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NanoString Technologies®: User Manual

1. Enter a valid user name and password and press the Sign In button nCounter amp Analysis System Dx Please enter a user name and password NanoString Diagnostics FIGURE 3 8 The sign in screen gt gt gt The Main Menu will appear FIGURE 3 9 nCounter amp Analysis System Main Menu NanoString Diagnostics Loggedin Test User FIGURE 3 9 The Digital Analyzer Main Menu in Diagnostics mode nanosStri g 18 2015 01 MAN C0034 02 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 gt gt gt The Exit Diagnostics Mode confirmation screen will appear nCounter amp Analysis System Dx Exit Diagnostics Mode NanoString Diagnostics This option will exit Diagnostics mode and return to the main select instrument mode screen Press OK to continue and exit Diagnostics mode or Cancel to return to the main menu FIGURE 3 10 The Digital Analyzer Exit Diagnostics Mode confirmation screen Touch OK to exit Diagnostics mode and return to the Select Instrument Mode screen FIGURE 3 6 Touch Cancel to return to the Main Menu nanostring TECHNoOoOLoGcGi es 2015 01 MAN C0034 02 19 USER MANUAL nCounter Dx Analysis System This chapter provides directions for using the nCounter web application which resides o
2. Last Update The date that the sample last changed status Created By The User ID that created the Run Set using the web application Lane The lane where the sample resides on the cartridge Memo optional Notes about the sample entered in the Memo field of the Run Set form Prep Station Name of the Prep Station on which the sample was processed useful if more than one Prep Station is connected to the Digital Analyzer nanostring 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL D Run Sets This section guides users through creating editing printing and deleting 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 Runs from the menu bar at the top of the page and choose Create New Run Set from the sub menu that appears below FIGURE 4 18 Logged inas _ Test User Prosigna NanoString Diagnostics Le Dashboard Runs M Samples Reports amp Admin My Profile Logout View Run Sets Create New Run Set COMMON TASKS m Run Sets Show All b View Run Sets gt Create New Run Set RUN SET ID STATUS CREATED CREATED BY gt Download Reports 20140912 BatchRegistered 9 12 2014 1 19 40 PM Test User gt Add New User 20140912GH BatchRegistered 9 12 2014 1 18 5
3. The four different functions described above are organized in different tabs The default tab displayed is Date and Time nanostring 2015 01 MAN C0034 02 45 USER MANUAL nCounter Dx Analysis System 46 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 Logged inas _ Test User Prosigna NanoString Diagnostics S a Dashboard mb Runs H Reports 2 Admin My Profile Logout amp System Settings Dateand Time Emaii Settings SSH Settings IP Address Usage Report DATE 09 12 2014 MM DD YYYY TIME 01 58 PM HH MM AM PM TIMEZONE GMT 08 00 Pacific Time US amp Canada Use Daylight Savings Time FIGURE 4 37 The Date and Time tab on the System Settings page L NOTE Administrators cannot adjust the Time Zone or Daylight Saving Time options Contact NanoString Support if these values need to be adjusted ps NOTE Changing the date and or time in the nCounter web application adjusts these values on the Digital Analyzer and Prep Station as well Take care when making changes to these settings nanostring 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL E mail Settings E mail settings must be configured in order for the nCounter system to successfully send automated e mai
4. nCounter Dx Analysis System User Manual NanoString Technologies Inc 550 Fairview Ave N Suite 2000 Seattle WA 98109 USA www nanostring com Phone 1 206 578 6266 1 888 558 NANO E mail dxsupport nanostring com LivD C 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 2015 01 MAN C0034 02 USER MANUAL nCounter Dx Analysis System Intellectual Property Rights 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 Analysis System including both its software and hardware components and this User Manual and any other documentation provided to you by NanoString in connection therewith are subject to patents copyright trade secret rights and other intellectual property rights owned by or licensed to NanoString No part of the software or hardware may be reproduced transmitted transcribed stored in a retrieval system or translated into other languages without the prior written consent of NanoString The manufacture use and or sale of NanoString product s may be subject to one or more patents or pending patent applications owned
5. 2015 01 MAN C0034 02 Es NanoString Technologies USER MANUAL 4 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 gt gt gt The Review Reaction Layout screen will appear nCounter amp Analysis System Dx Review Reaction Layout OO NanoString Diagnostics Run Set ID 20140912AB Assay Prosigna Creator Test User Date 9 12 2014 UU wi Name Value Sample ID Sample72306 Comment of Positive Nodes Zero Positive Nodes Tumor Size lt 2cm lt Back Cancel Next gt FIGURE 5 5 The Review Reaction Layout screen with two reference samples yellow and 10 patient samples blue One patient sample is selected green 5 Touch individual samples to view their details Verify that the Run Set and sample information are correct FIGURE 5 5 If not return to the web application and make the appropriate corrections First touch Cancel on the Prep Station to make them available for editing If they are correct touch Next gt gt gt The Scan CodeSet screen will appear nCounter Analysis System Dx Scan CodeSet OO NanoString Diagnostics Please scan or manually enter 10 digit barcode Manual Entry FIGURE 5 6 The Scan CodeSet screen nanostring ete ete UIDES Ze 05 USER MANUAL nCounter Dx Analysis System 6 The barcode for the CodeSet must be
