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NanoString Technologies nCounter User Manual

Dx analysis system
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nCounter
®
Dx Analysis System User Manual
NanoString Technologies
530 Fairview Ave N
Seattle, WA 98109 USA
www.nanostring.com
Phone:
+1 206.378.6266
+1 888.358.NANO
E-mail:
dxsupport@nanostring.com
For In Vitro Diagnostic Use
The nCounter Dx Analysis System that is the subject of this manual is for use with NanoString's Diagnostic Assays within their intended use in the EU,
United States, and other applicable markets.
, Inc.
®
2017-07 MAN-C0034-06

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Summary of Contents for NanoString Technologies nCounter

  • Page 1 For In Vitro Diagnostic Use The nCounter Dx Analysis System that is the subject of this manual is for use with NanoString’s Diagnostic Assays within their intended use in the EU, United States, and other applicable markets. 2017-07 MAN-C0034-06...
  • Page 2 The nCounter® Dx Analysis System User Manual and its contents are the property of NanoString Technologies, Inc. (“NanoString”) and are intended solely for the use of NanoString customers for the purpose of operating the nCounter Dx Analysis System. The nCounter Dx...
  • Page 3 NanoString Technologies USER MANUAL ® Contact Information NanoString Technologies, Inc. 530 Fairview Ave N Seattle, WA 98109 Phone: +1.888.358.NANO (+1.888.358.6266) Fax: +1.206.378.6288 E-mail: dxsupport@nanostring.com Website: www.nanostring.com EC REP EU Authorized Representative Emergo Europe Prinsessegracht 20 2514 AP The Hague The Netherlands E-mail: dxsupport@nanostring.com...

  • Page 4: Table Of Contents

    USER MANUAL nCounter Dx Analysis System ® Contents Introduction ..............7 A.
  • Page 5 NanoString Technologies USER MANUAL ® 4 Operating the Web Application ..........20 A.
  • Page 6 USER MANUAL nCounter Dx Analysis System ® 5 Operating the Prep Station ........... .67 A.

  • Page 7: Introduction

    A. Product Use Limitations The nCounter Dx Analysis System and the nCounter Dx Analysis System with the FLEX configuration (when run in IVD mode) is intended for in vitro diagnostic use when used in conjunction with specific IVD cleared or approved assays citing its use. The nCounter Dx Analysis System may only be used with NanoString’s nCounter test kits.

  • Page 8: Manual Conventions

    USER MANUAL nCounter Dx Analysis System ® D. Manual Conventions The following conventions are used throughout this manual and are described for your reference. 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.

  • Page 9: Additional Precautions

    • Ensure that all consumables are properly inserted into the system prior to starting a procedure. • Operate the system using only NanoString nCounter test kits in accordance with their Intended Use. • Wear gloves while operating or performing user maintenance on the instruments.

  • Page 10: Hardware Overview

    USER MANUAL nCounter Dx Analysis System ® Hardware Overview A. General Information The instrument serial number and compliance information can be found on the rating plate on the back panel of each instrument. Please refer to the rating plate and declaration of conformity (EU only) for compliance information.

  • Page 11: Prep Station

    ® B. Prep Station The Prep Station is a multi-channel pipetting robot configured specifically for use with NanoString nCounter Test Kits. The instrument 2.1). performs liquid transfers, magnetic bead separations, and immobilization of molecular labels on the Sample Cartridge surface (FIGURE FIGURE 2.1:...

  • Page 12: Digital Analyzer

    ® C. Digital Analyzer The Digital Analyzer is a multi-channel epifluorescence scanner configured specifically for use with NanoString’s nCounter Test Kit Cartridges. 2.3). When one or more scans have been completed, the instrument may be Up to six Cartridges can be loaded into the instrument (FIGURE paused to allow new Cartridges to be swapped in without disrupting the remaining Cartridges.

  • Page 13: Selecting The Instrument Mode

    For all other applications, individuals using nCounter CodeSets or nCounter Elements should choose the Life Sciences mode and refer to the nCounter Analysis System User Manual for further instruction.

