nanoString nCounter Pro User Manual
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nanoString nCounter Pro User Manual

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  • Page 2 Pro Analysis System User Manual SEV-00184-01 NanoString Technologies, Inc. 530 Fairview Ave N Seattle, Washington 98109 www.nanostring.com T: 206.378.6266 T: 888.358.6266 E: support@nanostring.com Sales Contacts United States: us.sales@nanostring.com EMEA: europe.sales@nanostring.com Asia Pacific & Japan: apac.sales@nanostring.com Other Regions: info@nanostring.com EU Authorized Representative...

  • Page 3: Rights, License, & Trademarks

    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.

  • Page 4: Table Of Contents

    Pro Analysis System User Manual SEV-00184-01 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 ..........................
  • Page 5 SEV-00184-01 nCounter Pro Analysis System User Manual 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 ....................

  • Page 6: Introduction

    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.

  • Page 7: Manual Conventions

    SEV-00184-01 nCounter Pro Analysis System User Manual 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 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.

  • Page 9: Informations De Sécurité (Français)

    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.

  • Page 10: Hardware Overview

    Pro Analysis System User Manual SEV-00184-01 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.

  • Page 11: Prep Station

    SEV-00184-01 nCounter Pro Analysis System User Manual NOTE: The Prep Station and the Digital Analyzer are stand-alone units. These instruments do not require connection to a personal computer and are not networked to one another. Connecting the Digital Analyzer to a network is optional and enables data delivery to the user via a network connection.

  • Page 12: Digital Analyzer

    Images are processed internally, and each lane produces one RCC (Reporter Code Count) file containing the counts for that lane. The RCC files are downloaded as a zipped folder of comma separated value (CSV) files. These can be imported and analyzed using NanoString's nSolver...

  • Page 13: Prep Station

    SEV-00184-01 nCounter Pro Analysis System User Manual Prep Station Select Instrument Mode After turning on the Prep Station, the first screen to appear is titled ‘Select Instrument Mode’ (Figure 6). Press the green icon labeled NanoString® Life Sciences to enter Life Sciences mode. The system will load the application and present the Main Menu (Figure 7).

  • Page 14: Digital Analyzer

    Pro Analysis System User Manual SEV-00184-01 Digital Analyzer Select Instrument Mode After turning on the Digital Analyzer, the first screen to appear is titled ‘Select Instrument Mode’ (Figure 9). Press the green icon labeled NanoString® Life Sciences to enter Life Sciences mode.
  • Page 15 SEV-00184-01 nCounter Pro Analysis System User Manual Exit Life Sciences Mode The user may exit Life Sciences mode by pressing the exit button located at the bottom of the Main Menu (Figure 11). The ‘Exit Life Sciences Mode’ confirmation screen will appear (Figure 12).

  • Page 16: Operating The Prep Station

    Pro Analysis System User Manual SEV-00184-01 Operating the Prep Station 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.

  • Page 17: Consumables Required

    SEV-00184-01 nCounter Pro Analysis System User Manual Consumables Required All the consumable items required to run the Prep Station are included in the nCounter Master Kit. This kit contains the reagents and consumables required to process 1, 4 or 16 cartridges depending on the Master Kit size purchased (12-rxns, 48-rxns, or 192-rxns).

