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nCounter Pro Analysis System User Manual

SEV-00184-01

FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.

100

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Authorized Representative in the European Community (Safety)

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Safety UK Conformity Assessed Mark

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Lower limit of temperature storage conditions

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For applications for which approval/clearance is not required and research use.

Summary of Contents for nCounter Pro

Page 1: ......

Page 2: ...m 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 Nano...

Page 3: ...ter 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 Pr...

Page 4: ...nformations de S curit Fran ais 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...

Page 5: ...mpleting 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...

Page 6: ...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...

Page 7: ...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...

Page 8: ...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 wi...

Page 9: ...che l applicationd une tensionpendantque laportede l instrument est ouverte Ne pasutiliserce dispositif proximit desourcesdefortesvibrationsouradiations lectromagn tiques car celles cipeuvent interf...

Page 10: ...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 op...

Page 11: ...ansfers magnetic bead separations and immobilization of molecular labels on the sample cartridge surface Figure 3 Prior to placing samples in the Prep Station samples need to be hybridized according t...

Page 12: ...he standard data resolution 280 fields of view FOV are collected per flow cell cartridge lane yielding data consisting of hundreds of thousands of target molecule counts The number of images taken cor...

Page 13: ...ication and present the Main Menu Figure 7 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 7 The Exit Life Scienc...

Page 14: ...login settings are enabled a Welcome screen will appear and the user will need to log in by pressing main menu Figure 10 see the section on Enterprise Package settings in the Operating the Digital An...

Page 15: ...ences 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 Press ok to exit Life Sciences mode and re...

Page 16: ...on AVERTISSEMENT Si lesr cipients d chetsne sont pasvid s lesemboutspeuvent entrer en contact avec des d chets liquides et contaminer les chantillons ou un trop grand nombred emboutspourraits accumule...

Page 17: ...e Master Kit size purchased 12 rxns 48 rxns or 192 rxns No reagent preparation or dilutions are required For each cartridge 12 lanes the components of the nCounter Master Kit include Two nCounter Prep...

Page 18: ...lect Protocol screen will appear Figure 14 Select one of three protocols for processing samples o High Sensitivity Recommended for most samples Increases the binding of all molecules to the slide by 2...

Page 19: ...es 1 6 of the 12 tube strip Any number of lanes between 1 12 will still consume an entire Cartridge 5 The Warm Reagents Cartridge screen will appear Figure 16 Cartridges and reagent plates prep plates...

Page 20: ...organization s laboratory procedures If the system is not being used to handle biohazardous samples liquid waste may be disposed of in the sink or other drain Press next 7 The Reagent Plate screen wil...

Page 21: ...Each side of the box serves as the opening for one set of tips Firmly grasp the bottom of the box when opening to avoid accidentally spilling the second set of tips Replace the loaded tip carrier bac...

Page 22: ...t is seated completely in the machined depression If it is not seated properly the electrodes may become bent Press next 11 The Electrode Fixture screen will appear Figure 26 Slowly lower the electrod...

Page 23: ...ectrodes workflow under the Maintenance menu The Prep Station will not be able to process any of the samples if there are bent electrodes 12 The Empty Strip Tubes screen will appear Figure 28 Place th...

Page 24: ...strip tube is placed incorrectly the lid won t close properly and the Prep Station will not be able to start processing Close the metal lid and press next Hybridized sample strip tubes have two notche...

Page 25: ...he 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 Finally select whether the Prep Stat...

Page 26: ...this is a part of normal operation If the Prep Station determines that a consumable is misplaced it will instruct the user to adjust the configuration The Validating deck layout screen will eventuall...

Page 27: ...The screen will update to show that the run has been paused Figure 35 After pausing an option to abort the run will appear Once the hybridized samples have been moved to the prep plate for processing...

Page 28: ...lease the fixture after the run is complete lift the lever in the center top of the device towards the front with a finger as shown in Figure 38 4 After processing is complete it is important to do th...

Page 29: ...or tracking and reporting needs Once enabled by NanoString users with the Enterprise Package will see an administration button on the Main Menu Figure 39 Below this there may be a second button to log...

Page 30: ...r erasing files after download cartridge tracking Set options for tracking nCounter Cartridge barcodes audit report Generate an audit log on demand For more information on the types of files managed b...