  • Page 14: Prep Station

    USER MANUAL nCounter Dx Analysis System ® A. Prep Station Select Instrument Mode After turning on the Prep Station, the first screen asks the user to select either Diagnostics mode (blue, on the left) or Life Sciences mode (green, on the right).
  • Page 15 NanoString Technologies USER MANUAL ® Enter a valid user name and password and touch the Sign In button. FIGURE 3.3: The sign in screen >>> The Main Menu will appear (FIGURE 3.4). FIGURE 3.4: The Prep Station Main Menu in Diagnostics mode...

  • Page 16: Switch Instrument Mode

    USER MANUAL nCounter Dx Analysis System ® Switch Instrument Mode The user may switch between Diagnostics mode and Life Sciences mode from the Main Menu. Press the Exit button located at the bottom of the Main Menu (FIGURE 3.4). >>> The ‘Exit Diagnostics Mode’ confirmation screen will appear.

  • Page 17: Digital Analyzer

    NanoString Technologies USER MANUAL ® B. Digital Analyzer Select Instrument Mode After turning on the Digital Analyzer, the first screen to appear asks the user to select either Diagnostics mode (blue, on the left) or Life Sciences mode (green, on the right).
  • Page 18 USER MANUAL nCounter Dx Analysis System ® Enter a valid user name and password and press the Sign In button. FIGURE 3.8: The sign in screen >>> The Main Menu will appear (FIGURE 3.9). FIGURE 3.9: The Digital Analyzer Main Menu in Diagnostics mode...

  • Page 19: Switch Instrument Mode

    NanoString Technologies USER MANUAL ® Switch Instrument Mode The user may switch between Diagnostics mode and Life Sciences mode from the Main Menu. Press the Exit button located at the bottom of the Main Menu (FIGURE 3.9). >>> The ‘Exit Diagnostics Mode’ confirmation screen will appear.

  • Page 20: Operating The Web Application

    Sign In The local nCounter system administrator must provide each user with the URL to access the nCounter web application and will also set up the user account. Navigate to the URL provided from any computer connected to the organization’s local network. (It must be the same network used by the Digital Analyzer.)

  • Page 21: Forgot User Id/Password

    The Assay Type control on the Sign In page Forgot User ID/Password • If you forget your user ID, contact your local nCounter system administrator to retrieve it. • If the password is forgotten, the nCounter web application may be able to retrieve it.
  • Page 22 • If the nCounter system finds a matching profile, the password will be e-mailed to the address on record (FIGURE 4.4). • If a matching profile is not found, you will be instructed to contact your nCounter system administrator in order to reset the password. FIGURE 4.4:...

  • Page 23: Updating My Profile

    NanoString Technologies USER MANUAL ® Updating My Profile User information can be updated by selecting the My Profile button from the menu bar at the top of the page 4.5). (FIGURE FIGURE 4.5: Location of the My Profile button The My Profile page enables the user to change the account password and/or e-mail address associated with the profile and view other 4.6).

  • Page 24: Application Layout And Navigation

    B. Application Layout and Navigation Menu The nCounter web application has a menu bar at the top that enables users to quickly navigate from one area of the application to another 4.7). The menu items separate the application into five sections: (FIGURE •...

  • Page 25: Tables

    Filter Tables can become large after frequent use of the nCounter web application, making it difficult to find the data of interest. Filtering is available in all tables to enable users to search for and view only data of interest.
  • Page 26 USER MANUAL nCounter Dx Analysis System ® FIGURE 4.10: An example of filter settings on the Run Sets page Click Apply when finished. Only relevant rows will be displayed in the table 4.11). (FIGURE NOTE: The presence or absence of a funnel icon next to the page title indicates whether or not filtering is applied.

  • Page 27: Sort

    NanoString Technologies USER MANUAL ® Sort All table columns allow users to sort the displayed rows in ascending or descending order. Click on the column heading for the data of interest to sort the rows (FIGURE 4.13). To re-sort the data in the reverse order, click again on the same column heading.

