAs at single-base resolution. Each CodeSet contains a comprehensive collection of miRNAs in a single, highly multiplexed assayHighly multiplexed, direct digital detection and counting of miRNAs in a single reaction without amplification.

Feature
Accurate Identification with High Specificity
At single-base resolution, the nCounter miRNA assay can accurately distinguish between highly similar miRNAs with great specificity. The innovative protocol is highly sensitive and requires no amplification steps.
Comprehensive Transcriptome Coverage
Comprehensive CodeSets are available for human, mouse, rat and fly miRNA transcriptomes. High levels of multiplexing, digital counting, and the capacity to process up to 96 samples per 24-hour time period* provide fast and cost-effective access to thousands of data points per day.
miRNA Expression Panels
nCounter Human miRNA Assay Kit
: A comprehensive collection of 800 human miRNAs derived from miRBase v.18
nCounter Mouse miRNA Assay Kit
:A comprehensive collection of more than 600 mouse and mouse-associated viral miRNAs derived from miRBase.
nCounter Rat miRNA Assay Kit
:A comprehensive collection of more than 400 Rat miRNAs derived from miRBase.
nCounter Fly miRNA Assay Kit

Elegant, Simple with Remarkable results
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To prepare a sample containing miRNA molecules for hybridization in the nCounter assay, proprietary DNA sequences called miRtags are ligated to the mature miRNAs
through complementarity with sequence-specific bridging oligonucleotides (bridges). This multiplexed reaction leads to the highly precise, sequence-specific tagging of all miRNAs in a single tube. Excess tags and bridges are removed via a simple enzymatic step in the same tube. No further purification is required.

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The miRtagged mature miRNA is then hybridized to a probe pair in the standard nCounter gene expression assay workflow. The Reporter Probe carries the signal; the
Capture Probe allows the complex to be immobilized for data collection. Hybridization occurs in one multiplexed reaction.


Sensitivity - Single base resolution

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The Let7 family of miRNAs contains several members differing in sequence by as littleas a single nucleotide. Percent cross-hybridization for the Let7 probes was assessed
by tagging and hybridizing individual Let7 family miRNAs in the presence of the comprehensive human miRNA CodeSet including probes to eight Let7 family members.
The minimal cross-hydridization observed (with no probe exceeding 6%) indicates that the nCounter miRNA assay can accurately discriminate similar sequence miRNAs with great specificity.


FFPE samples 

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Formalin-Fixed Paraffin-Embedded (FFPE) samples are difficult to analyze with many techniques due to RNA degradation. To demonstrate the ability of the miRNA assay to analyze degraded RNA samples, we tested FFPE-derived purified total RNA from liver samples against purified total RNA from matched fresh-frozen tissue using the nCounter Human miRNA Expression Assay Kit. Counts for all detected miRNA species were highly correlated (R2 > 0.95) between the two sample types.

Assay Reproducibility
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To demonstrate the reproducibility of the miRNA assay, we used the nCounter Human miRNA Expression Assay Kit to analyze commercially purchased human total RNA. The samples were prepared and run on the system separately. When plotted against one another, the assay demonstrated very high reproducibility, with R2 values of greater than 0.99.



4. nCounter® Plex2™ Expression Assay

The nCounter® Plex2™ Assay offers a cost-effective way to analyze expression levels of hundreds of gene targets in multiple samples simultaneously in a single tube. The system can directly assay tissue and blood lysates as well as Formalin-Fixed Paraffin-Embedded (FFPE) extracts in a high-throughput workflow that is ideal for researchers with large numbers of samples

Feature
Multiplex in 2-dimensions –  multiplex hundreds of targets and multiple samples in a single tube
Customizable to study size – measure between 20–400 customizable targets in a single tube
Digital counting – digital data in a high throughput format 
Directly assay tissue extracts and whole-blood lysates, total RNA, cell lysates, and FFPE

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To determine assay precision when 4 multiple samples are profiled in a single tube, 4 samples derived from 2.5μl of Hela cell lysates were independently hybridized with 200 probe CodeSets each targeting the same 200 genes (each CodeSet contained 200 independent barcodes). After hybridization, the 4 samples were combined into a single tube for processing on the nCounter System. Technical replicate data were normalized and gene expression counts were then plotted to determine assay precision across all replicates. The plot below displays the correlation of 2 replicate samples. Comparisons between replicates showed R2 ≥ 0.99.


5. nCounter® lncRNA Expression Assay
    The nCounter® Custom lncRNA Assay enables researchers to study focused sets of up to 800 lncRNAs with high
    precision and minimal hands-on time.

    Feature
    High precision, digital quantification of lncRNAs
    Analyze up to 800 lncRNAs (and mRNAs) in a single reaction
    Quantify immunoprecipitated RNA directly with no amplification
    15 minutes of hands-on time for up to 9,600 data points
    Compatible with FFPE, crude cell lysates, and other challenging sample types


    6. nCounter® ChIP-String Expression Assay

    The nCounter ChIP-String Assay is a read-out method designed to measure dsDNA fragments enriched via user-defined chromatin immunoprecipitation protocols. Based on nCounter Technology, the assay reliably quantifies as few as 5,000 molecules of DNA without amplification. The assay is ideal for validating ChIP-Seq results and screening large sample sets against focused sets of loci involved in chromatin remodeling and gene expression. Additionally, streamline the screening of ChIP antibodies, library pre-sequencing, or optimize IP protocols. nCounter ChIP-String delivers the same level of performance, flexibility, and low hands-on time as other nCounter assays.