6. CONFIRM PASSWORD E MAIL ADDRESS USERTYPE Administrator General no admin privileges PERMISSIONS RUN POST HYBRIDIZATION Prosigna Assay 2 ACCESS REPORTS Prosigna Assay 2 CREATE RUN SET Prosigna Assay 2 FIGURE 4 31 The Add New User form nanostring 2015 01 MAN C0034 02 4 USER MANUAL nCounter Dx Analysis System Enter the following information and click the Save button e User ID required Password required Confirm Password required e E mail address required e User type required choose either e General Access to standard functionality including creating a Run Set access does not include processing samples e Administrator General user access plus administrative access including user management and system settings Permissions at least one permission is required choose all that apply e Run Post Hybridization This permission is required to operate the Prep Station and initiate the post hybridization process for the assay s selected e Access Reports This permission is required to view the Reports tab on the Web Application and download diagnostic reports for the assay s selected e Create Run Set This permission is required to create a new Run Set or edit an existing Run Set on the Web Application for the assay s selected n NOTE Administrators do not automatically have permission to access diagnostic reports and initiate post hybridization processing o
7. appear Touch the appropriate buttons to enter the number If you make a mistake touch del to backspace or clear to start over Press enter when finished b Remove the clear plastic lids and place the reagent plates on the deck as indicated on the screen FIGURE 5 10 The deck has alignment pins that will allow the plates to sit flat only if they are in the correct orientation The reagent plate should be oriented with the barcode facing the user FIGURE 5 11 If the plate is placed in the wrong direction the Prep Station will pause the protocol at the validation step until the user intervenes ps NOTE Only one reagent plate is required for runs performed using a 1 2 3 or 4 test kit For these kits load the reagent plate into the front position nearest the user on the Prep Station deck E NOTE The Prep Station will not accept barcodes for plates that have expired Make sure the plates are used prior to the expiration date 312006 WM oO 3 30 0170 Me Ee iio n m M A e 4 e TUS Raum NS f etn tiet L A wy FIGURE 5 11 Use the positioning pins to ensure correct placement of the reagent plates O IMPORTANT Do not remove the foil or pierce the wells on the reagent plates The Prep Station pierces the aluminum foil during processing nanostring 56 2015 01 MAN C0034 02 m um C HN O LO GI M NanoString mm Toi alate eTe 1 08 USER MANUAL c Touch Next gt gt gt The Tips and Foi
8. code 9 Lkyy59D2x0 4 CodeSet Kit Number 012345019 Scan or manually enter the barcode labeled Run z orn enter the Kit Lot Ni e 5 Enter Sample Data prese DOM HP HM CY RHONE PNE sticker included in the CodeSet box be r mpie Data WELL SAMPLE ID LABEL OF POSITIVE NODES TUMOR SIZE Sample12353 Zero Positive Nodes Sample24213 Zero Positive Nodes Sample32365 1 3 Positive Nodes Sample48456 1 3 Positive Nodes FIGURE 4 24 The Edit Run Set page kh NOTE Clicking on the Run Set ID hyperlink will NOT open the Run Set for editing Clicking the hyperlink will open the Samples status page pre filtered to view only that Run Set Verify that the correct Run Set has been opened and then edit the Run Set as needed Save changes by clicking the Save Run Set button at the top When prompted print the worksheet as recommended earlier in this section nanostring rECHNOLOGieEs 2015 01 MAN C0034 02 S7 USER MANUAL nCounter Dx Analysis System 58 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 25 Logged inas _ Test User NanoString Diagnostics My Profile Logout RUN SET ID STATUS CREATED CREATED BY INITIATED BY 201409121J BatchRegistered 9 12 2014 1 19 40 PM Test User 20140912GH BatchRegistered 9 12 2014 1 18 56 PM Test User 2014091 2EF BatchRegistered 9 12 2
9. lifting it straight up and out of the Prep Station 2 Remove the liquid waste container from the combined receptacle by using the latch on the front and dispose of the liquid appropriately e Tips should be discarded into the appropriate waste receptacle as outlined in the local organization s laboratory procedures e f biohazardous samples are not being used in the system and if permitted by the laboratory procedures liquid waste may be disposed of in the sink or other drain 3 Verify that the plastic rack holding the used piercers tip sheaths reagent plates and strip tubes from the previous run have all been removed from the deck Consumables Required The consumables required for each run are available as part of the test kit The kit contains the reagents and consumables required to process 1 2 3 4 10 20 30 or 40 patient samples The components of a test kit required to operate the Prep Station include e CodeSet Barcode included inside CodeSet box e Sample Cartridges e Reagent Plates e Pipette Tips e Tip Sheaths e 12 Tube Strips and Caps e Cartridge Adhesive Covers nanostring 50 2015 01 MAN COQDJS4 07 T E C H NOLO GIE s NanoString Technologies USER MANUAL B Initiating a Run The following steps summarize the workflow beginning from the Welcome screen on the Prep Station touchscreen 1 To process samples using the Prep Station a user must log on to the instrument In order to log on touch Main
