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 COHR: Center for Oral Health Research | Oral Histology & Digital Imaging Core | nanostring

nCounter Analysis System from Nanostring Technologies

The nCounter Analysis System offers researchers the ability to easily profile hundreds of mRNAs, miRNAs, or DNA targets in a single tube.  All reaction steps are performed in a single tube and processed on the fully automated system.  NanoString Technologies offers several predefined gene sets for human and mouse research topics including cancer, inflammation and immunology or you can define your genes, miRNAs or DNA regions of interest to create a customized CodeSet for your research.

If you are interested in more information on how your research may benefit from the nCounter Analysis System, please complete the attached interest survey and return it to the COHR by e-mail ( or in person (BSB 129).

The nCounter Analysis System is operational and available to researchers.  To schedule training on operation of the system, please contact Johannes Aartun.  Once personnel are trained, they will be able to schedule time on the system to conduct their own analyses.

                                                            **PROMOTIONAL OFFER DETAILS**

Free NanoString Trials: Beginning January 2, 2014, we will be accepting up to six (6) RNA samples (100 ng total RNA) for processing and analysis on the system using the custom CodeSets we have purchased.  The first 32 faculty members submitting up to 6 samples will receive analysis at no cost (all samples must be submitted at the same time; only the custom CodeSets detailed below are available for the promotion).  Additional samples can be run at $600/up to 6 samples until the custom CodeSets are exhausted.  This offer is open to all MUSC faculty members and will be offered until all of the custom CodeSets have been utilized.

Interested users should bring RNA samples along with the attached sample submission form to BSB 129.  For standard analyses, RNA should be diluted to 20 ng/µl in RNase-free water; 33 ng/µl for miRNA analyses.  A total of 100 ng of total RNA is recommended.  Be sure to indicate which CodeSet you would like to utilize or if you will be doing miRNA analyses. Additional information for RNA preparation and the nCounter Analysis process can be found in the below links.

NanoString Manuals
Gene Expression Assay ManualmiRNA Expression Assay Manual

Custom CodeSet: We have two custom CodeSets available for RNA analysis based on the genes submitted by MUSC researchers through this promotional offer.  CodeSet-1 should be used for mouse studies, while genes from a variety of species including human, rat, C. glabrata, zebrafish and other marine organisms are included in CodeSet-2.  Gene lists for the two CodeSets can be downloaded from the links below.  

CodeSet Gene Lists

(human, rat, C. glabrata,

zebrafish, marine species)

Training: We will also be providing training on the nCounter Analysis System to a limited number of interested users at no charge during the promotional period.  If you are interested in receiving training, please contact Johannes Aartun to obtain information regarding available times.

After the promotional period, all users will conduct their own analyses and be charged a nominal fee ($150/12 samples run) to cover the costs of system maintenance and service.  Users will be responsible for all materials and consumables needed for analyses. 

Data Analysis: Data from the nCounter Analysis System will be emailed directly to the contact listed on the sample submission form. nSolver analysis software is available as a free download on the NanoString website. Additional information for data analysis can be found in the below link.

nCounter Expression Data Analysis Guide

Pre-defined CodeSets available from NanoString include (pdf attached for each):

Human Cancer Panel
Human Kinase PanelHuman Inflammation Panel
Human miRNA Panel
Human Immunology Panel
Mouse Immunology Panel
Mouse Inflammation PanelMouse miRNA Panel

NanoString nCounter Brochure

For more information or to discuss your project, please contact:

Johannes Aartun
Research Specialist II
BSB 129

Courtney J. Haycraft, PhD
Assistant Professor
BSB 230D


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