    Specification
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    Performance
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    nCounter Analysis System
    Overview of the nCounter Analysis System and critical performance specifications.
    nCounter Single Cell Gene Expression Assay
    Analyze multiple pathways for up to 800 genes, eliminate sample splitting, minimize amplification - get better data from every cell.
    nCounter Plex2 Assay
    Analyze expression levels in multiple samples and hundreds of gene targets simultaneously in a single tube.
    nCounter v2 Cancer CN Assay
    Copy number analysis of 87 genes commonly amplified or deleted in cancer.
    nCounter Human v2 miRNA Expression Assay
    Overview of the nCounter Human v2 miRNA Expression Assay Kit, an off-the-shelf panel profiling of 800 human miRNAs from miRBase v.18.
    nCounter Mouse miRNA Expression Assay
    Overview of the nCounter Mouse miRNA Expression Assay Kit, an off-the-shelf panel profiling of more than 600 murine and murine-associated viral miRNAs.
    nCounter Rat miRNA Expression Assay
    Overview of the nCounter Rat miRNA Expression Assay Kit, an off-the-shelf panel profiling of 423 rat miRNAs.
    nCounter D. melanogaster (Fly) miRNA Expression Assay
    Overview of the nCounter Fly miRNA Expression Assay Kit, an off-the-shelf panel profiling of 184 D. melanogaster miRNAs.
    nCounter miRGE Assay CodeSet
    Overview of the nCounter miRGE Expression Assay Kit, a customized CodeSet which can measure between 5-30 miRNAs and 100-200 mRNAs in a single reaction.
    nCounter Custom lncRNA Assay
    Study focused sets of up to 800 lncRNAs in a single reaction.
    nCounter ChIP-String Assay
    Customized CodeSet for analysis of DNA enriched by chromatin immunoprecipitation.
    nCounter Leukemia Fusion GX Assay
    Overview of the nCounter Fusion Gene Expression Assay and critical performance specifications.
    nCounter Copy Number Variation Assay
     
    nCounter Human Karyotype
     
    nCounter GX Human Immunology
    Gene Expression CodeSet profiling 511 immunology-related human genes and 15 internal reference genes. CodeSets are available in quantities to run 12, 24, 48 or 96 assays.
    nCounter GX Human Kinase
    Overview of the nCounter GX Human Kinase Kit, an off-the-shelf panel enabling gene expression profiling of 519 human Kinase genes in a single reaction.
    nCounter Mouse miRNA Expression Assay
    Overview of the nCounter Mouse miRNA Expression Assay Kit, an off-the-shelf panel profiling of over 600 mouse and mouse-associated viral miRNAs derived from miRBase.
    nCounter Rat miRNA Expression Assay
    Overview of the nCounter Rat miRNA Expression Assay, an off-the-shelf panel profiling of 400 rat miRNAs in a single reaction.
    nCounter Custom Copy Number Variation Assay (Early Access)
    Overview of the nCounter Customer Copy Number Variation Assay Kit, a custom assay for human genomic DNA that allows users to analyze up to 200 genomic regions in a single multiplexed reaction.
    nCounter Human Cancer Reference
    Overview of the nCounter Human Cancer Reference Kit, an off-the-shelf panel enabling gene expression profiling of 230 cancer-related human genes in a single reaction.
    nCounter Human Inflammation
    Overview of the nCounter Human Inflammation Kit, an off-the-shelf panel enabling gene expression profiling of 184 inflammation-related human genes in a single reaction.
    nCounter Mouse Inflammation
    Overview of the nCounter Mouse Inflammation Kit, an off-the-shelf panel enabling gene expression profiling of 179 inflammation-related mouse genes in a single reaction.
    nCounter Virtual Angiogenesis Gene Set
    Pre-selected angiogenesis gene set to accelerate your research; Made to order, rapidly delivered.
    nCounter Virtual Breast Cancer-Estrogen Receptor Gene Set
    Pre-selected breast cancer-estrogen receptor gene set to accelerate your research; Made to order, rapidly delivered.
    nCounter Virtual p53 Pathway Gene Set
    Pre-selected p53 pathway gene set to accelerate your research; Made to order, rapidly delivered.
    nCounter Virtual Apoptosis Gene Set
    Pre-selected apoptosis gene set to accelerate your research; Made to order, rapidly delivered.
    nCounter Virtual Cell Cycle Gene Set
    Pre-selected cell cycle gene set to accelerate your research; Made to order, rapidly delivered.
    nCounter Virtual Jak-Stat Pathway Gene Set
    Pre-selected jak-stat pathway gene set to accelerate your research; Made to order, rapidly delivered.
    nCounter Virtual Stem Cell Gene Set
    Pre-selected stem cell gene set to accelerate your research; Made to order, rapidly delivered.
    nCounter Virtual Wnt Pathway Gene Set
    Pre-selected wnt pathway gene set to accelerate your research; Made to order, rapidly delivered.
    nCounter Virtual Mouse Cancer Gene Set
    Pre-selected mouse cancer gene set to accelerate your research; Made to order, rapidly delivered.
    nCounter Virtual Mouse Stem Cell Gene Set
    Pre-selected mouse stem cell gene set to accelerate your research; Made to order, rapidly delivered.

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