10. nanostring NOoutoGies 2015 01 MAN CO0034 02 29 USER MANUAL nCounter Dx Analysis System The following information is available 1 RunSetID The Run Set ID entered when the Run Set was created 2 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 PostHybProcessing Prep Station Processing Run Set is currently processing on the Prep Station PostHybComplete Prep Station Completed Run Set has completed on the Prep Station PostHybAbort Prep Station Abort manual abort on the Prep Station PostHybError Prep Station Error an error occurred during processing on the Prep Station ScanProcessing DA Scan Processing currently processing on the Digital Analyzer ScanError DA Scan Error an error occurred during processing on the Digital Analyzer ScanAbort DA Scan Abort manual abort on the Digital Analyzer BatchComplete Batch Complete Run Set has completed processing ReportPending Report Pending scanning complete but waiting for the algorithm to complete ReportProcessing Report Processing algorithm is running but the report has not been produced yet ReportComplete Report Complete Digital Analyzer has finished scanning and reports are available for download from the Reports page ReportError Report Failed all processing for the Run Set is complete but a report was not generated
11. performing user maintenance on the instruments e Donot attempt to wash the Prep Station s electrodes or allow water or other solvents to come into contact with the electrodes e Donot attempt to wash either instrument s touchscreen or allow water or other solvents to come into contact with the touchscreens G Caution Symbols AA BIOHAZARD Potential hazard from a biological source exists If you choose to use biohazardous materials on your Prep Station the instrument may become contaminated with biohazardous materials Please affix the proper warning labeling to your Prep Station if you use biohazardous inputs Be careful not to touch this area without gloves or other personal protective equipment AN ELECTRICAL HAZARD A CAUTION HOT SURFACE H Environmental Requirements e Temperature 18 28 C e Humidity lt 80 relative humidity non condensing nanostring 2015 01 MAN C0034 02 9 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 Both instruments contain a touchscreen to enable operation of the instrument The touchscreen is a touch sensitive method of controlling the instrument that enables the user to operate the system by touching a selection on the screen The
12. scanned before proceeding Hold the barcode of the CodeSet in front of the barcode reader A red beam will appear Move the barcode in front of the red beam until it is read When the barcode is successfully entered the barcode number will appear in the box FIGURE 5 6 ps NOTE The CodeSet barcode must match the CodeSet Kit Number entered when the Run Set was created using the web application FIGURE 4 19 gt gt gt The Reagents And Cartridge screen will appear nCounter amp Analysis System Dx Reagents And Cartridge 00 NanoString Diagnostics Allow the plates to warm to room temperature for 10 15 minutes prior to proceeding Before loading centrifuge reagent plates at 2000 g for 2 minutes FIGURE 5 7 The Reagents And Cartridge screen 7 Cartridges and reagent plates FIGURE 5 8 must be at room temperature prior to processing a 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 sealed sample cartridge left and Dx reagent plate right Lh NOTE Only one reagent plate is required for runs performed using a 1 2 3 or 4 test kit NOTE Do not open the cartridge pouch until it has reached room temperature This will prevent condensation from forming on the cartridge nanostring 54 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL b Ce
13. see Chapter 5 Selecting the Instrument Mode O IMPORTANT To ensure proper communication between instruments after a power cycle always restore power to the Digital Analyzer first and allow the instrument to fully initialize before restoring power to the Prep Station nanostring TECHNOLO G ces 2015 01 MAN C0034 02 15 USER MANUAL nCounter Dx Analysis System 76 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 In addition to instrument power cycling see previous section users are expected to perform two principal tasks when required electrode alignment and O ring lubrication Additional less frequent maintenance functions include homing the robot and downloading log files Electrode Alignment From time to time the electrodes used for stretching the reporters may become bent out of alignment and no longer fit into the cartridge properly This usually occurs if the cartridge was not aligned properly when the electrode fixture was depressed causing the electrode to make contact with the cartridge and bend The following describes a method for re alignment of the electrodes using the system hardware interface This method allows the electrode fixture to tilt at an angle that makes it much easier to view the electrodes durin
14. the appropriate nCounter reports NOTE A user must have proper permissions set in their user profile in order to be able to receive e mail report notifications Attempts to assign a user without appropriate access to receive report notifications will result in an error message To change these permissions an administrator must edit the user s profile and add the privilege nanostring 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL SAMPLE ID LABEL OF POSITIVE NODES TUMOR SIZE Sample1 Zero Positive Nodes Sample2 Zero Positive Nodes Sample3 1 3 Positive Nodes Sample4 Zero Positive Nodes Sample5 Zero Positive Nodes Sample6 1 3 Positive Nodes Sample Zero Positive Nodes Samples 1 3 Positive Nodes Sample9 Zero Positive Nodes Sample10 Zero Positive Nodes Set E mail Recipients E mail STATUS UPDATES to Administrator Test User Alpha Beta Charlie David Elena Frank Gamma E mail REPORT NOTIFICATIONS to Helen Test User Karen Test User FIGURE 4 20 The location of the contact list and email alerts on the Create New Run Set form It is crucial that sample information is entered correctly Each well must be completed with all required information before sample information is entered for the next well When all information for the Run Set has been entered click on Save Run Set After the Run Set has been saved a prompt to print a worksheet will appear gt Print Worksheet Do you want to
