nanoString nCounter Pro User manual

nCounter Pro Analysis System User Manual SEV-00184-01
2
NanoString Technologies, Inc.
530 Fairview Ave N
Seattle, Washington 98109
www.nanostring.com
T: 206.378.6266
T: 888.358.6266
E: [e-mail]
Sales Contacts
United States: [e-mail]
EMEA: [e-mail]
Asia Pacific & Japan: [e-mail]
Other Regions: [e-mail]
EU Authorized Representative
NanoString Technologies
Germany Gmbh
Birketweg 31
80639 Munich
Germany
UK Authorized Representative
NanoString Technologies
Europe Limited
11th Floor Whitefriars
Lewins Mead
Bristol BS1 2NT
United Kingdom

SEV-00184-01 nCounter Pro Analysis System User Manual
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
3
Rights, License, & Trademarks
Use
For research use only. Not for use in diagnostic procedures.
Intellectual Property Rights
This nCounter® Pro Analysis System User Manual and its contents are the property of NanoString
Technologies, Inc. (“NanoString”), and are intended solely for use by NanoString customers, for the
purpose of operating the nCounter Pro Analysis System. The nCounter Pro Analysis System
(including both its software and hardware components) and this User Manual and any other
documentation provided to you by NanoString in connection therewith, are subject to patents,
copyright, trade secret rights and other intellectual property rights owned by, or licensed to,
NanoString. No part of the software or hardware may be reproduced, transmitted, transcribed,
stored in a retrieval system, or translated into other languages without the prior written consent of
NanoString. For a list of patents, see https://www.nanostring.com/about-us/legal/patents/.
Limited License
Subject to the terms and conditions of the nCounter Pro Analysis System contained in the product
quotation, NanoString grants you a limited, non-exclusive, non-transferable, non-sublicensable,
research use only license to use the proprietary nCounter Pro Analysis System only in accordance
with the manual and other written instructions provided by NanoString. Except as expressly set
forth in the terms and conditions, no right or license, whether express, implied or statutory, is
granted by NanoString under any intellectual property right owned by, or licensed to, NanoString
by virtue of the supply of the proprietary nCounter Pro Analysis System. Without limiting the
foregoing, no right or license, whether express, implied or statutory, is granted by NanoString to
use the nCounter Pro Analysis System with any third-party product not supplied or licensed to you
by NanoString or recommended for use by NanoString in a manual or other written instruction
provided by NanoString.
Trademarks
NanoString, NanoString Technologies, the NanoString logo, and nCounter are trademarks or
registered trademarks of NanoString Technologies, Inc., in the United States and/or other countries.
All other trademarks and/or service marks not owned by NanoString that appear in this document
are the property of their respective owners.
Copyright
©2022 NanoString Technologies, Inc. All rights reserved.

nCounter Pro Analysis System User Manual SEV-00184-01
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
4
Table of Contents
Rights, License, & Trademarks ................................................................................................................... 3
Introduction ................................................................................................................................................. 6
Product Use Limitations.......................................................................................................................... 6
Product Components .............................................................................................................................. 6
Overview of the Procedure..................................................................................................................... 6
Online Training at NanoString University.............................................................................................. 6
Manual Conventions ................................................................................................................................ 7
Instrument Specifications ....................................................................................................................... 7
Environmental Requirements................................................................................................................. 7
Safety Information (English) .................................................................................................................. 8
Caution Symbols .................................................................................................................................. 8
Informations de Sécurité (Français) ...................................................................................................... 9
Symboles Attention ............................................................................................................................. 9
Hardware Overview.................................................................................................................................. 10
General Information............................................................................................................................... 10
Prep Station............................................................................................................................................ 11
Digital Analyzer...................................................................................................................................... 12
Prep Station............................................................................................................................................ 13
Select Instrument Mode .................................................................................................................... 13
Exit Life Sciences Mode..................................................................................................................... 13
Digital Analyzer...................................................................................................................................... 14
Select Instrument Mode .................................................................................................................... 14
Exit Life Sciences Mode..................................................................................................................... 14
Operating the Prep Station ...................................................................................................................... 16
Prior to Initiating a Run......................................................................................................................... 16
Waste Removal .................................................................................................................................. 16
Consumables Required...................................................................................................................... 17
Initiating a Run....................................................................................................................................... 18
Pausing or Aborting a Run................................................................................................................ 27
When Run is Complete...................................................................................................................... 27
Operating the Digital Analyzer ................................................................................................................ 29
Enterprise Package................................................................................................................................ 29
User Management.............................................................................................................................. 30
Login Settings .................................................................................................................................... 32
Archive Settings................................................................................................................................. 33
Cartridge Tracking Settings .............................................................................................................. 34
Audit Report Generation................................................................................................................... 34