  • Page 28: Forms

    USER MANUAL nCounter Dx Analysis System ® Forms Forms are pages for manual data entry changes. Users with the ‘Create Run Set’ account privilege have access to the ‘Create Run Set’ and ‘Edit Run Set’ forms. Users who lack this privilege may view Run Set and sample statuses, but may not create or edit Run Sets. Administrators may also access other forms, which include: •...

  • Page 29: Dashboard And Status

    Dashboard 4.15). The Dashboard The Dashboard is the landing page, the first screen displayed after logging into the nCounter web application (FIGURE can be accessed from other pages by clicking on the Dashboard menu item, but it will be unavailable when editing a form until that form has been saved or discarded.

  • Page 30: Run Set Status

    USER MANUAL nCounter Dx Analysis System ® Run Set Status The Run Sets page can be accessed from the Dashboard as described above, and is also available by clicking Runs on the menu bar. 4.16) The Run Sets page displays the statuses of all Run Sets that have been created (FIGURE FIGURE 4.16:...
  • Page 31 NanoString Technologies USER MANUAL ® The following information is available: Run Set ID – The Run Set ID entered when the Run Set was created Status – The current condition or state of the Run Set. Status possibilities include: • BatchRegistered – Run Set Registered (Run Set is defined but has not started processing yet) •...

  • Page 32: Sample Status

    USER MANUAL nCounter Dx Analysis System ® Sample Status Similar to the Run Sets page, the Samples page can be accessed from the Dashboard and is also available from the Samples menu option at the top of the page (FIGURE 4.17).
  • Page 33 NanoString Technologies USER MANUAL ® The following information is available: Sample ID – The Sample ID entered manually or via a barcode scanner when creating the Run Set Run Set ID – The Run Set ID entered when creating the Run Set in the web application Status –...

  • Page 34: Run Sets

    Create a Run Set Users are required to create a Run Set associating the sample IDs with their strip tube well locations using the nCounter web application. A user can choose to create a new Run Set from several places within the web application. The most common way is to select the option...
  • Page 35 Enter the following information to create a Run Set: nCounter Assay Type – If the user has access to more than one nCounter assay type, the assay that was previously selected during 4.2). To change this selection, the user must log out, then sign in again and select a different assay...
  • Page 36 USER MANUAL nCounter Dx Analysis System ® FIGURE 4.21: The location of the contact list and e-mail alerts on the Create New Run Set form It is crucial to correctly enter sample information. Complete each well with all required information before entering sample information for the next well.
  • Page 37 NanoString Technologies USER MANUAL ® >>>The worksheet will appear in a new window (FIGURE 4.23). FIGURE 4.23: An example worksheet Select Print to print the worksheet, and then close the worksheet. The application will return to the Run Sets page.

  • Page 38: Edit A Run Set

    USER MANUAL nCounter Dx Analysis System ® Edit a Run Set Run Sets with the status ‘BatchRegistered’ can be edited. Users should edit a Run Set to match the final hybridization record if sample information was altered. For example, the Sample ID Labels may be updated if patient samples are swapped out or if a new sample ID is assigned.

  • Page 39: Delete A Run Set

    NanoString Technologies USER MANUAL ® Delete a Run Set Run Sets with the status ‘BatchRegistered’ can be deleted if necessary. To delete a Run Set, select the appropriate Run Set from the list and click the Delete button (FIGURE 4.26).

  • Page 40: Print Worksheets

    It is highly recommended that worksheets be used when setting up hybridization reactions. As described earlier, when a Run Set is saved the system will prompt the user to print the worksheet. However, it is also possible to print Run Set worksheets at any time from the nCounter web application.

  • Page 41: Reports

    A link to download reports from the web application is included within the e-mail notification. NOTE: The download link requires the user to log in to the nCounter web application before diagnostic reports can be accessed. From the Reports page, select the row(s) of samples to be downloaded and click the Download button (FIGURE 4.30).