15. the network administrator for Static IP address e Subnet Subnet provided by the network administrator for Static IP address e Gateway Gateway address provided by the network administrator for Static IP address e DNS1 Domain Name Server provided by the network administrator for Static IP address e DNS2 A second DNS is optionally provided by the network administrator and used as a backup for Static IP address 5 NOTE A Static IP Address is particularly useful because it ensures more reliable communication between the Digital Analyzer and the Prep Station If the Dynamic IP Address option is chosen the Digital Analyzer may sometimes acquire a different IP address giving rise to the possibility of intermittent communication issues nanostring 2015 01 MAN C0034 02 49 USER MANUAL nCounter Dx Analysis System 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 A 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 A CAUTION Used plastic ware such as reagents cartridges and pipetting tips must be collected and disposed of properly in accordance with local safety regulations and laboratory procedures 1 Remove the combined waste receptacle by
16. to a specified location on a computer or network 5 NOTE Remember that reports contain confidential information Be careful when saving to a network or location that may be accessed by others nanostring 40 2015 01 MAN C0034 02 tec HN OLOGI NanoString Technologies USER MANUAL G Administration For users designated with the Administrative role the Admin button is available in the top menu bar of the web application Administrators can choose from three main functions e Manage Users e System Settings e Add User Add Delete and Manage Users To add a new user select Admin from the top menu bar and click on Add User Logged inas _ Test User Prosigna NanoString Diagnostics Emu A2 1l oo li Reports a Admin My Profile Logout Runs M Samples Manage Users System Settings Add User COMMON TASKS E Run Sets Show AII b View Run Sets gt Create New Run Set RUN SET ID STATUS CREATED CREATED BY Dashboard gt Download Reports 20140912 BatchRegistered 9 12 2014 1 19 40 PM Test User b Add New User 20140912GH BatchRegistered 9 12 2014 1 18 56 PM Test User 20140912EF BatchRegistered 9 12 2014 1 17 51 PM Test User 20140912CD BatchRegistered 9 12 2014 1 16 52 PM Test User 20140912AB BatchRegistered 9 12 2014 1 13 56 PM Test User FIGURE 4 30 The location of the Add User button in the Admin sub menu gt gt gt The Add New User form will appear Add New User USERID PASSWORD
17. to continue or Maintenance to return to the maintenance menu NanoString Diagnostics nCounter amp Analysis System Lubricate O Rings Preparing Station Please wait while preparing the prep station nCounter Analysis System Lubricate O Rings Close Door NanoString Diagnostics Please close the instrument door Press Finish to complete the operation FIGURE 7 9 Screens shown for the different steps in the Lubricate O rings workflow nanostring 2015 01 MAN CO034 02 trecHNoOtocies NanoString Technologies USER MANUAL 2 Follow the directions on the screens 3 To lubricate the O rings take a small amount of silicone grease and rub a finger round the O ring using a gloved hand as shown in FIGURE 7 10 FIGURE 7 10 Use a finger to apply a small amount of NanoString silicone grease to the O rings 4 Using lint free paper thoroughly wipe off any excess silicone grease from the nozzles and Tip Ejectors 5 Gently move that finger around each ring to distribute the grease evenly 6 Following the instructions on the screen touch the Next and Finish buttons to complete the procedure 7 Completing the Lubricate O rings workflow will reset the internal timer and remove the yellow warning icon if it is present Q IMPORTANT Excess grease may cause equipment malfunction Avoid applying grease to the metal portion of the nozzle nanostring c4 FO 2015 01 MAN C0034 02 31 USER MANUAL nCounter Dx An
18. v E son see en ence octet E meinen ta E E A enacts racine 24 FFU EEE EOE E AEEA VA EENS E AAEE TEE E O AA E E 24 gt E A EATE EA T TE E E E E E E N E E E E T E E EE E EE 26 PON e A E A E E E E A coecetneurenee 27 C Dashboard and Status Pages sostenere EEEIEE EREEREER EEEa 28 BE aS ee PR NR TT 28 Fe ng c c 29 SairiDI S SPSBS coconut MM MM uM 31 D lile 33 Ce FIN sce A m 33 EAN O RUN AM OOKX O 37 Delete a RUN Set oo ccccccessssssessessssssssssecussessesussnssesseesssssssaussussesssansesssesseasssessssusavssesusevsssssesusassaseasansevsseeussessssesausassseensersasaneansass 38 Xximbpcil lcw 59 BS RN REIR RR RUE E N E a 40 A OMINIE NON ues oratum ns ERAN MUR UNE MUNI MN E E 41 Add Delete and Manage Users seen ertet tette tette 41 SN EAC GG O bs cac usn A MM UM DE MM ME ME MM EE 45 Chapter 5 Operating the Prep Station sss 50 67 A Prior to Initiating a RUN sse eren rentrer eerte erred 50 MS SU c M T ae 50 Be gol gars 8 ercal REQUE NENNT TENE E O 50 B Initiating a od en re cease we vn a ee Ce en ene ee Te 51 Chapter 6 Operating the Digital Analyzer sss 68 72 A Initiating a R
19. 014 1 17 51 PM Test User BatchRegistered 9 12 2014 1 16 52 PM Test User 20140912AB BatchRegistered 9 12 2014 1 13 56 PM Test User FIGURE 4 25 Location of the Delete button on the Run Sets page gt gt gt A prompt will appear to confirm deletion of the Run Set a Delete runset Are you sure you want to delete runset 20140912CD ELI NNNM FIGURE 4 26 The Delete runset prompt Click OK to delete the Run Set or Cancel to return to the Run Sets page nanostring 2015 01 MAN C0034 02 trecHnNnoi NanoString Technologies USER MANUAL E 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 To print a Run Set worksheet navigate to the Run Sets page select the Run Set row of interest and click the Print Worksheet button FIGURE 4 27 Logged inas _ Test User NanoString Diagnostics E X eee eee ae Reports x Admin My Profile Logout Print Worksheet Delete RUN SET ID CREATED CREATED BY INITIATED BY 201408121J BatchRegistered 9 12 2014 1 19 40 PM Test User 20140812GH BatchRegistered 9 12 2014 1 18 56 PM Test User 20140912EF BatchRegistered 9 12 2014 1 17 51 PM Test User 20140912CD BatchRegistered 9 12 2014 1 16 52 PM Test Us
