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SEV-00184-01

nCounter Pro Analysis System User Manual

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

SSH (SFTP) Setup

NanoString personnel can configure the Digital

Analyzer if users prefer to use SSH (SFTP) rather

than FTPS to transfer data files. Contact NanoString

[email protected]

to have SFTP

configured and enabled on the Digital Analyzer

(Figure 148).

System Software

Select software from the Maintenance Menu to

update Digital Analyzer’s system software when a

new release occurs, view the current software

version information, and restart the system in

troubleshooting situations (Figure 149).

Should assistance with the Digital Analyzer be

necessary, please identify the system software

version 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 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. The update file (*.cab) needs to

be at the root directory of the 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. The system will

automatically perform the software update.

Restart

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.

Figure 148: The ‘SSH configuration’ screen.

Figure 149: The ‘System Software’ screen.

Figure 150: The ‘About’ screen.

Содержание nCounter Pro

Страница 1: ......

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

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

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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...

Страница 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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