  • Page 42: Administration

    USER MANUAL nCounter Dx Analysis System ® G. Administration For Administrators, the Admin button is available in the top menu bar of the web application. Administrators can choose these functions: • Manage Users • System Settings • Add User • Configure Report In addition to the functions listed in the Admin menu, two additional areas are restricted to Administrators: •...

  • Page 43: Add, Delete, And Manage Users

    NanoString Technologies USER MANUAL ® Add, Delete, and Manage Users To add a new user, select Admin from the top menu bar and click on Add User 4.31). (FIGURE FIGURE 4.31: The location of the Add User button in the Admin sub-menu >>>...
  • Page 44 USER MANUAL nCounter Dx Analysis System ® Enter the following information and click the Save button. • User ID (required) • Password (required) • Confirm Password (required) • E-mail Address (required) • User Type (required) – choose either: • General – Access to standard functionality including creating a Run Set (access does not include processing samples) •...
  • Page 45 NanoString Technologies USER MANUAL ® To edit a user, select the User ID link or select the row for the specified user and click the Edit button. >>> The Edit User Data form will appear (FIGURE 4.34). FIGURE 4.34: The Edit User Data form Edit any of the following information and click the Save button to save any changes made.
  • Page 46 USER MANUAL nCounter Dx Analysis System ® To delete a user, open the Manage Users page, select the row for the appropriate user, and click the Delete button (FIGURE 4.35). FIGURE 4.35: Location of the Delete button on the Manage Users page >>>...

  • Page 47: System Settings

    NanoString Technologies USER MANUAL ® System Settings System settings are available to users with the Administrative user type. The System Settings page supports four main functions, which are displayed in separate tabs: • Date and Time (default tab) • E-mail Settings •...
  • Page 48 ® Date and Time Date and time settings are initially set when NanoString personnel set up the nCounter. Change these settings only when necessary. Click Save to save any changes or Cancel to discard changes and perform another function. NOTE: Administrators cannot adjust the Time Zone or Daylight Saving Time options.
  • Page 49 NanoString Technologies USER MANUAL ® E-mail Settings 4.39) must be configured in order for the nCounter system to successfully send automated e-mails for status E-mail settings (FIGURE updates such as Prep Station run completion or diagnostic report notifications. FIGURE 4.39:...
  • Page 50 4.40) allows an Administrator to configure the Secure Shell server (SSH server). The SSH server allows users (FIGURE to programmatically pull nCounter report data or system backup data from the system in a secure manner. It also allows for unlimited concurrent client connections. See the section “LIS Integration” below for more information.
  • Page 51 NanoString Technologies USER MANUAL ® Once the Enable SSH Server checkbox is enabled, the Administrator can select which type of assay or backup data to configure for SSH 4.41). access (FIGURE FIGURE 4.41: Assay / Backup menu is active after the Enable SSH Server checkbox is selected...
  • Page 52 4.42) is an essential function to enable networking of the instruments. The Prep Station, Digital Analyzer, and IP address function (FIGURE nCounter web application are all in frequent communication. The IP address is the basis for setting up this communication. Avoid errors when making changes to fields under the IP Address tab. FIGURE 4.42:...