20. 6 PM Test User 20140912EF BatchRegistered 9 12 2014 1 17 51 PM Test User 20140912CD BatchRegistered 9 12 2014 1 16 52 PM Test User 20140912AB BatchRegistered 9 12 2014 1 13 56 PM Test User FIGURE 4 18 The Create New Run Set option is in the Runs sub menu gt gt gt The Create New Run Set form will appear Logged inas _ Test User Prosigna NanoString Diagnostics lt gt Dashboard mb Runs Il Al My Profile Logout Cancel SAVE RUN SET Create New Run Set 2 Enter Run Set ID 20140912AB Every Run Set ID must be unique Example 20120701LB2 3 Test Configuration code wL28s0 w14 4 CodeSet Kit Number 012345019 Scan or manually enter the barcode labeled Run Scan or manually enter the Kit Lot Number from the Configuration Code that came in the CodeSet box sticker included in the CodeSet box 5 Enter Sample Data WELL SAMPLE ID LABEL Sample1 Zero Positive Nodes Sample2 Zero Positive Nodes Sample3 1 3 Positive Nodes Sample4 Zero Positive Nodes Sample5 Zero Positive Nodes Sample6 1 3 Positive Nodes Sample Zero Positive Nodes Samples 1 3 Positive Nodes Sample9 Zero Positive Nodes Sample10 Zero Positive Nodes FIGURE 4 19 The Create New Run Set form nanostring Notocgies 2Q15 01 MAN C0034 02 53 USER MANUAL 54 nCounter Dx Analysis System Enter the following information to create a Run Set 1 nCounter Assay Type The nCounter assay type was prev
21. 7 51 PM 9 12 2014 1 16 52 PM 9 12 2014 1 13 56 PM CREATED BY Test User Test User Test User Test User Test User FIGURE 4 16 The location of the Samples menu option The Samples page allows users to view the statuses of all samples for all Run Sets RUN SET ID Sample14578 Sample27456 Sample34352 Sample48724 Sample52968 Sample65702 Sample72306 Sample82380 Sample91306 Sample10410 20140912AB 20140912AB 20140912AB 20140912AB 20140912AB 20140912AB 20140912AB 20140912AB 20140912AB 20140912AB SampleRegistered SampleRegistered SampleRegistered SampleRegistered SampleRegistered SampleRegistered SampleRegistered SampleRegistered SampleRegistered SampleRegistered 9 12 2014 1 36 07 PM 9 12 2014 1 36 07 PM 9 12 2014 1 36 07 PM 9 12 2014 1 36 07 PM 9 12 2014 1 36 07 PM 9 12 2014 1 36 07 PM 9 12 2014 1 36 07 PM 9 12 2014 1 36 07 PM 9 12 2014 1 36 07 PM 9 12 2014 1 36 07 PM Test User Test User Test User Test User Test User Test User Test User Test User Test User Test User FIGURE 4 17 The statuses of all samples contained within all Run Sets nanostring N C O G 2015 01 MAN C0034 02 Logged inas _ Test User NanoString Diagnostics My Profile Logout 5 USER MANUAL o2 nCounter Dx Analysis System The following information is available o Ngon p Sample ID The Sample ID entered manually or via a barcode scanner when creating the Run Set Run Set I
22. 73 nCounter Dx Analysis System 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 nCounter amp Analysis System Dx Main Menu NanoString Diagnostics Process Samples Maintenance LoggedIn Test User FIGURE 7 1 This example shows the Maintenance button on the Prep Station Main Menu E NOTE Users must be assigned Administrator privileges by an Administrator to perform these functions Only Administrators may shut down the system E NOTE Shutting down the IVD system will interrupt cartridge preparation and analysis Please ensure that all cartridges have finished processing on the Digital Analyzer and the Prep Station is not in use before cycling instrument system power The following instructions may be used to cycle the system power on either instrument 1 Select Power Off from the Maintenance Menu nCounter amp Analysis System nCounter Analysis System m i DX Maintenance Maintenance NanoString Diagnostics Home Robot Home Stage Align Electrodes Lubricate O Rings Download Logs Download Logs FIGURE 7 2 The Prep Station Maintenance Menu left and Digital Analyzer Maintenance Menu right gt gt gt The system will shut down nanos
23. D The Run Set ID entered when creating the Run Set in the web application Status The condition or state that the sample is currently in The following are possible statuses for a sample SampleRegistered Sample Registered Sample is defined has not started processing yet PostHybProcessing Prep Station Processing Run Set is currently processing on the Prep Station PostHybComplete Prep Station Completed Run Set has completed on the Prep Station PostHybAbort Prep Station Abort manual abort on the Prep Station PostHybError Prep Station Error an error occurred during processing on the Prep Station ScanProcessing DA Scan Processing currently processing on the Digital Analyzer ScanError DA Scan Error an error occurred during processing on the Digital Analyzer ScanAbort DA Scan Abort manual abort on the Digital Analyzer ReportPending Report Pending Scanning complete but waiting for the algorithm to complete ReportProcessing Report Processing Algorithm is running but the report has not been produced yet ReportComplete Report Complete Digital Analyzer has finished scanning and reports are available for download from the Reports page ReportError Report Failed All processing for the run set is complete but a report was not generated due to an error in the algorithm ReportCompleteWithError Report Complete with Error All processing for the run set is complete and a report generated but the assay failed