  • Page 18: Initiating A Run

    Pro Analysis System User Manual SEV-00184-01 Initiating a Run The following workflow begins after samples have been hybridized overnight, according to the protocol outlined in the user manual specific to the assay (such as the nCounter miRNA Assay Manual...
  • Page 19 SEV-00184-01 nCounter Pro Analysis System User Manual The ‘Select sample tubes’ screen will appear (Figure 15). Select the sample positions that will be processed. Green tubes will be processed, and grey tubes will not be processed. If processing fewer than 12 tubes, begin with tube 1.
  • Page 20 Pro Analysis System User Manual SEV-00184-01 Centrifuge the prep plates at 2000g for 2 minutes to collect all liquids in the bottom of the wells prior to loading the prep plates onto the Prep Station deck. After centrifugation, visually inspect plates to ensure that reagents have collected at the bottom of each well.
  • Page 21 SEV-00184-01 nCounter Pro Analysis System User Manual Lanes 7-12 Lanes 1-6 Figure 20: Use the positioning pin (circled in red for the front plate) to ensure correct placement of the Prep Plates. The plate catch (circled in purple) contains a spring clip that ensures the plate is positioned securely.
  • Page 22 Pro Analysis System User Manual SEV-00184-01 The ‘Tip Sheaths’ screen will appear (Figure 23). Tip sheaths are used to reduce the amount of consumable waste. They allow the system to dedicate tips to a set of 6 samples and store them while processing the other 6 samples.
  • Page 23 SEV-00184-01 nCounter Pro Analysis System User Manual IMPORTANT: If any resistance is felt while lowering the fixture, stop and adjust the position of the cartridge slightly. Make sure that the electrodes are correctly aligned. If the electrodes are not aligned, use the ‘Align Electrodes’ workflow under the Maintenance menu.
  • Page 24 Pro Analysis System User Manual SEV-00184-01 The ‘Hybridized Samples’ screen will appear (Figure 29). Lift the metal lid to place the hybridized sample strip tube in the sample strip holder, ensuring that tube 1 aligns with position 1 (Figure 30). Note that the strip tube is asymmetrically keyed, and if the strip tube is placed incorrectly, the lid won’t close properly, and the Prep Station will not be able to start processing.
  • Page 25 SEV-00184-01 nCounter Pro Analysis System User Manual The ‘Notification Options’ screen will appear (Figure 31). Figure 31: The ‘Notification Options’ screen. Select the email addresses where error and completion confirmation emails should be sent. To add a new address, press add email, type in the address, and press enter (Figure 32).
  • Page 26 Pro Analysis System User Manual SEV-00184-01 The ‘Start Processing’ screen will appear (Figure 33). Press start when ready to begin processing. Figure 33: The ‘Start Processing’ screen. The ‘Validating deck layout’ screen will appear (Figure 34). The nCounter Prep Station will first check that all consumables and reagents have been placed properly on the deck.

  • Page 27: Pausing Or Aborting A Run

    SEV-00184-01 nCounter Pro Analysis System User Manual Pausing or Aborting a Run IMPORTANT: When a run is paused, resume as quickly as possible. Incubation times are very important and pausing the instrument can affect data quality and consistency. Runs should be paused only to avoid data loss due to operator error.
  • Page 28 Pro Analysis System User Manual SEV-00184-01 Press next. The ‘Run Successfully Completed’ screen will appear (Figure 37). The ‘Run Successfully Completed’ screen lists the steps to follow once the run is complete, including: Remove and discard empty reagent plates.

  • Page 29: Operating The Digital Analyzer

    This initial account has the user name “admin” and the default password “NanoString!”. Set your own password immediately after logging in for the first time. Press the administration button to open the Administration Menu; users will be required to enter a valid administrator user name and password.

  • Page 30: User Management

    Pro Analysis System User Manual SEV-00184-01 Administration Menu will appear (Figure 40). The Administration Menu provides access to six functions: • user management: Create new user profiles, define user access privileges, and disable existing user accounts. • login settings: Choose to require that users login before using the instrument.
  • Page 31 SEV-00184-01 nCounter Pro Analysis System User Manual Add a User To create a new user, press the add button. The ‘Create User’ screen will appear (Figure 42). Figure 42: The ‘Create User’ screen: top half (left) and bottom half (right).

  • Page 32: Login Settings

    Pro Analysis System User Manual SEV-00184-01 Update or Disable User To update an existing user profile, select that profile and press the update button (Figure 41). The user information will appear, very similar to the process of creating a new user. Select and edit fields as necessary, then press the save button.

  • Page 33: Archive Settings

    SEV-00184-01 nCounter Pro Analysis System User Manual USB/FTP Settings The ‘USB/FTP Settings’ screen (Figure 44) enables the administrator to choose which data transfer options are available to upload RLFs and CDFs and to download RCC files. For more information on these files and their...

