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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 would like 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).  Researchers interested in purchasing CodeSets and supplies should contact Beth Nye ( for pricing and ordering information.  To discuss project design, custom CodeSet degign, please contact Christine Hipsky ( Additional information about the technology and products available from NanoString Technologies can be found on their website (

Gene Expression Assay ManualmiRNA Expression Assay Manual

MUSC Custom CodeSet: We have two custom CodeSets available for RNA analysis based on genes requested by MUSC researchers.  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.  Samples can be run at a cost of $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 129For standard analyses, RNA should be diluted in RNase-free water.  A minimum of 100 ng of total RNA is recommended in a volume of 3-5 ul.  Be sure to indicate which Custom CodeSet you would like to utilize. Additional information for RNA preparation and the nCounter Analysis process can be found in the above manual links.


(human, rat, C. glabrata,

zebrafish, marine species)

Training: If you are interested in receiving training, please contact Johannes Aartun to obtain information regarding available times.

Fees: All users will conduct their own analyses and be charged a nominal fee ($75/12 samples run) to cover the costs of system maintenance and service.  Users will be responsible for all materials and consumables needed for analyses. Custom or predefined CodeSets can be ordered through NanoString Technologies directly.  A thermocycler is available in the L-COHR for hybridization.

Data Analysis: Data from the nCounter Analysis System will be emailed directly to the user. 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 PanelHuman Kinase PanelHuman Inflammation PanelHuman miRNA Panel
Human Immunology PanelMouse Immunology PanelMouse Inflammation PanelMouse miRNA Panel

NanoString nCounter Brochure

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

James Cray Jr, PhD
Assistant Professor

Lixia Zhang, PhD
Research Specialist
BSB 129