Page 31: ...Administration Menu Figure 40 and can create other user profiles email address Enter the email address that will be associated with the User display name The display name will appear when selecting em...

Page 32: ...the update function See the user jdb in Figure 41 as an example Be aware that user profiles can never be truly deleted as this would invalidate the audit trail Login Settings The Login Settings scree...

Page 33: ...tions If desired the RCC checksum option can create a separate checksum file stored in the same directory as the RCC file This checksum can be used to check that the RCC file was not altered during fi...

Page 34: ...he cartridge barcode scanner will be disabled when both audit log and RCC file are set to False Audit Report Generation The Audit Report Generation screen Figure 47 enables the administrator to create...

Page 35: ...uring image processing to assign target identities to the barcodes The Reporter Code Count file is generated by the Digital Analyzer Each one contains the data for one of the twelve lanes in a cartrid...

Page 36: ...ate the folder contents NOTE nCounter TagSets do not ship with a USB flash drive the RLF is provided via email Navigating File Folder Screens The file folder structure is similar to a personal compute...

Page 37: ...ive The RLF corresponding to a specific CodeSet must be uploaded before setting up a run using that CodeSet Once an RLF has been uploaded it will always be available until it is manually deleted from...

Page 38: ...es 38 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 4 Select one or more files and press...

Page 39: ...FTP client will need to support FTPS and TLS SSL implicit encryption NOTE Windows Explorer and Mac OS Finder do not support FTPS WinSCP is used for the following example steps and images 1 On a Window...

Page 40: ...3 Open the RLFData folder The RLFData folder will open and display the available files Figure 56 4 Copy and paste RLFs from the personal computer into the RLFData folder Figure 55 The contents of the...

Page 41: ...ls regarding the project or a specific sample Details are output within the RCC file as general information Date Optional This field can contain any date in the YYYYMMDD format The date of a scan is a...

Page 42: ...enario 1 Create a CDF using the CDF Utility on a personal computer This is the easiest and recommended method for creating CDFs See Creating a CDF Using the CDF Utility on a Personal Computer Scenario...

Page 43: ...tal 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: ...er the CartridgeID 2 Optional Enter the Email where the data should be sent 3 Enter the SampleID for each of the 12 samples These can be cut and pasted from another spreadsheet but you will not be abl...

Page 45: ...the RLF name will usually contain an underscore character _ but this character is allowed in this field in the CDF and are required to recognize the correct RLF name Do not include the rlf extension...

Page 46: ...ate CDF files on a personal computer see Creating a CDF Using the CDF Utility on a Personal Computer Users can modify this CDF template to contain personalized sample information it can be imported an...

Page 47: ...underscore cannot be used 2 Append the extension csv to the end of the file name 3 Double click the file to open it in Excel 4 Fill in the CDF as shown in Figure 60 Enter Cartridge ID here Enter vali...

Page 48: ...file name will include BOTH cdf and csv extensions as shown in Figure 61 top 6 Close the file 7 Remove the extra csv file extension leaving the file extension cdf Figure 61 bottom If a warning appear...

Page 49: ...ppropriate for the experiment Under Header Do not alter any of the existing text Enter the cartridge ID and user Email address after the comma Do not use spaces Under Samples Do not alter the definiti...

Page 50: ...he USB transfer option may be disabled 1 Insert the USB flash drive containing the CDF saved in the CDFData folder into the USB port on the side of the touchscreen 2 From the Main Menu press Upload Fi...

Page 51: ...the Digital Analyzer from a personal computer There are many FTP applications available For transferring data between the Digital Analyzer and a personal computer the FTP client will need to support...

Page 52: ...Connect The contents of the instrument server will appear Figure 68 3 Open the CDFData folder The CDFData folder will open and display the available files Figure 69 4 Copy and paste CDFs from the per...

Page 53: ...ples as no unique identifying information besides the sample cartridge ID will be contained in the data output The instructions below will discuss the entire process of creating a CDF on the Digital A...

Page 54: ...d If a higher throughput is preferred on the analyzer the user may opt to collect fewer images if sensitivity is less important For example rescanning a cartridge to check for data quality at low reso...

