Difference between revisions of "NanoString"

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The nCounter™ Analysis System measures transcript abundance by tagging and counting individual mRNA molecules using a novel fluorescent barcoding technology. The system is able to detect 1 copy of mRNA per cell, can measure up to 800 genes per reaction, and requires only 10-100 ng of total RNA for analysis. The nCounter can also be used for miRNA profiling and CNV analysis.
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|title=nCounter System
 
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|subtitle=nCounter System (NanoString)
 
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Highlights:
  
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ChIP-Sequencing (or ChIP-Seq) combines chromatin immunoprecipitation (ChIP) with DNA sequencing allowing researchers to identify the binding sites of DNA-associated proteins. a
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* Fills the throughput niche between qPCR and microarrays for "mid-multiplex" assays
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* Ideal for assays of dozens to hundreds of genes in 50+ samples
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* More time-efficient and cost-effective than qPCR
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* Direct measurement of transcript abundance (No amplification, digital readout)
  
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Please see below for further details about the service.
 
  
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== Sample Submission Guidelines ==
 
  
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Users are required to prepare their own sequencing libraries. Samples should be gel-purified and provided UNDILUTED in EB.
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== Sample Submission/Preparation ==
  
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Users should submit 5uL of undiluted sample. We will determine the concentration by RT-PCR and make the appropriate dilutions. Excess sample will be retained in our freezers for potential future re-run. Users are also strongly encouraged to retain a portion of their samples in case of emergency.  
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New users should contact WIGTC for training and consultation. Custom CodeSets* are designed by Nanostring specifically for your assay. CodeSet pricing varies with number of targets and samples. Delivery times for CodeSet design and synthesis can be several weeks.  
  
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GTC will provide sequencing primers for libraries prepared with standard Illumina adapters. If custom sequencing primers are required they must be provided at the time of sample submission.  
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Typically 100 ng of total RNA is recommended though the assay is very tolerant to smaller inputs or partially degraded samples such as from FFPE.  
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(*A CodeSet is the collection of reporter and capture probes for all genes of interest in the assay).
  
 
== Data ==
 
== Data ==
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=== Is there documentation available about analyzing my data? ===
 
=== Is there documentation available about analyzing my data? ===
 
Yes, there is a data analysis guidelines document that is available in the Product Literature from Nanostring. You can download it here:  
 
Yes, there is a data analysis guidelines document that is available in the Product Literature from Nanostring. You can download it here:  
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== Turnaround Time ==
 
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Wait times vary but are generally two weeks or less.
 
  
 
== Pricing ==
 
== Pricing ==
  
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{{PricingHeader}}
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Please refer to the [[Pricing]] Section
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{{PricingRow|Sequencing - 36 bp Single Read|Sample|~$850|Cluster, Sequence, Pipeline}}
 
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{{PricingRow|Sequencing - 36 bp Paired-End Reads|Sample|~$1,500|Cluster, Sequence, Pipeline}}
 
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{{PricingRow|Sample prep - ChIP Seq|Sample|Inquire|-}}
 
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{{PricingLastRow|Genome Alignment and other analysis|Sample|Inquire|-}}
 

Latest revision as of 17:43, 21 September 2010

The nCounter™ Analysis System measures transcript abundance by tagging and counting individual mRNA molecules using a novel fluorescent barcoding technology. The system is able to detect 1 copy of mRNA per cell, can measure up to 800 genes per reaction, and requires only 10-100 ng of total RNA for analysis. The nCounter can also be used for miRNA profiling and CNV analysis.

Highlights:

  • Fills the throughput niche between qPCR and microarrays for "mid-multiplex" assays
  • Ideal for assays of dozens to hundreds of genes in 50+ samples
  • More time-efficient and cost-effective than qPCR
  • Direct measurement of transcript abundance (No amplification, digital readout)


Sample Submission/Preparation

New users should contact WIGTC for training and consultation. Custom CodeSets* are designed by Nanostring specifically for your assay. CodeSet pricing varies with number of targets and samples. Delivery times for CodeSet design and synthesis can be several weeks.

Typically 100 ng of total RNA is recommended though the assay is very tolerant to smaller inputs or partially degraded samples such as from FFPE.

(*A CodeSet is the collection of reporter and capture probes for all genes of interest in the assay).

Data

How do you normalize the data?

First normalize using the internal system controls to remove any slight assay-to-assay system variation and then normalize using 3-4 validated endogenous controls.

Can I compare the nCounter System with my microarray data?

Yes. The fold change data obtained from an nCounter analysis should correlate with fold change results obtained from microarray analyses.

Can nCounter data be used together with qPCR data?

Yes, both in terms of relative expression levels and fold changes.

How do I analyze my data?

The comma separated value file returned by the nCounter system is easily imported and analyzed in other programs, including Excel.

Is there documentation available about analyzing my data?

Yes, there is a data analysis guidelines document that is available in the Product Literature from Nanostring. You can download it here:

Pricing

Please refer to the Pricing Section

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