  • Page 34: Cartridge Tracking Settings

    Pro Analysis System User Manual SEV-00184-01 Cartridge Tracking Settings ‘Cartridge Tracking Settings’ screen (Figure 46) allows the administrator to enable two features that track which nCounter Cartridge barcodes have been run on the Digital Analyzer. The first, audit log, instructs the instrument to save the cartridge barcode for inclusion in future audit reports (see the next section).

  • Page 35: Overview Of File Structure

    Digital Analyzer during image collection and processing. • The Reporter Library File is generated by NanoString and is unique to each custom CodeSet. It contains the information used during image processing to assign target identities to the barcodes.

  • Page 36: Navigating File/Folder Screens

    Pro Analysis System User Manual SEV-00184-01 Users may provide their own USB flash drive to transfer files but must create the same three folders (CDFData, RLFData, and RCCData) in order to interface with the nCounter system. NOTE: The USB flash drive and the Digital Analyzer have been designed specifically to enable quick and accurate file transfers.

  • Page 37: Reporter Library Files

    SEV-00184-01 nCounter Pro Analysis System User Manual Reporter Library Files Users need only upload Reporter Library Files (RLFs) when they first receive a new CodeSet. If the Enterprise Package is configured, RLFs may also be transferred automatically by FTPS (certain configurations may disable transfer by USB flash drive).
  • Page 38 Pro Analysis System User Manual SEV-00184-01 The ‘Select RLF Source’ screen will appear (Figure 52). Those folders and RLFs found on the USB flash drive that have not already been uploaded will be displayed. Select one or more files and press next to upload the file(s).

  • Page 39: Upload Rlfs Via Ftps

    SEV-00184-01 nCounter Pro Analysis System User Manual Upload RLFs via FTPS Acquire the IP address, or instrument serial number, and FTPS password prior to completing the following instructions to transfer data from a personal computer to the Digital Analyzer. See...
  • Page 40 Pro Analysis System User Manual SEV-00184-01 Open the RLFData folder. The RLFData folder will open and display the available files (Figure 56). Copy and paste RLFs from the personal computer into the RLFData folder. Figure 55: The contents of the instrument server when using an FTPS client.

  • Page 41: Cartridge Definition Files

    Users can create a new CDF on a personal computer or directly on the Digital Analyzer using the touchscreen. NanoString recommends users create CDFs on their computer if detailed information for each sample is required. In this case, a USB flash drive can be used to transfer the CDF to the imaging instrument.
  • Page 42 Pro Analysis System User Manual SEV-00184-01 When on the ‘Select Sample Tubes’ screen (Figure 57), tubes will be shown in three different colors. Blue: Defined. Blue tubes have the required information associated with them. Green: Selected. Green tubes are currently selected.

  • Page 43: Creating A Cdf On A Personal Computer

    Digital Analyzer (see section below). Because of these challenges, NanoString has created a macro-driven Excel file with built-in instructions as well as safeguards to prevent the more common sources of error.
  • Page 44 Pro Analysis System User Manual SEV-00184-01 Highlighted yellow cells indicate information is required, including CartridgeID, SampleID, FOVCount, and GeneRLF. Green cells are optional for additional information, including Email (if enabled on the Digital Analyzer), Owner, Comments, and Date (note that for tracking purposes the date of the scan will be automatically added to the start of each cartridge ID name as well as each sample File name).
  • Page 45 SEV-00184-01 nCounter Pro Analysis System User Manual IMPORTANT: The name entered in the GeneRLF column must be identical to the RLF loaded into the scanner. To prevent errors in transcribing, simply copy and paste the name from the RLF itself. Navigate to the RLF location using File Explorer (PC) or Finder...
  • Page 46 Pro Analysis System User Manual SEV-00184-01 Creating a CDF Manually on a Personal Computer Each USB flash drive that comes with a new CodeSet has a CDF template loaded onto it in the folder titled “CDFData”. If you received your RLF in an email from Bioinformatics, that email will also contain the CDF template that comes on the USB drive for CodeSets.
  • Page 47 SEV-00184-01 nCounter Pro Analysis System User Manual Modify an Existing CDF in Excel Available characters for renaming a file include: @ ^ + - # % ( ~ & ) NOTE: Filenames of CDFs cannot contain any characters in the filename not displayed on the touchscreen keypad.
  • Page 48 Pro Analysis System User Manual SEV-00184-01 When complete, save to the CDFData folder as file type “.csv”; the file name will include BOTH “.cdf” “.csv” extensions shown Figure 61, top. Close the file. Remove the extra “.csv” file extension,...
  • Page 49 SEV-00184-01 nCounter Pro Analysis System User Manual Modify an Existing CDF in Notepad NOTE: To avoid errors in file content and format. this method is not recommended unless necessary. Open the CDF in Notepad (or TextEdit). Note that all the information present in the Excel spreadsheet is also visible in Notepad (Figure 62).