24. Environmental ReQulFemells mei rri MER RR E IE AU REDE HET ru dE M GR ER ESRB NEL IA MACH LOREM MR ICA CMM EL CREE LMLUS 9 Chapter 2 Hardware Overview sse eren tnn 10 12 A General Information 1 1 0 sse terere terere rrr tete 10 B Prop SEO c NRRRRUPRR ERN 11 C Digital Analyzer tessisnsssssesissetnssevevvirnseetesvevisnssesveveseecesevevereesesevevverererseneneren 12 Chapter 3 Selecting the Instrument Mode osse 15 19 A Prep Station 14 Select Instramesnt MOUSL aieo ee ran Pm een ub eS ut tnu eerte Run De E d d 14 SWiteh Instrument e e NEMPE DEREN 16 B Digital AnalyZer iii sse mmn mener nene eret treten 17 Sale INS TUNENE MOOG eom Ur i mum Vade on Oe nT Ee Cabe cod bm ene Da 17 SWiten NStiruUment MOOG oec retenti eT rotae ave CET ee eS 19 nanostring 4 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL Chapter 4 Operating the Web Application sss 20 49 A Sign In and Profile Management sss tenerent 20 legc RR TR 20 Forgot User ID PassSWOTd ssssseteetetetet eret tret terra rer teret 21 Updating My M igo i RRNRRRERRERRRRENM AA EOCDIIIIII 22 B Application Layout and Navigation sss tnnt 23 PS 23 Jem c
25. Menu on the Welcome Screen nCounter amp Analysis System Dx Welcome Select an option ooooot FIGURE 5 1 The Prep Station Welcome screen 2 Enter a valid user name and password and touch Sign In nCounter Analysis System Dx Please enter a user name and password NanoString Diagnostics FIGURE 5 2 The sign in screen gt gt gt The Main Menu will appear FIGURE 5 3 nanostring 2015 01 MAN C0034 02 5 USER MANUAL nCounter Dx Analysis System 3 Toset up a new run touch Process Samples from the Main Menu nCounter amp Analysis System Dx Main Menu Dx NanoString Diagnostics Process Samples Maintenance LoggedIn Test User FIGURE 5 3 The Prep Station Main Menu gt gt gt The Process A Run Set screen will appear nCounter Analysis System Dx Process A Run Set NanoString Diagnostics Select a Run Set Creator 201409121J 1 Prosigna Test User 9 12 2014 20140912GH 2 Prosigna Test User 9 12 2014 20140912EF 3 Prosigna Test User 9 12 2014 o 20140912CD 4 Prosigna Test User 9 12 2014 v FIGURE 5 4 The Process a Run Set screen displays the name of each Run Set the assay type and the number of samples it contains E 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 52 nanostring
26. Technologies Inc All rights reserved nanostring 2 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL Contact Information NanoString Technologies Inc 550 Fairview Ave N Suite 2000 Seattle WA 98109 USA Phone 1 888 558 NANO 41 888 558 6266 Fax 1 206 5 8 6288 E mail dxsupport nanostring com Website www nanostring com EU Authorized Representative Emergo Europe Molenstraat 15 2515 BH The Hague The Netherlands EU 451 0 545 6570 Registration Holder in Israel Emergo Israel Hashita St 19 1 Yokneam Illit 20692 Israel Israel 972 77 5361147 E mail dxsupport nanostring com Website www nanostring com nanostring 2015 01 MAN C0034 02 5 USER MANUAL nCounter Dx Analysis System CONTENTS Chapter 1 Introduction sssssssssennnmnnenmmmenenreen entente ttr ttn 7 9 A Product Use EIDIEaEIORIS eoa etter neces at RR IRURE MEIN DNI A MU NEN MM UEM UM 7 B Product Components 5 sss ener tert teet tete te tete tr tr ESEESE NEEESE EEEE EEEE 7 C Overview of the Procedure sss ttt ttt nc 7 D Manual Conventions emeret tnr tren treten ttr EEs 8 E Instrument Specifications s esses tnter tette ttt trt tent 8 F Additional Precautions T Guusssseeeeeenneenet tette ttt tel 9 G Caution Symbols 7 sse teet tenet ertet sss serere rte re reste sesso se EEEE 9 H
27. UAL nCounter Dx Analysis System 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 completed FIGURE 5 28 Touch Next nCounter Analysis System Dx Post Hybridization Successful NanoString Diagnostics Time Finished 9 15 12 21 02 PM Time Elapsed 0 Hours 0 Minutes 9 Seconds FIGURE 5 28 The System Processing Complete screen 18 The Run Successfully Completed screen lists the steps to follow after sample processing including a Remove and discard empty reagent plates b Remove and discard the empty tip racks and foil piercers c Remove and discard the sample strips d Remove the sample cartridge and seal the wells nanostring 66 2015 01 MAN C0034 02 teEcHNOLOGIEsS NanoString Technologies USER MANUAL 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 finger as shown in FIGURE 5 29 FIGURE 5 29 Releasing the fixture after a completed run 20 After processing is complete it is important to do the following a Sealthe wells immediately with the adhesive cover provided to prevent evaporation b Samples should be protected from as much light as possible c If the cartridge will not be scanned on the Digital Analyzer within an hour the sealed cartridge should be stored at 4 C in an opaque box The cartridge can be stored this way
28. Un ssssssssssemmenmmnennmmem enne rere sre 68 nanostring 2015 01 MAN C0034 02 5 USER MANUAL nCounter Dx Analysis System Chapter 7 Technical Support and Maintenance sss 75 81 A Technical Support reete tnter tnter tnter sesso tee 73 B Jhnstrument POWEF CUEITIQ sioe nmi ne Ense Rire M MEA DEDI M E EL LUE MM MEER 74 C Prep Station Maintenance 7 5st entren teer t testet cssc 76 EEC HOGE AA IMNE BORNE m 76 Orina CUr atO eee e atten coed E E E TEES 79 OVO CIS EOS I mi cS 82 POMER ODOT ear E T E E EE A inte 82 D Digital Analyzer Maintenance eren enean 83 D wnNoading Log FS NN RRRRRRRRRee m u 83 E Clean mem 84 Misekcu is RR ra Ei e a TODE Eaa S E E E ET SE NEE TEA EES 84 DOIAN NR 84 F Disposal of Electronic Equipment sess tnmen 84 Symbols and Definitions sse trennt 85 nanostring 6 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL E C H N 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 The nCounter Dx Analysis System may only be operated by appropriately trained professional users NanoSt
