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nCounter Academy: MAX/FLEX

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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 instruments. 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.

Training for the nCounter MAX and FLEX instrument on this document is for RESEARCH USE ONLY. Not for use in diagnostic procedures.

Introduction
Before Training
Sample Hybridization
Probe Purification
Digital Counting
Instrument Maintenance
Troubleshooting
Need Help?
Introduction

Introduction: nCounter Technology Overview

Now that you are preparing to take on biomolecule profiling using the nCounter platform, 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 instruments. For a quick orientation on the nCounter technology, check out this short 2 minute video:

Before Training

Before Training on the nCounter MAX/FLEX Instruments

Before beginning training on the nCounter MAX/FLEX instruments, 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 instruments, all assays require the Master Kit consumables.

For information on RNA preparation and sample quality control for the nCounter MAX/FLEX, instruments please consult the sample preparation manuals for RNA from FFPE tissue or fresh frozen materials.

Sample Hybridization

Sample Hybridization for the nCounter MAX/FLEX Instruments

For training on the nCounter® platform, we will be demonstrating how to perform the CodeSet gene expression assay using the reagents supplied with the nCounter Training kit. For a step-by-step protocol of the CodeSet hybridization process, please consult the CodeSet Hybridization Setup user manual. This video will walk you through the steps of preparing the CodeSet hybridization reaction using the Customer Assay Evaluation (CAE) training kit.

Probe Purification

nCounter MAX/FLEX 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. Detailed information on operating the nCounter MAX/FLEX Prep Station can be found in the nCounter User Manual or the MAX/FLEX quick start guide.

Digital Counting

Processing samples on the MAX/FLEX

nCounter MAX/FLEX Digital Analyzer Training

The nCounter digital analyzer images the NanoString barcodes and quantifies the abundance of each target in the samples. Detailed information on operating the nCounter MAX/FLEX Digital Analyzer can be found in the nCounter User Manual or the MAX/FLEX quick start guide.

Download the CDF utility tool here.

Instrument Maintenance

nCounter MAX/FLEX Instrument Maintenance

In this section, you will find resources for routine maintenance for your nCounter MAX or FLEX instruments to ensure the longevity of your instrument. For any questions or further information on instrument maintenance, please contact our technical support team.

Top 10 Tips and Tricks on the nCounter MAX/FLEX instruments

  1. Always handle the cartridge by the left and right edges, “NanoString and barcode” ends of the cartridge.
  2. After a run, store your cartridge at 4°C in the dark in case a re-scan is needed. Cartridges can last for up to 5 scans or 1–2 weeks before significant attenuation of signal if stored properly.
  3. Use a twisted lint-free lab tissue or lens cloth to “floss” between the pipette nozzles and remove any grease from the white tip ejector block above the nozzles. If necessary, pull the tip ejector block down to thoroughly clean it.
  4. Use a small amount of grease during o-ring maintenance and make sure to wipe excess grease from the nozzles. Excess grease on the white tip ejector block may interfere with proper tip ejection.
  5. If the instrument has been idle for more than a month, always perform a dry run before processing precious samples. Contact support@nanostring.com for more information.
  6. Keep a blank cartridge in the electrode fixture between processing runs to avoid accidental bending of the electrodes.
  7. Always use new consumables (including cartridge, reagent plates, and tips) when restarting a sample processing run.
  8. If you are advised to restart a run, it is recommended to power down and restart the instrument before re-initiating the run. Use the shutdown button in the maintenance menu.
  9. When loading your cartridge into the prep station, never press down on the middle of the cartridge to seat it in the electrode deck, doing so will bend the electrodes.
  10. It is highly recommended that Prep Stations are on at least a 600 Watt uninterruptable power supply, and Digital Analyzers are on at least a 600 Watt uninterruptable power supply.

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.

Troubleshooting

nCounter MAX/FLEX Troubleshooting

In this section, you will find resources that can be used for troubleshooting any issues with assays on the nCounter MAX/FLEX instruments. This information is also available in the nCounter User Manual. The quick guide on sending log files to the NanoString support team can be found here. For any questions or for further information on instrument maintenance, please contact our technical support team.

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

Need Help?

Need Help? Contact Support:

Have data analysis questions or what to learn more about options to analyze your nCounter data? Make sure to check out the nCounter Academy Data Analysis section!