  • Page 50: Upload Cdfs Via Usb Flash Drive

    Pro Analysis System User Manual SEV-00184-01 Upload CDFs via USB Flash Drive Users can upload a CDF created on a personal computer to the Digital Analyzer from a USB flash drive. If the Enterprise Package is configured (see the...

  • Page 51: Upload Cdfs Via Ftps

    SEV-00184-01 nCounter Pro Analysis System User Manual The ‘Select CDF Destination’ screen will appear (Figure 65). Browse to the folder CDFData and press save. Figure 65: The ‘Select CDF Destination’ screen. Upload CDFs via FTPS Acquire the IP address, or instrument serial...
  • Page 52 Pro Analysis System User Manual SEV-00184-01 Enter ‘technician’ as the FTPS user name as shown in Figure 67, enter the password as defined in the maintenance menu, and then click Log On or Connect. Figure 67: Enter 'technician' as the user name in the FTPS client connection.

  • Page 53: Creating A Cdf On The Digital Analyzer

    SEV-00184-01 nCounter Pro Analysis System User Manual Creating a CDF on the Digital Analyzer The fastest method for data entry on the Digital Analyzer is to create a template CDF for each CodeSet. To accomplish this, the user would select all tubes, use default sample IDs of 01–12, select an RLF, and press done on the confirmation screen.
  • Page 54 Pro Analysis System User Manual SEV-00184-01 The Digital Analyzer will return to the ‘Cartridge information’ screen (Figure 72). Press fov count to change the data resolution. The ‘Select Data Resolution’ screen will appear (Figure 73). Figure 72: The ‘Cartridge information’ screen Select the desired data resolution.
  • Page 55 SEV-00184-01 nCounter Pro Analysis System User Manual The system will return to the ‘Cartridge Information’ screen (Figure 72). Press email to select an email address; if the Enterprise Package enabled, some configurations disable email notifications. The ‘Select email address’ screen will appear (Figure 74).
  • Page 56 Pro Analysis System User Manual SEV-00184-01 Select the samples field. The ‘Select sample tubes’ screen will appear (Figure 76). Figure 76: The ‘Select sample tubes’ screen. Select the tubes for which sample information will be entered by pressing the appropriate tube on the screen.
  • Page 57 SEV-00184-01 nCounter Pro Analysis System User Manual d. Select the library RLF data field. The ‘Select Reporter Library File’ screen will appear (Figure 78). e. Select the RLF to use with this sample and press enter. The RLF contains the...
  • Page 58 Pro Analysis System User Manual SEV-00184-01 If all samples for the selected cartridge are defined appropriately, press done. To define more samples for the cartridge, press the samples button continue enter information as described in Steps 9–11 until all desired tubes in the cartridge have been defined.

  • Page 59: Initiating A Run

    SEV-00184-01 nCounter Pro Analysis System User Manual Initiating a Run From the Main Menu (Figure 83) select start counting. The ‘Select Stage Position’ screen will appear (Figure 84). NOTE: The administration button will only appear if the user has the Enterprise Package...
  • Page 60 Pro Analysis System User Manual SEV-00184-01 If a Cartridge Definition File (CDF) was already created and uploaded/saved to the system, press load existing. Otherwise, create a new CDF by pressing create new (see the previous section on Cartridge Definition Files instructions to create a new CDF).
  • Page 61 SEV-00184-01 nCounter Pro Analysis System User Manual Place cartridges into the stage position corresponding to the data entered in Steps 2–7 above. Use the orientation shown in Figure 89, with the barcode closest to the front of the instrument. Be sure that each cartridge is seated flat in the slot. Close the magnetic clips gently.
  • Page 62 Pro Analysis System User Manual SEV-00184-01 If the Enterprise Package has been configured to require user login (see the Enterprise Package section), then the screen will dim and lock automatically after begins (Figure 91). Press the light grey unlock button to log in. The...