29. alysis System 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 Multiple dated folders may be selected for download by touching each one Selected folders will be highlighted in blue 1 Insert a USB flash drive into the Prep Station s front USB port 2 When the desired folders have been selected touch Download to transfer them to the flash drive nCounter amp Analysis System Dx nCounter Analysis System Download Logs Download Logs NanoString Diagnostics NanoString Diagnostics This function allows the user to selectively X 20140501 download log files E 20140514 Make sure a USB flash drive is inserted E 20140515 Press Next to continue or Maintenance 1 20140530 to return to the maintenance menu X 20140709 E 20140714 E 20140716 Maintenance Next gt Maintenance FIGURE 7 11 Screens that appear when downloading log files Home Robot If the robot enters into an undesirable state selecting the Home Robot button can home all the motors This button should not be needed under normal operation nCounter Analysis System Dx nCounter Analysis System Dx Maintenance Home Robot NanoString Diagnostics NanoString Diagnostics Home Robot Align Electrodes Lubricate O Rings Please wait while homing the robot Dow
30. artridge screen will display ABORTED for that cartridge To re scan a cartridge press on the cartridge s icon A screen will appear with the option to scan again If this is performed while a cartridge is scanning be aware that the cartridge status will remain pending until either all other cartridges have been scanned or until scanning has been paused and resumed nanostring 2015 01 MAN C0034 02 7 USER MANUAL nCounter Dx Analysis System 5 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 6 To add a cartridge to a Digital Analyzer that is already counting touch the Pause button on the Counting Cartridges screen It might take a few minutes for the Digital Analyzer to reach a suitable stopping point FIGURE 6 7 The door will unlock when it does Place the new cartridge in an empty slot or replace a cartridge that has already been scanned Touch the Resume button The door should re lock and resume counting nCounter amp Analysis System Dx Pause Counting Job NanoString Diagnostics Please wait while pausing the current counting job FIGURE 6 7 The Pause Counting Job screen 7 When a cartridge is finished scanning an e mail notification will be sent to the user and the processing screen will change to reflect that the cartridge has completed FIGURE 6 8 Upon receiving the
31. 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 lk NOTE The Prep Station will not accept barcodes for cartridges that have expired Make sure the cartridge is used prior to its expiration date E NOTE It is not possible to manually enter the barcode for the cartridge If a barcode will not scan or is not accepted use another cartridge from the same kit lot for the run nanostring 2015 01 MAN C0034 02 59 USER MANUAL nCounter Dx Analysis System b Insert a Sample Cartridge under the electrode fixture in the orientation shown in FIGURE 5 18 Place the cartridge on the deck and slide it into position avoiding the electrodes Make sure that it is seated completely in the machined depression When positioned properly a latch will activate and hold the fixture in place If it is not seated properly the electrodes may become bent when the electrode fixture is closed FIGURE 5 18 Insert an unused cartridge into the Prep Station in the orientation shown c Touch Next gt gt gt The Secure Electrode Fixture screen will appear nCounter Analysis System Dx Secure Electrode Fixture NanoString Diagnostics Secure electrode fixture over sample cartridge FIGURE 5 19 The Secure Electrode Fixture screen nanostring 60 2015 01 MAN C0034 02 tec LOGIE NanoString Technologies USER MANUAL 14 Carefully lower the electrode fixt
32. 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 By default filtering is turned off for most status pages There is one exception reference samples are filtered out by default on the Samples page To turn filtering on click on the next to the Filter Settings header The header will expand and display available filter settings FIGURE 4 8 Logged inas _ Test User Prosigna NanoString Diagnostics 4 Dashboard Runs M Samples IE Reports 2 Admin My Profile Logout Run Sets RUN SET ID STATUS CREATED CREATED BY INITIATED BY 201409121J BatchRegistered 9 12 2014 1 19 40 PM Test User 20140912GH BatchRegistered 9 12 2014 1 18 56 PM Test User 20140912EF BatchRegistered 9 12 2014 1 17 51 PM Test User 20140812CD BatchRegistered 9 12 2014 1 16 52 PM Test User 20140912AB BatchRegistered 9 12 2014 1 13 56 PM Test User FIGURE 4 8 Filter settings are available when viewing most data I NOTE Filtering is not available for the Manage Users page Users can filter data by using any of the fields displayed in the table This will return any items that match the entered text anywhere in that field Likewise users can choose to show all items or only items created recently by specifying the time frame of interest To change the number of items displayed per page sel
33. bridized sample strip tubes have two notches to ensure proper orientation FIGURE 5 22 Hybridization sample strip tubes with notched orientation guides 0 IMPORTANT Do not let the hybridized samples sit at room temperature longer than 15 minutes If there are delays between removing the hybridized samples from the heat block and starting the Prep Station return the samples to 65 C until they can be processed Do not exceed the maximum hybridization time stated in the assay package insert D IMPORTANT All tubes should be seated fully and evenly in the rack to ensure proper processing Ensure that all tube caps are removed from the hybridized samples prior to placing tubes on the deck Leaving the caps on will pause the protocol and require user intervention Q IMPORTANT Only use strip tubes provided by NanoString Other tubes have different dimensions and will cause system failure nanostring 62 2015901 MAN COO0584 02 T E CH NOLO GIES NanoString Technologies USER MANUAL a Securely close the lid that flips down over the tubes FIGURE 5 23 b Touch Next gt gt gt The Notification Options screen will appear FIGURE 5 24 FIGURE 5 23 Lid closed over tubes Q 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 nanostrin