  • Page 53: Configure Report

    Personally Identifiable Information (PII) desired. (Users will need to save the completed forms outside the nCounter system as it is not currently engineered to support storage of PII). The report body, including assay results, logos, and explanatory graphs and text, may not be modified.
  • Page 54 • Discard Production Report – Selecting this button will remove all user-generated customization of the report and will revert to the default, nCounter Dx Analysis System-provided patient report. • Move to Production – Move the current draft report to production. This erases the current production report and cannot be undone.
  • Page 55 NanoString Technologies USER MANUAL ® If there is no working draft in progress (See FIGURE 4.45), then a dropdown listing of available templates is displayed instead of the thumbnail of the draft report, along with a control to start a new draft. Drafts may be started from the current production report, the NanoString standard header and footer, blank header and footer, or one of a number of pre-supplied templates.
  • Page 56 USER MANUAL nCounter Dx Analysis System ® Header Tab The Header tab allows administrators to modify the header for the report (see FIGURE 4.46). FIGURE 4.46: The Header tab of the Configure Report page, displaying the NanoString standard header The main body of the Header tab is a text entry area for specifying the content and layout of the customized report header. There is a vertical ruler to assist in placement of content items.
  • Page 57 • Sample ID – The Sample ID entered on the Create New Run Set page. • Run Date – The date that the sample was run on the DA. This date is automatically recorded by the nCounter Dx Analysis System.
  • Page 58 USER MANUAL nCounter Dx Analysis System ® Footer Tab The Footer tab 4.50), allows administrators to modify the footer for the report. The footer is always placed at the bottom of each (FIGURE page, leaving any empty space between the end of the body and the start of the footer. The formatting controls available for the header are available for use in the footer area as well.
  • Page 59 NanoString Technologies USER MANUAL ® Header Configuration Example To further illustrate how the header can be configured, consider the case of a laboratory with a standard header consisting of the organization logo; patient family name, given name, birth date, and gender; and assay-specific fields. This header example has been customized for 4.52), and demonstrates how to combine and nest multiple elements and adjust their individual configuration.
  • Page 60 USER MANUAL nCounter Dx Analysis System ® 13. Right click on the logo, then select Merge Down from the presented menu. This will merge the top 2 cells of the leftmost column of the table. Repeat until there is only 1 cell in the leftmost column of the table.

  • Page 61: Report Integration With External Systems

    Report Integration with External Systems The nCounter Dx Analysis System supports direct integration with existing report generation and management systems, such as Laboratory Information Systems (LIS). Using SFTP for file transfers, external automated processes may retrieve the output report (either in whole or in part), as well as the system backup archive.
  • Page 62 USER MANUAL nCounter Dx Analysis System ® Filenames All formats share a common basename format: <YYMMDD>_<cartridgeID>_<scan>_<sampleName>_<Lane> Where: <YYMMDD> Last 2 digits of the year, 2-digit (numeric) month, 2-digit numeric day <cartridgeID> Barcode found on the Cartridge <scan> Assigned by the system. Typically defaults to 1.

  • Page 63: Editing Sample Information

    NanoString Technologies USER MANUAL ® Assay Export (XML) Files The export XML file is intended for advanced users who need access to the underlying data elements, and is typically useful when integrating results with external systems. It is expected that most users will not need access to this level of detail and will be able to either use a customized PDF file or the modular image files to meet their customization needs.
  • Page 64 USER MANUAL nCounter Dx Analysis System ® Click the Edit Sample button. >>> The Edit Sample page will appear (FIGURE 4.54). FIGURE 4.54: Edit Sample page The sample parameter fields (# of Positive Nodes and Tumor Size in this example) and Memo (for adding comments, if desired) can be revised.
  • Page 65 NanoString Technologies USER MANUAL ® Please ensure that the correct sample is being updated and the revised fields are correct. Once a justification is entered, click the Revise 4.55). Sample button. This will bring up a final confirmation of the revision (FIGURE FIGURE 4.55:...

  • Page 66: System Backup Archive

    • To ensure that the backup data is available in the event of a system failure, IT administrators will need to arrange a regular scheduled “pull” of the encrypted backup data from the nCounter system to their own internal networked server. (This would rely on access to the nCounter SSH server and a scheduled SFTP pull of the backup data.)

  • Page 67: Operating The Prep Station

    NanoString Technologies USER MANUAL ® Operating the Prep Station A. Prior to Initiating a Run Waste Removal Prior to starting a new run, ensure that the waste containers have been emptied. Empty waste containers are required for every run. CAUTION: If waste containers are not emptied, tips could come into contact with waste liquids and contaminate samples, or excess tips could pile up and cause a system malfunction.