SEV-00184-01 nCounter Pro Analysis System User Manual
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
5
Overview of File Structure.................................................................................................................... 35
Navigating File/Folder Screens ........................................................................................................ 36
Reporter Library Files............................................................................................................................ 37
Upload RLFs via FTPS........................................................................................................................ 39
Cartridge Definition Files ...................................................................................................................... 41
Creating a CDF on a Personal Computer......................................................................................... 43
Upload CDFs via USB Flash Drive .................................................................................................... 50
Upload CDFs via FTPS....................................................................................................................... 51
Creating a CDF on the Digital Analyzer........................................................................................... 53
Initiating a Run....................................................................................................................................... 59
Pausing a Run..................................................................................................................................... 63
Completing a Run .............................................................................................................................. 65
Download RCC Files via USB Flash Drive ........................................................................................ 66
Download RCC Files via Email .......................................................................................................... 67
Download RCC Files via SSH (SFTP)................................................................................................ 67
Download RCC Files via FTPS........................................................................................................... 68
Technical Support & Maintenance ........................................................................................................... 70
Technical Support.................................................................................................................................. 70
Online Training at NanoString University............................................................................................ 70
Prep Station Maintenance..................................................................................................................... 71
System Setup ..................................................................................................................................... 72
System Hardware............................................................................................................................... 74
System Software................................................................................................................................ 84
Troubleshoot ...................................................................................................................................... 85
Shutdown System.............................................................................................................................. 90
Digital Analyzer Maintenance............................................................................................................... 91
System Setup ..................................................................................................................................... 92
System Software................................................................................................................................ 95
Troubleshoot ...................................................................................................................................... 96
User Profile ......................................................................................................................................... 97
System Information ........................................................................................................................... 97
Disk Cleanup....................................................................................................................................... 97
Shutdown System.............................................................................................................................. 99
Cleaning.................................................................................................................................................. 99
Prep Station........................................................................................................................................ 99
Digital Analyzer.................................................................................................................................. 99
Disposal of Electronic Equipment........................................................................................................ 99
Symbols and Definitions......................................................................................................................... 100

nCounter Pro Analysis System User Manual SEV-00184-01
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
6
Introduction
Product Use Limitations
The nCounter Pro Analysis System is intended for applications for which approval/clearance is not
required and for research use. This system may only be used with NanoString’s nCounter reagents.
See the documentation that accompanies the reagents for information regarding performance and
sample type limitations.
Product Components
The nCounter Analysis System consists of two instruments: The Prep Station and the Digital
Analyzer. A power cable is included with each instrument. The Prep Station also includes a pipette
tip rack, a liquid waste container, a solid waste container, and silicone grease. Customers may
expand the system by adding additional Prep Stations.
Overview of the Procedure
1. After sample processing and hybridization has been completed according to the assay or reagent
instructions, samples are loaded onto the Prep Station, where they are purified and immobilized
onto the internal surface of a sample cartridge. This process takes 2–3 hours, depending on the
number of samples run and the sensitivity setting selected.
2. The sample cartridge is then transferred to the Digital Analyzer for imaging and analysis.
3. During processing with the nCounter Analysis System, email alerts may be used to track sample
status if the system has been networked and properly configured (optional).
4. Finally, results are available for download directly from the Digital Analyzer.
Online Training at NanoString University
NanoString University is an online training platform for instructional videos and documents to
accompany your NanoString instrument and assays. Create a free account at
https://university.nanostring.com.