Page 55: ...ear next to each email address and users will have the option to select more than one email address Data will be stored in the older data section of the Digital Analyzer after being sent by email and...

Page 56: ...ar Figure 77 IMPORTANT When multiple samples are selected the information entered will be applied to all selected samples in this case Sample tubes 1 3 as the top of the screen indicates 11 On the Sam...

Page 57: ...the digital color coded reporter signals to their target identities IMPORTANT Selecting the wrong RLF during CDF creation will result in incorrect Reporter Code Counts 12 Once information for selected...

Page 58: ...sting folder or create a new folder in which to save the CDF Press next The Enter new cdf name screen will appear Figure 81 14 Enter the CDF name using the screen s keyboard and press enter If the CDF...

Page 59: ...ed and is logged in as an administrator see the Enterprise Package section 2 Select the cartridge position for which cartridge information will be entered by tapping that cartridge position on the scr...

Page 60: ...ppear Figure 87 NOTE If a cartridge ID or an email address was already entered into the CDF template then the following screens and steps may not apply to the workflow Skip to Step 9 6 To change any o...

Page 61: ...cartridge ID for the active cartridge the cartridge currently being scanned Cartridge scan status progress o Blue cartridge scan completed and or in progress o Green cartridge yet to be scanned durin...

Page 62: ...anually 13 The screen image in Figure 93 provides an example of a completed run Button options during and after a run download data Press download data to access data that has already been collected w...

Page 63: ...ta from cartridges that have already been imaged will be saved upload files New CDFs or RLFs can be uploaded if for example incorrect files were originally assigned when the run was initiated NOTE The...

Page 64: ...th the same cartridges following the instructions outlined above in Initiating aRun Abort a Cartridge When a single cartridge is aborted data on cartridges and lanes that have completed imaging are sa...

Page 65: ...tridge Definition Files section Completing a Run When the data collection has completed the stage will move to the home position for the door to be opened and the cartridges removed A Reporter Code Co...

Page 66: ...een until it has been downloaded once After the initial download data will be moved to the Older Data page NOTE If the Enterprise Package has been enabled it may be configured to prevent transferring...

Page 67: ...ly removed Download RCC Files via Email If Digital Analyzer networking and email have been configured via the maintenance screens and a valid email address was entered into a CDF template or during se...

Page 68: ...data between the Digital Analyzer and a personal computer the FTP client will need to support FTPS and TLS SSL implicit encryption NOTE Windows Explorer and Mac OS Finder do not support FTPS WinSCP is...

Page 69: ...e RCCData folder will open and display the available files Figure 105 4 Copy and paste files from the RCCData folder to the personal computer NOTE RCC files can be downloaded from the Digital Analyzer...

Page 70: ...l number in all communications NanoString Technologies Inc 530 Fairview Avenue North Seattle Washington 98109 USA Website https www nanostring com Support Email support nanostring com Phone 1 888 358...

Page 71: ...are Home robot align electrodes lubricate O rings and perform a dry run software Update Prep Station s system software when a new release occurs and view the current software information troubleshoot...

Page 72: ...on the Maintenance Menu Figure 107 The System Setup Menu will appear Figure 108 Setting the System Clock Setting the system clock ensures the accurate time is displayed on the screen and in the log fi...

Page 73: ...d correctly or outgoing email will not be sent Enter the name of the SMTP server for outgoing email SMTP port Enter the name of the port used by the SMTP server from address Enter a valid email addres...

Page 74: ...re Menu press hardware on the Maintenance Menu The System Hardware Menu Figure 112 enables the user to home robot Homes all the motors should the robot enter an undesired state align electrodes Guides...

Page 75: ...ndicates a bent electrode error message contact support nanostring com before attempting to re align an electrode NanoString Support can assess whether the electrode is the true root cause of the erro...

Page 76: ...stem Hardware Menu The Align Electrodes STEP 1 screen will appear Figure 114 2 If the electrode is severely bent such that a cartridge cannot be inserted first close the electrode fixture without a ca...

Page 77: ...he electrodes Two screens will appear in succession ending on Step 3 Figure 116 3 Using a pair of tweezers or fine tip pliers bend the electrodes into alignment Try to align the tip of the electrode t...

