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nanostring nCounter™ system
Cost-sharing strategy:
The cost-effectiveness of NanoString technology is evident when a large number of genes (ie. more than 30), or a large number of samples (ie. more than 50), are processed.
At the UHNMAC, we understand that evaluating new technologies can be expensive. Thus, we have launched a cost-sharing strategy that will enable researchers to detect and profile 10 gene transcripts of their choice, plus profile an additional 70 transcripts (chosen by other researchers), for $125 per sample with a minimum of 12 samples.
Why choose nanostrings for gene quantification?
- more time-efficient and cost-effective than qPCR, especially if you have more than 10 genes to evaluate
- no assay optimisation - custom probes are created for you (you can even select the region of the gene!)
- nanostring assays are highly reproducible
- the nanostring assay does not involve enzymology or amplification
- digital detection, which uses discrete units for measurement, rather than analogue detection, which uses the relative level of signal, is used to detect and quantify the mRNA transcripts
Genes included in the trial CodeSet
The CodeSet is a collection of all reporter probes and capture probes for all genes of interest in an assay. For the purposes of this trial offer, the "trial CodeSet" will consist of a total of 80 genes (10 genes will be selected by each of 8 researchers, assuming each researcher submits 12 samples; if 24 samples are submitted by one researcher, he/she can select 20 genes).
Researchers will be able to view the gene profiles of the entire trial CodeSet (80 genes), even though some of these genes may not be relevant to their research. In order to select 10 custom genes to add to the Trial CodeSet, we require a minimum of 12 samples. If you have less than 12 samples, you are welcome to team up with another researcher!
If you would like an idea of genes that have already been used for nanostring assays, NanoString Technologies has comprehensive lists of genes available for various disease states and biological processes including angiogenesis, apoptosis, breast cancer-estrogen receptor, cancer, cell cycle, inflammation, and stem cells. NanoString also offers gene expression panels for human kinase genes and GPCR genes.
Please visit the NanoString website to view the genes included in these sets.
Please note that this pricing is for academic groups. Commercial customers, please inquire.
Contact: Kelly Jackson at
How the cost-sharing strategy will work:
First, please email Kelly and let her know how many samples you would like to evaluate and provide your list of 10 genes of interest. Once a set of 80 genes has been collected, the probes will be designed and manufactured by NanoString Technologies.
Once the trial CodeSet has been shipped to us from NanoString Technologies, the samples will be processed.
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Once you send us this information, the UHN Customs Officer will generate the appropriate Customs document and send it to you via e-mail. This document must be included with the waybill on your package.
Return to the NanoString service webpage.
Quick questions:
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- How much total RNA is required?
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100 ng of high quality total RNA is required for analysis using NanoStrings. We request an additional 100 ng of total RNA for analysis on the Agilent Bioanalyzer.
- As part of the trial offer, can I run less than 12 samples?
Yes, you can run less than 12 samples. However, the NanoString nCounter System processes 12 samples at a time, so we will wait until we accumulate a total of 12 samples before proceeding. Also, you will not be able to choose 10 custom genes to add to the Trial CodeSet unless you have at least 12 samples. You can always team up with another researcher!
- Can I run FFPE samples?
Total RNA, including RNA from FFPE samples, should meet minimal integrity requirements (more than 50% greater than 300bp) in order to obtain good results. Total RNA from FFPE samples will be analysed on the Agilent Bioanalyzer prior to setting up the nanostring assay.
- What is a CodeSet?
Each unique mRNA sequence has its own pair of reporter and capture probes. The CodeSet is the collection of all reporter probes and capture probes for all genes of interest in an assay. For the purposes of this trial offer, the "Trial CodeSet" will consist of 110 pre-selected cancer-associated genes plus 10 genes chosen by the researcher(s), with a minimum of 12 samples.
- Are there control samples in the CodeSets?
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The nCounter CodeSets include positive control codes and synthetic RNA targets that have been spiked in to the CodeSets at concentrations ranging from 0.1fM -100fM which roughly correspond to 0.2-200 copies per cell of mRNA.
There are six internal reference transcripts included in the Trial CodeSet, including GAPDH, CLTC (heavy chain clathrin), GUSβ (beta glucuronidase), HPRT1 (hypoxanthine phosphoribosyltransferase 1), PGK1 (phosphoglycerate kinase 1), and TUBβ (beta tubulin). - How is the nCounter™ data analysed?
The nCounter system provides a comma separated value file that can be imported and analysed in programs like Excel, Open Office, or Matlab. NanoString Technologies has provided guidelines for normalisation and data analysis. The nCounter Data Analysis Guidelines will provide more information.
- How long does it take to get results from one sample?
The entire assay takes 22 hours of one 12-sample cartridge (including the 16 hour -overnight hybridisation, two hours on the liquid-handling Prep Station, and four hours on the Digital Analyzer). The time to run the assay is independent of the number of genes analysed (the assay time is the same for a 20-plex assay and a 550-plex assay).
For researchers submitting multiples of 12 samples, it should take us about one week to schedule your samples for processing once we have received the Trial CodeSet from NanoString Technologies.- How is the nCounter™ system quantitative, and how sensitive is it?
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The nCounter system is able to detect, count and report molecules across all biological levels of expression. The nCounter CodeSets include positive control codes and synthetic RNA targets that have been spiked in to the CodeSet at concentrations ranging from 0.1fM -100fM which roughly correspond to 0.2-200 copies per cell of mRNA. Using these internal controls, users can plot a regression line and quantify relative levels of expression for each of the genes in the CodeSet. The sensitivity of the nCounter system is comparable to qPCR.