  • Page 68: Initiating A Run

    USER MANUAL nCounter Dx Analysis System ® B. Initiating a Run The following steps summarize the workflow beginning from the Welcome screen on the Prep Station touchscreen. To process samples using the Prep Station, a user must log on to the instrument. In order to log on, touch Main Menu on the Welcome Screen.
  • Page 69 The ‘Process A Run Set’ screen displays the name of each Run Set, the assay type, and the number of samples it contains. NOTE: The Exit button will only appear on the Welcome screen and Main Menu if the user has the nCounter Dx Analysis System with FLEX configuration (see Chapter 3 – Selecting the Instrument Mode).
  • Page 70 USER MANUAL nCounter Dx Analysis System ® Select the Run Set to be processed by touching the Run Set name. Use the arrow keys on the right side of the screen to scroll through the selections. Touch Next to continue.
  • Page 71 (FIGURE 5.8) must be at room temperature prior to processing. Remove the nCounter Reagent Plates from storage at 4°C and the nCounter Cartridges from storage at -20°C. Allow them to equilibrate to room temperature for 10–15 minutes. FIGURE 5.8: A...
  • Page 72 USER MANUAL nCounter Dx Analysis System ® Centrifuge the Reagent Plates at 2000 x g for 2 minutes to collect liquids at the bottom of the wells prior to loading the Reagent Plates onto the Prep Station deck. While the Cartridges and Reagent Plates come to room temperature, continue setting up the Prep Station. Touch Next.
  • Page 73 NanoString Technologies USER MANUAL ® Instructions for the ‘Reagent Plate’ screen: The barcode for the Reagent Plates must be scanned before proceeding. Hold the barcode in front of the barcode reader. A red beam will appear. Move the barcode in front of the red beam until it is recorded. When the barcode is successfully recorded, the barcode number will appear in the box and the Manual Entry button will change to Clear Entry.
  • Page 74 USER MANUAL nCounter Dx Analysis System ® Touch Next. >>> The ‘Tips and Foil Piercers’ screen will appear (FIGURE 5.12). FIGURE 5.12: The ‘Tips And Foil Piercers’ screen 10. Instructions for the ‘Tips and Foil Piercers’ screen: Remove the metal tip carrier from the Prep Station deck by lifting straight up.
  • Page 75 NanoString Technologies USER MANUAL ® Replace the loaded metal tip carrier back onto the Prep Station deck with the foil piercers closest to the front of the deck 5.14). (FIGURE FIGURE 5.14: Proper placement of rack containing pipette tips and foil piercers Touch Next.
  • Page 76 USER MANUAL nCounter Dx Analysis System ® 11. Place the tip sheaths on the deck and press firmly into place. Touch Next. >>> The ‘Empty Strip Tubes’ screen will appear (FIGURE 5.16). FIGURE 5.16: The ‘Empty Strip Tubes’ screen 12. Place the empty strip tubes in the heater on the deck. Touch Next.
  • Page 77 NanoString Technologies USER MANUAL ® 13. Instructions for the ‘Sample Cartridge’ screen: The barcode for the Sample Cartridge must be scanned before proceeding. Hold the barcode in front of the barcode reader. A red beam will appear. Move the barcode in front of the red beam until it is scanned and the barcode number appears in the entry field.
  • Page 78 USER MANUAL nCounter Dx Analysis System ® 14. Carefully lower the electrode fixture in place over the Cartridge (FIGURE 5.20). The 24 electrodes should insert easily into the 24 wells. Touch Next. FIGURE 5.20: Carefully lower the electrode fixture into place over the Cartridge.
  • Page 79 NanoString Technologies USER MANUAL ® >>> The ‘Hybridized Samples’ Screen will appear (FIGURE 5.21). FIGURE 5.21: The ‘Hybridized Samples’ screen 15. Place the hybridized sample strip tube on the deck of the Prep Station, ensuring that well 1 aligns with position 1 (FIGURE 5.22).
  • Page 80 USER MANUAL nCounter Dx Analysis System ® Securely close the lid that flips down over the tubes (FIGURE 5.23). FIGURE 5.23: Lid closed over tubes Touch Next. IMPORTANT: Failure to securely close the lid over the tubes can result in a system malfunction. If the metal lid is not closed completely, then the sensor will return an error message and the run will not initiate until the error is corrected.
  • Page 81 NanoString Technologies USER MANUAL ® >>> The ‘Notification Options’ screen will appear (FIGURE 5.24). FIGURE 5.24: The ‘Notification Options’ screen 16. Select whether the Prep Station should make an audible alarm when processing is finished. Touch Next. >>> The ‘Start Deck Validation’ screen will appear.
  • Page 82 ® The nCounter Prep Station will now check that all of the consumables and reagents have been placed properly on the deck 5.26). To do this, the Prep Station confirms that the sensors for the Sample Cartridge, electrode fixture, and heater lid (FIGURE are all in the correct state.
  • Page 83 NanoString Technologies USER MANUAL ® 17. When the sample processing is finished, a blue screen will appear and the timer will start to count up from when the run was 5.28). Touch Next. completed (FIGURE FIGURE 5.28: The System Processing Complete screen 18.
  • Page 84 USER MANUAL nCounter Dx Analysis System ® 19. To release the fixture after the run is complete, pull the latch on the top of the device up and towards the front of the system using a FIGURE 5.29. finger as shown in FIGURE 5.29:...