  • Page 63: Pausing A Run

    SEV-00184-01 nCounter Pro Analysis System User Manual Pausing a Run From the ‘Counting Cartridge’ screen (Figure 92), runs can be paused to perform any of several actions: • add cartridge: A cartridge can be added if, for example, the device is in use, but the Prep Station has recently finished processing samples.
  • Page 64 Pro Analysis System User Manual SEV-00184-01 Abort a Run When a run is aborted, data on cartridges and lanes that have completed imaging are saved and available for download. On the ‘Counting Cartridge ID’ screen, press pause. The ‘Imaging Paused’ screen will appear (Figure 94).

  • Page 65: Completing A Run

    SEV-00184-01 nCounter Pro Analysis System User Manual Upload Files The Digital Analyzer can be paused in order to upload a new CDF or RLF. If the Enterprise Package has been enabled (see the Enterprise Package section), it may be configured to require that users log in before pausing the instrument.

  • Page 66: Download Rcc Files Via Usb Flash Drive

    Pro Analysis System User Manual SEV-00184-01 Download RCC Files via USB Flash Drive From the Main Menu (Figure 98), press download data. The ‘Select Data to Download’ screen will appear (Figure 99). Select data for download to the RCCData folder on a USB flash drive.

  • Page 67: Download Rcc Files Via Email

    Download RCC Files via SSH (SFTP) If SSH (SFTP) rather than FTPS is preferred to transfer data files, this can be configured on the Digital Analyzer by NanoString personnel. Contact NanoString Support at support@nanostring.com to have SSH (SFTP) configured and enabled on the Digital Analyzer.

  • Page 68: Download Rcc Files Via Ftps

    Pro Analysis System User Manual SEV-00184-01 Download RCC Files via FTPS Acquire the IP address and FTPS password prior to completing the following instructions to transfer data from the Digital Analyzer to a personal computer. Go to the Maintenance Menu on the Digital Analyzer and press system info to open the ‘System Information’...
  • Page 69 SEV-00184-01 nCounter Pro Analysis System User Manual The contents of the instrument server will appear (Figure 104). Figure 104: The contents of the instrument server when using an FTPS client. Open the RCCData folder. The RCCData folder will open and display the available files (Figure 105).

  • Page 70: Technical Support & Maintenance

    Seattle, Washington 98109 USA Website: https://www.nanostring.com/ Support Email: support@nanostring.com Phone: +1 888 358 NANO (+1 888 358 6266) Online Training at NanoString University NanoString University is an online training platform for instructional videos and documents to accompany your NanoString instrument assays. Create...

  • Page 71: Prep Station Maintenance

    SEV-00184-01 nCounter Pro Analysis System User Manual Prep Station Maintenance Several tasks can be accomplished using the Maintenance Menu on the Prep Station: • system setup: Set the date and time on the system clock and configure email. • hardware: Home robot, align electrodes, lubricate O-rings and perform a dry run.

  • Page 72: System Setup

    Pro Analysis System User Manual SEV-00184-01 System Setup The System Setup Menu allows the user to set the Prep Station’s date and time and configure email settings. To access it, press system setup on the Maintenance Menu (Figure 107).
  • Page 73 SEV-00184-01 nCounter Pro Analysis System User Manual Email Access Email addresses can be added, deleted, and managed on the Prep Station. This function allows users to receive notifications via email. Email must be configured for the notifications to work properly.

