nCounter® Academy


Welcome to training on the nCounter Analysis System!

The content on this page is applicable to learning how to utilize the nCounter® MAX or the nCounter® FLEX instrument. For information on differences between the two instruments, please consult the nCounter Analysis System user manual. Although these videos are tailored to the nCounter MAX, both instruments follow the same protocol for training and the videos and support resources below are applicable for both platforms.

nCounter Technology Overview

Now that you are preparing to take on biomolecule profiling using the nCounter, it is necessary to get an overview of the assay and the functions of the instrumentation. Below you will find resources highlighting the capabilities of the nCounter MAX and FLEX profilers.

Before Training on the nCounter MAX/FLEX Platforms

Before beginning training on the nCounter MAX/FLEX platforms, it is necessary to gather all the reagents needed for the training. For any NanoString Assay on the nCounter® Platform, please consult the appropriate hybridization manual for a list of required ancillary equipment required for the assay, such as a thermocycler and pipettes.

In addition to laboratory equipment, please confirm all assay reagents are present and stored at the correct temperature. For the nCounter MAX/FLEX, all assays require the Master Kit consumables.

Sample Preparation

For training on the nCounter Analysis System, we will be demonstrating how to perform the assay using the reagents supplied with the nCounter Training kit. Please select the appropriate training path for the specific NanoString product you will be performing to get an in-depth tutorial on preparing the samples for analysis on the nCounter MAX or FLEX.

nCounter MAX Prep Station Training

The nCounter prep station functions to purify the target samples for profiling and prepares them for imaging in an automated fashion using internal robotics.

nCounter MAX Digital Analyzer Training

The nCounter digital analyzer images the NanoString barcodes and quantifies the abundance of each target in the samples.

Download the CDF utility tool here.

nCounter Maintenance and Troubleshooting

In this section, you will find resources for routine maintenance for your nCounter MAX or FLEX to ensure the longevity of your instrument. We have also included information that can be used for troubleshooting issues with assays on the nCounter Analysis System. For any questions or further information on instrument maintenance, please contact our technical support team.

nCounter MAX/FLEX instrument maintenance:

If the Prep Station has been idle for more than a month, it is highly recommended to perform a dry run on this equipment, preferably several days in advance of the planned run. The purpose of a dry run is to lubricate hardware which would ordinarily be lubricated by routine use. This will help ensure that moving parts do not get stuck while processing precious samples, and will thus reduce the risk of losing precious samples. For information on how to perform this maintenance, please consult the nCounter User Manual.

nCounter MAX/FLEX instrument troubleshooting:

For further information on the nCounter MAX/FLEX instruments, please consult our FAQ.

nCounter Data Analysis

Here you will find all resources for data analysis using nSolver™ and OnRamp’s Rosalind™.

nSolver Analysis Software

Download nSolver and the advanced analysis module to get the most of your nCounter data set. Please also consult the user manuals for nSolver and the advanced analysis module for information on installing and running these applications. For more information, please visit the nSolver support webpage or our FAQs on data analysis.

Please join our weekly nSolver data analysis webinars with chat support from one of our technical support team members. Each week the content alternates between analysis with the basic suite of nSolver and with the advanced analysis module. For new users, we will cover how to import your nCounter® data, perform quality control, normalize, and generate data plots. For advanced users, we help you build a custom Advanced Analysis and review the module outputs generated with your dataset.

Data Analysis with Rosalind

NanoString has partnered with OnRamp Bioinformatics to integrate our knowledge and expertise into an optimized analysis experience for nCounter with the ROSALIND Analysis Platform. ROSALIND is cloud-based, runs in a web browser, and provides an intuitive experience that is designed with life scientists in mind. Please visit the website to sign up for a free account to analyze your nCounter data.

OnRamp Bioinformatics also offers a weekly webinar and Q&A session covering the basics of analyzing nCounter data with ROSALIND.  During these sessions, they will cover the ROSALIND functionality for Experimental Set Up, Data QC, and Interactive Analysis and address participant questions.

Consultation and Data Analysis Services (DAS)

NanoString is dedicated to helping you get the most out of your data. In addition to technical support with nSolver, NanoString also offers customizable data analysis services for a fee. Our highly trained and experienced staff will partner with you in designing and executing a personalized comprehensive data analysis plan. Contact us for more information and pricing.

Download a Data Analysis Brochure. Visit the DAS website for more information on available data analysis services.

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