  • Page 85: Operating The Digital Analyzer

    NanoString Technologies USER MANUAL ® Operating the Digital Analyzer A. Initiating a Run To scan a Cartridge using the Digital Analyzer, log on to the instrument. In order to log on, touch Main Menu on the Welcome screen. FIGURE 6.1: The Digital Analyzer ‘Welcome’...
  • Page 86 The Digital Analyzer Main Menu NOTE: The Exit button will only appear on the Welcome screen and Main Menu if the user has the nCounter Dx Analysis System with FLEX configuration (see Chapter 3 – Selecting the Instrument Mode). IMPORTANT: If a laboratory has more than one Digital Analyzer, the Cartridge must be scanned on the same instrument registered to the Prep Station used to process the samples (see Chapter 4 –...
  • Page 87 NanoString Technologies USER MANUAL ® Place the Sample Cartridge into an empty slot. Make sure the Cartridge is inserted in the correct orientation (the slot and Cartridge 6.4). Close are keyed to help ensure the correct orientation), and is completely flat in the slot. The barcode will be facing up...
  • Page 88 USER MANUAL nCounter Dx Analysis System ® The scanner will use the barcode to look up the Run Set associated with that Cartridge and determine whether the Cartridge is ready to be scanned. Once the six positions have been checked, the Counting Cartridge screen will appear. Each slot has five possible states: •...
  • Page 89 NanoString Technologies USER MANUAL ® Confirm that a small blue bar appears at the bottom of the scanning Cartridge, indicating the scan has started. There will be a series of rhythmic clicks as the images are collected. To add a Cartridge to a Digital Analyzer that is already counting, touch the Pause button on the ‘Counting Cartridges’ screen. It might 6.7).

  • Page 90: Technical Support And Maintenance

    A. Technical Support Technical support is available by phone, fax, mail, or e-mail. Please be sure to include the product number and serial number in all communications. U.S. Contact Information: NanoString Technologies, Inc. 530 Fairview Ave N Seattle, WA 98109, U.S.A. Phone: +1.888.358.NANO (+1.888.358.6266)

  • Page 91: Instrument Power Cycling

    NanoString Technologies USER MANUAL ® B. Instrument Power Cycling It is recommended that the system power for each instrument is cycled periodically (for example, once every two weeks after Prep Station O-ring lubrication). Maintenance and support functions can be accessed from the Main Menu of the Prep Station and Digital Analyzer.
  • Page 92 USER MANUAL nCounter Dx Analysis System ® Select Confirm to continue the system shutdown. FIGURE 7.3: System shutdown messages displayed by the Prep Station (left) and the Digital Analyzer (right). >>> The system will shut down. After the system shuts down (there is a delay of approximately 30 seconds), locate the power switch on the back of the instrument and turn off the power.