SEV-00184-01 nCounter Pro Analysis System User Manual
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
7
Manual Conventions
The following conventions are used throughout this manual and are described for your reference.
NOTE: This notation indicates general information that may be useful for improving assay
performance. These notes may clarify other instructions or provide guidance to improve
the efficiency of the assay workflow.
IMPORTANT: This notation indicates important information that is critical to ensure a
successful assay. Following these instructions may help improve the quality of your data.
CAUTION: This notation indicates the potential for bodily injury or damage to the
instrument if the instructions are not followed correctly. Always carefully read and follow
the instructions accompanied by this symbol to avoid potential hazards.
Instrument Specifications
Test Lanes per Run
1–12
Weight
Prep Station 5s: 150 lbs/68 kg
Digital Analyzer 5s: 265 lbs/120 kg
Dimensions (W x D x H)
Prep Station 5s: 35.0 x 26.4 x 24.6 in/89 x 67 x 63 cm
Digital Analyzer 5s: 26 x 26 x 19 in/66 x 66 x 48 cm
Power Requirements
100–240 VAC, 610 VAC
Fuse
8A (100–120 VAC) or 4A (200–240 VAC)
Environmental Requirements
Temperature: 18–28°C
Humidity: < 80% relative humidity (non-condensing)
Text Style
Meaning
Bold
Bold text is typically used to highlight a specific button, keystroke, or menu option. Bold text
may appear elsewhere to highlight important text or terms.
Italic Italic text is typically used to highlight references to another section of the manual. Italic text
may also be used to highlight references to other manuals or instructional material. These are
often accompanied by a hyperlink that will take you directly to the referenced document or
section.

nCounter Pro Analysis System User Manual SEV-00184-01
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
8
Safety Information (English)
The nCounter Analysis System may only be operated by appropriately trained, professional users.
NanoString recommends that all users read and understand this manual prior to attempting to
operate the system. Keep this manual with the instruments for easy access to instructions and safety
information. Failure to comply with the instructions in this manual may pose a dangerous risk to the
operator and void the manufacturer’s warranty.
•The Digital Analyzer is a Class 1 laser product. The instrument contains an internal Class 2 laser
barcode reader. Class 2 laser radiation exposure is possible while the Digital Analyzer cover is
opened. Do not stare into the barcode reader laser beam.
•The Prep Station is a piece of electrical equipment for measurement, control, and laboratory
use. It contains high voltage and heater modules indicated by symbols on the deck. Avoid
contacting the heater module and electrodes. The instrument is equipped with a safety
interlock that will prevent voltage from being applied while the door of the instrument is open.
•Do not use this device in close proximity to sources of strong electromagnetic radiation or
vibration, as it may interfere with proper operation.
•Do not attempt to install, move, or disassemble the instrumentation.
•Do not override the door sensors (pinch hazard exists).
•Ensure that all consumables are properly inserted into the system prior to starting.
•Operate the system using only NanoString nCounter reagents in accordance with their
indications for use.
•Wear gloves while operating or performing user maintenance on the instrumentation.
•Do not attempt to wash the Prep Station’s electrodes or allow water or other solvents to come
into contact with the electrodes.
•If it becomes necessary to wash either instrument’s touchscreen, use a damp cloth to gently
wipe the surface. Do not use excessive water or other solvents, which may damage the screen.
Caution Symbols
BIOHAZARD: Potential hazardfrom a biologicalsource exists.If you chooseto use biohazardous materials on yourPrep Station,
the instrument may become contaminated with biohazardous materials. Please affix the proper warning labels to your Prep
Station if you use biohazardous inputs. Be careful not to touch this area withoutgloves or other personal protective equipment.
ELECTRICAL HAZARD
CAUTION HOT SURFACE