  • Page 74: System Hardware

    O-rings need to be lubricated and guides the user in the process. • calibration check: NanoString recommends that customers do not run the calibration check program. If the Prep Station has been idle for more than 1 month, it is recommended to perform a run.
  • Page 75 SEV-00184-01 nCounter Pro Analysis System User Manual Home Robot If the robot enters an undesirable state, pressing the home robot button can home all the motors. Pressing home robot will open the 'Home Prep Station' screen (Figure 113). This button should not be needed under normal operation.
  • Page 76 Pro Analysis System User Manual SEV-00184-01 NOTE: The Prep Station checks electrode function during the validation steps of the process before any samples are processed. If it detects problems with an electrode, the processing will halt and wait for user intervention. The screens described below will then appear, allowing the user to fix the bent electrodes.
  • Page 77 SEV-00184-01 nCounter Pro Analysis System User Manual Close the door and select next. The electrode fixture will tilt towards the operator for easier access to the electrodes. Two screens will appear in succession, ending on Step 3 (Figure 116). Figure 116: The ‘Align Electrodes—STEP 3’ screen.
  • Page 78 The Prep Station Maintenance Menu has an interface to make O-ring lubrication easier. Following the user interface brings the pipetting head to the front of the deck for access during lubrication. Required materials: • Silicone grease (transparent grease in a plastic container, provided by NanoString) • Lint-free paper (e.g., Kimwipe) •...
  • Page 79 SEV-00184-01 nCounter Pro Analysis System User Manual An alert will appear on the main screen and maintenance screen when it is time to lubricate the O- rings (Figure 119). Figure 119: The ‘lubricate O-rings’ maintenance alert screens. NOTE: The Prep Station will continue to function normally even though the yellow alert icon is present.
  • Page 80 Pro Analysis System User Manual SEV-00184-01 Follow the instructions as directed on the screen (Figure 121). Figure 121: The ‘Lubricate O-rings—STEP 2’ screen. To lubricate the O-rings, first use a twisted Kimwipe or lens cloth to “floss” between the nozzles and remove any grease from the white tip ejector block above the nozzles.
  • Page 81 SEV-00184-01 nCounter Pro Analysis System User Manual Continue following the instructions in each step of the workflow. Using lint-free paper, thoroughly wipe off any excess silicone grease from the nozzles and tip ejectors. Be careful not to get grease into any nozzles. If grease does get in the nozzle, open up a paperclip and use the wire to carefully scrape the grease back out.
  • Page 82 Pro Analysis System User Manual SEV-00184-01 nCounter Prep Station: Maintenance Dry Run NOTE: When conducting maintenance activities, always use appropriate safety precautions including wearing safety glasses and gloves. 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.
  • Page 83 SEV-00184-01 nCounter Pro Analysis System User Manual Approximately 10 minutes after initiating the dry run, the system will display a ‘bent electrode’ error message (Figure 125). This is expected as there is no liquid in the blank cartridge. To continue with the run, choose ignore and the Prep Station will continue running the rest of the protocol.

  • Page 84: System Software

    Periodically, NanoString will release a new version of software for the instruments. Users can download the latest version of the software from the NanoString website and transfer the update files to a USB flash drive. To update the software, insert the USB flash drive into the USB port on the side of the touchscreen and select the update button.

  • Page 85: Troubleshoot

    SEV-00184-01 nCounter Pro Analysis System User Manual Troubleshoot To access the Troubleshoot Menu, press troubleshoot on the Maintenance Menu. The Troubleshoot Menu (Figure 128) displays options to download log files (to submit to NanoString Support for diagnosing instrument issues) or run specialized procedures that may assist in recovering failed runs.
  • Page 86 Pro Analysis System User Manual SEV-00184-01 Start Binding The ‘Start Binding’ protocol can assist in running specialized procedures or in recovering failed runs. The process will start from the step after the hybridized samples are pulled away from the unbound probes and proceed to binding the purified samples to the surface of the cartridge.
  • Page 87 SEV-00184-01 nCounter Pro Analysis System User Manual The ‘Sample Selection’ screen will appear (Figure 132). After selecting the samples to be processed, press finish. Figure 132: The ‘Sample Selection’ screen. The ‘Notification Options’ screen will appear (Figure 133). Select an email address to receive an email alert when the protocol is complete and set the system to produce an audio alert if desired.
  • Page 88 Pro Analysis System User Manual SEV-00184-01 Start Immobilizing The ‘Start Immobilizing’ protocol can assist in running specialized procedures or in recovering failed runs. The process will start from the step after the hybridized samples are bound to the functionalized surface of the cartridge and proceed to immobilization of the bound samples.
  • Page 89 SEV-00184-01 nCounter Pro Analysis System User Manual Additional instructions will appear. These instructions apply only to recovery of 12 samples (Figure 137). Press next. Figure 137: Additional instructions for the ‘Surface Immobilization Protocol Recovery’ workflow. The ‘Sample Selection’ screen will appear (Figure 138).