  • Page 93: Prep Station Maintenance

    NanoString Technologies USER MANUAL ® C. Prep Station Maintenance Maintenance and support functions can be accessed from the Main Menu of the Prep Station. Users must be assigned the necessary permissions by an Administrator to perform these functions. Only Administrators may shut down the system.
  • Page 94 USER MANUAL nCounter Dx Analysis System ® If the electrode is severely bent to the point where a Cartridge cannot be inserted, close the electrode fixture without a Cartridge in it and adjust the position of the electrode such that it is positioned similarly to the other electrodes. If it is only slightly bent and a Cartridge can be inserted by carefully maneuvering the bent electrode, then insert a Cartridge before closing the electrode fixture.
  • Page 95 NanoString Technologies USER MANUAL ® Using a pair of tweezers, gently bend the electrodes into alignment by trying to align the tip of the electrode to the center and bottom of the Cartridge well. Touch Next. >>> The final screen will appear when the procedure is complete.

  • Page 96: O-Ring Lubrication

    USER MANUAL nCounter Dx Analysis System ® O-ring Lubrication The O-rings on the pipetting nozzles in the Prep Station are present to ensure a seal with the pipette tips thus ensuring accurate liquid volume control. O-rings are the small black rings found on the lower end of the nozzle. These O-rings must be lubricated regularly in order to ensure a good seal.
  • Page 97 NanoString Technologies USER MANUAL ® Select Lubricate O-Rings on the Maintenance Menu. >>> A series of ‘Lubricate O-rings’ maintenance screens will appear. FIGURE 7.9: Screens displayed for the different steps in the Lubricate O-rings workflow. 2017-07 MAN-C0034-06...
  • Page 98 USER MANUAL nCounter Dx Analysis System ® Follow the directions on the screens. To lubricate the O-rings, take a small amount of silicone grease and rub a finger around the O-ring using a gloved hand as shown in FIGURE 7.10.

  • Page 99: Downloading Log Files

    NanoString Technologies USER MANUAL ® Downloading Log Files If an issue is encountered, NanoString Support may request a download of the system log files. In the Maintenance Menu, select the Download Logs button. Log files are stored according to the date of each run (FIGURE 7.11).

  • Page 100: Digital Analyzer Maintenance

    USER MANUAL nCounter Dx Analysis System ® D. Digital Analyzer Maintenance Maintenance and support functions can be accessed from the Main Menu of the Digital Analyzer. Users must be assigned the necessary permissions by an Administrator to perform these functions. Only Administrators may shut down the system.

  • Page 101: Cleaning Instructions

    F. Disposal of Electronic Equipment IMPORTANT: This symbol on the nCounter Dx Analysis System is required in accordance with the Waste Electrical and Electronic Equipment (WEEE) Directive of the European Union. The presence of this marking on the product indicates that: •...

  • Page 102: Symbols And Definitions

    USER MANUAL nCounter Dx Analysis System ® Symbols and Definitions – Manufacturer – Authorized Representative in the European Community – In vitro diagnostic medical device – Consult Instructions for Use – CE Mark – Catalogue or Reference Number – Batch code / Lot number –...
  • Page 103 USER MANUAL ® NanoString Technologies, Inc. CONTACT US INFORMATION 530 Fairview Ave N info@nanostring.com United States: us.sales@nanostring.com europe.sales@nanostring.com Seattle, Washington 98109 USA Tel: +1.888.358.6266 Europe: info@nanostring.com Fax: +1.206.378.6288 Other Regions: www.nanostring.com © 2013-2017 NanoString Technologies, Inc. All rights reserved. 2017-07 MAN-C0034-06...

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