SEV-00184-01 nCounter Pro Analysis System User Manual
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
9
Informations de Sécurité (Français)
Le système d’analyse nCounter ne peut être utilisé que par des professionnels dûment formés.
NanoString recommande que tous les utilisateurs lisent et comprennent ce manuel avant toute
tentative d’utilisation du système. Garder ce manuel à proximité des instruments pour pouvoir
accéder facilement aux instructions et aux informations de sécurité. Le non-respect des instructions
décrites dans ce manuel peut présenter un risque élevé pour l’opérateur et invalider la garantie du
fabricant.
•L’analyseur numérique est un produit laser de classe 1. L’instrument contient un lecteur de codes-barres laser
de classe 2 lecteur interne. Une exposition à des rayonnements laser de classe 2 est possible lorsque le capot
de l’analyseur numérique est ouvert. Ne pas fixer du regard le faisceau laser d’un lecteur de codes-barres.
•La station de préparation est un équipement électrique pour la mesure, le contrôle et l’utilisation en
laboratoire. Celle-ci utilise des modules chauffants et de la haute tension indiquées par des symboles sur le
châssis. Évitez tout contact avec le module chauffant et les électrodes. L’instrument est doté d’un
mécanisme de verrouillage de sécurité qui empêche l’application d’une tension pendant que la porte de
l’instrument est ouverte.
•Ne pas utiliser ce dispositif à proximité de sources de fortes vibrations ou radiations électromagnétiques, car
celles-ci peuvent interférer avec le bon fonctionnement de l’équipement.
•Ne pas essayer d’installer, de déplacer ou de démonter les instruments.
•Ne pas court-circuiter les capteurs de la porte en raison des risques de pincement.
•S’assurer que tous les consommables sont correctement insérés dans le système avant de commencer une
procédure.
•N’utiliser le système qu’avec les kits de test nCounter de NanoString et conformément à leur mode d’emploi.
•Porter des gants pendant l’utilisation et la maintenance des instruments.
•Ne pas essayer de laver les électrodes de la station de préparation et éviter que de l’eau ou tout autre
solvant entre en contact avec les électrodes.
•Ne pas essayer de laver l’écran tactile des instruments et éviter que de l’eau ou tout autre solvant entre en
contact avec les écrans tactiles.
Symboles Attention
BIOHAZARD: Existence d’un danger potentiel provenant d’une source biologique. Si vous choisissez d’utiliser du matériel
biologique
dangereux sur votre station de préparation, l’instrument peut être contaminé par ce matériel à risque biologique. S’ il
vous
plaît apposer l’étiquetage de mise en garde appropriée à votre station de préparation si vous utilisez des échantillons
biologiques
dangereux. Faites attention de ne pas toucher cette zone sans gants ou sans autres équipements de protection
personnelle.
RISQUE ÉLECTRIQUE
ATTENTION SURFACE CHAUDE

nCounter Pro Analysis System User Manual SEV-00184-01
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
10
Hardware Overview
General Information
The instrument serial number and compliance
information can be found on the rating plate on
the back panel of each instrument (Figure 1).
Please refer to the rating plate and declaration
of conformity (EU only) for compliance
information.
Figure 1: Serial number and compliance information
for the Prep Station (left) and Digital Analyzer (right).
Both instruments contain a touchscreen to enable operation of the instrument. The touchscreen
enables the user to operate the system by touching a selection on the screen. There are several
buttons that appear in the touchscreen user interface. The Main Menu for each instrument is shown
in Figure 2.
Figure 2: Main Menu on the touchscreens of the Prep Station (left) and the Digital Analyzer (right).