  • Page 90: Shutdown System

    Pro Analysis System User Manual SEV-00184-01 The ‘Start Processing’ screen will appear (Figure 140). Press start to initiate the protocol. Refer to the Operating the Prep Station section for further instructions. Figure 140: The ‘Start Processing’ screen. Shutdown System If the system needs to be shut down, it is preferable to use the shutdown system button on the Maintenance Menu to power off the system before using the switch on the back of the Prep Station.

  • Page 91: Digital Analyzer Maintenance

    SEV-00184-01 nCounter Pro Analysis System User Manual Digital Analyzer Maintenance Several tasks can be accomplished using the Maintenance Menu on the Digital Analyzer: access Maintenance Menu, press maintenance on the Main Menu (Figure 141). The Maintenance Menu will appear (Figure 142). The...

  • Page 92: System Setup

    Pro Analysis System User Manual SEV-00184-01 System Setup The ‘System Setup’ screen (Figure 143) in the Maintenance section allows the user to set the Digital Analyzer’s date and time, configure email settings, and set the FTPS server password. Figure 143: The ‘System Setup’ screen.
  • Page 93 After entering the above information, enter a valid email address to test the email settings. NOTE: NanoString recommends testing email settings prior to setting up a run. Press the test button and confirm that a message was delivered to the inbox of the test email address.
  • Page 94 Pro Analysis System User Manual SEV-00184-01 The ‘Manage email addresses’ screen will appear (Figure 146). Email addresses associated with a user profile are not listed on this screen. Instead, use this screen to enter additional email addresses without creating a user profile.

  • Page 95: System Software

    Restart Figure 150: The ‘About’ screen. In rare troubleshooting situations, a NanoString representative may ask the user to restart the Digital Analyzer. Ensure that the cartridge door is closed, and then select the restart button. FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

  • Page 96: Troubleshoot

    Pro Analysis System User Manual SEV-00184-01 Troubleshoot Use the Troubleshoot Menu to download log files to send to NanoString Support for assistance in diagnosing a problem. Press troubleshoot on the Maintenance screen. ‘Troubleshoot’ screen will appear (Figure 151). Press the download log files button.

  • Page 97: User Profile

    System Information The ‘System Information’ screen (Figure 154) contains key information about the configuration of the Digital Analyzer. Some of these settings can only be configured by NanoString Support or from other screens accessed from the Maintenance Menu. These include: •...
  • Page 98 Pro Analysis System User Manual SEV-00184-01 Cleanup RCC Files To cleanup RCC files, press RCC on the ‘Disk Cleanup’ screen. The ‘Select Files to Delete’ screen will appear (Figure 156). Select one or more files to delete and press delete.

  • Page 99: Shutdown System

    IMPORTANT: For products under the requirement of WEEE directive, please contact your dealer or local NanoString office for the proper decontamination information and take back program, which will facilitate the proper collection, treatment, recovery, recycling, and safe disposal of the device.

  • Page 100: Symbols And Definitions

    Pro Analysis System User Manual SEV-00184-01 Symbols and Definitions Manufacturer Authorized Representative in the European Community (Safety) Safety CE Mark Safety UK Conformity Assessed Mark Catalogue or Reference Number Batch code / Lot number Serial number Temperature range storage conditions...
  • Page 101 NanoString Technologies, Inc. CONTACT US SALES CONTACTS 530 Fairview Ave North info@nanostring.com United States: us.sales@nanostring.com Seattle, Washington 98109 USA Tel: +1 888 358 6266 EMEA: europe.sales@nanostring.com www.nanostring.com Fax: +1 206 378 6288 Asia Pacific & Japan: apac.sales@nanostring.com Other regions: info@nanostring.com...

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