Page 78: ...r caution appropri es notamment le port de gants et de lunettes de s curit The O rings on the pipetting nozzles in the Prep Station are present to ensure a good seal with the pipette tips thus ensurin...

Page 79: ...e to lubricate the O rings Figure 119 NOTE The Prep Station will continue to function normally even though the yellow alert icon is present 1 Select lubricate O rings on the Main Menu or on the System...

Page 80: ...ub between gloved thumb and forefinger to yield a sheen of grease Then apply greased thumb and forefinger to the nozzle around the O ring as shown Figure 122 After applying grease to the front and bac...

Page 81: ...se 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 4 At th...

Page 82: ...m the dry run you will need the following blank reagent components It is appropriate to employ used reagents for this protocol Full set of used pipette tips 2x blank prep plates opened foil on the top...

Page 83: ...the Prep Station during the dry run to correct any issues that may occur 6 When the dry run is complete save the discarded tips by loading them back into the tip rack as well as the empty plates tubes...

Page 84: ...e the system software version prior to calling NanoString This information can be found by pressing about on the System Software Menu to open the About screen Figure 127 Update Periodically NanoString...

Page 85: ...s that may assist in recovering failed runs Download Log Files Access log files by pressing download log files on the Troubleshoot Menu Figure 128 Log files are labeled with the date of each run Multi...

Page 86: ...ol recovery workflow press start binding on the Troubleshoot Menu The Surface Binding Protocol Recovery screen will appear Figure 130 Press next 2 Instructions will appear on the next screen Figure 13...

Page 87: ...screen will appear Figure 133 5 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 Press next 6 The Start Processi...

Page 88: ...press start immobilizing on the Troubleshoot Menu The Surface Immobilization Protocol Recovery screen will appear Figure 135 Press next to proceed with the protocol 2 Instructions will appear on the...

Page 89: ...n will appear Figure 138 After selecting the samples to be processed press finish 5 The Notification Options screen will appear Figure 139 Select an email address to receive an email alert when the pr...

Page 90: ...re 140 Press start to initiate the protocol Refer to the Operating the Prep Station section for further instructions Shutdown System If the system needs to be shut down it is preferable to use the shu...

Page 91: ...rs view the current software version information and restart the system in troubleshooting situations troubleshoot Download log files for remote analysis by NanoString Support user profile Edit the cu...

Page 92: ...t the Digital Analyzer s date and time configure email settings and set the FTPS server password Setting the System Clock The data files created by the Digital Analyzer are named with a date and time...

Page 93: ...et This setting must be configured correctly or outgoing email will not be sent Enter the name of the SMTP server for outgoing email SMTP port Enter the name of the port used by the SMTP server from a...

Page 94: ...access to the Digital Analyzer select FTP on the System Setup screen The FTP configuration screen will appear Figure 147 The default FTPS user name is set to technician The user name cannot be changed...

Page 95: ...ion prior to calling NanoString This information can be found in the about section on the System Software screen Figure 150 Update Periodically NanoString will release a new version of software for th...

Page 96: ...of the touchscreen 4 Navigate to the appropriate log file directory by pressing on the folder Log files are organized by date the scan was initiated Press the download logs button 5 When the files hav...

Page 97: ...or from other screens accessed from the Maintenance Menu These include Software Version Instrument Name Current Date Current Time IP Address MAC Address Additional settings are configured through the...

Page 98: ...on Files press CDF on the Disk Cleanup screen The Select Files to Delete screen will appear Figure 157 2 Select one or more files to delete and press delete 3 At the prompt confirm the files to delete...

Page 99: ...excessive water or other solvents which may damage the screen Digital Analyzer Clean the exterior periodically using a diluted neutral soap followed by water NOTE If it becomes necessary to wash the...

Page 100: ...ty Safety Safety CE Mark Safety UK Conformity Assessed Mark Catalogue or Reference Number Batch code Lot number Serial number Temperature range storage conditions Lower limit of temperature storage co...

Page 101: ...ton 98109 USA www nanostring com CONTACT US info nanostring com Tel 1 888 358 6266 Fax 1 206 378 6288 SALES CONTACTS United States us sales nanostring com EMEA europe sales nanostring com Asia Pacific...

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