34. by NanoString or licensed to NanoString from Life Technologies Corporation and other third parties Limited License Subject to the terms and conditions of sale of the nCounter Dx Analysis System contained in the product quotation NanoString grants you a limited non exclusive non transferable non sublicensable license to use the proprietary nCounter Dx Analysis System only in accordance with the manual and other written instructions provided by NanoString Except as expressly set forth in the terms and conditions no right or license whether express implied or statutory is granted by NanoString under any intellectual property right owned by or licensed to NanoString by virtue of the supply of the proprietary nCounter Dx Analysis System Without limiting the foregoing no right or license whether express implied or statutory is granted by NanoString to use the nCounter Dx Analysis Sytem with any third party product not supplied or licensed to you by NanoString or recommended for use by NanoString in a manual or other written instruction provided by NanoString Trademarks NanoString Technologies NanoString the NanoString logo nCounter and Prosigna are registered trademarks or trademarks of NanoString Technologies Inc in the United States and or other countries All other trademarks and or service marks not owned by NanoString that appear in this manual are the property of their respective owners Copyright 2015 2015 NanoString
35. c All rights reserved nanostring CONTACT US info nanostring com Tel 1 888 358 6266 Fax 1 206 378 6288 www nanostring com INFORMATION United States us sales nanostring com Europe europe sales nanostring com Other Regions info nanostring com 2015 01 MAN C0034 02
36. code 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 Empty location no graphic This slot is empty and can be loaded with a new cartridge e White cartridge This slot contains a cartridge that is registered but has not yet been scanned DO NOT REMOVE THIS CARTRIDGE Partial blue cartridge This slot contains a cartridge that has been incompletely scanned DO NOT REMOVE THIS CARTRIDGE e Completely blue cartridge Scanning of that cartridge is complete e icon and text over a cartridge There may have been a problem encountered during a scan of the cartridge Touch the icon or cartridge to get more information In the example shown in FIGURE 6 6 the cartridge in slot 1 is being scanned and cartridges in slots 2 5 4 5 and 6 are waiting to be scanned nCounter amp Analysis System s Dx Counting Cartridge 1 NanoString Diagnostics Logged in Test User Current Time 9 15 07 23 05 AM Time Left 1 00 51 17 Time Left All 05 41 19 Finish Time 9 15 01 14 PM Scanning lane 1 in cartridge 280002690315 for run set 20140912IJ FIGURE 6 6 The Counting Cartridge screen with the current cartridge indicated E NOTE Cartridges previously aborted may be able to be re scanned When placed in the Digital Analyzer the counting c
37. cs Confirm tip sheaths on deck FIGURE 5 15 The Tip Sheaths screen E NOTE 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 the other 6 samples are being processed 11 Place the tip sheaths on the deck and press firmly into place Touch Next gt gt gt The Empty Strip Tubes screen will appear FIGURE 5 16 nanostring 58 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL nCounter Analysis System Empty Strip Tubes NanoString Diagnostics Confirm empty strip tubes on deck FIGURE 5 16 The Empty Strip Tubes screen 12 Place the empty strip tubes in the heater on the deck Touch Next gt gt gt The Scan Sample Cartridge screen will appear k NOTE Only one empty heater strip tube is required for runs performed using a 1 2 5 or 4 test kit For these Run Sets load the empty heater strip tube into the front position of the heat block nearest the user on the Prep Station deck nCounter amp Analysis System Scan Sample Cartridge O 0 0 0 0 NanoString Diagnosticg Please scan 12 digit barcode Clear Entry Next gt FIGURE 5 17 The Scan Sample Cartridge screen 13 Instructions for the Sample Cartridge screen a The barcode for the sample cartridge must be scanned before proceeding Hold the barcode in front of the barcode reader A red
38. d to test if the e mail settings are configured correctly Enter an e mail address you have access to and press the Test button Check your e mail account to confirm that the settings are working and the test e mail was received nanostring 2015 01 MAN C0034 02 47 USER MANUAL nCounter Dx Analysis System 48 SSH Settings The SSH Settings tab allows an Administrator to configure the Secure Shell server SSH server The SSH server allows users to programmatically pull nCounter report data from the system in a secure manner It also allows for unlimited concurrent client connections mes Logged inas _ Test User Prosigna NanoString Diagnostics 7A M Dashboard Runs H Samples amp Admin My Profile Logout LZ System Settings SSH HOST NAME 100940002 SSH PORT NUMBER 22 w Enable SSH Server ASSAY Prosigna SSH USER NAME Prosigna PASSWORD FIGURE 4 39 The SSH Settings tab The following fields are available Pre configured fields e SSH host name The name of the host used by the client for connecting to the SSH server SSH port number The port used by the client for connection to the SSH server e SSH user name SSH server account name used by the client for authenticating the connection Configurable fields e Enable SSH server Check box for enabling or disabling the SSH server e Password SSH server account password used by the client for authenticating the connection require
39. d when enable SSH server is checked e Confirm Password Same password entered as above required when enable SSH server is checked nanostring 2015 01 MAN C0034 02 trecHnNnoi NanoString Technologies USER MANUAL IP Address IP address function is an essential function to enable networking of the instruments The Prep Station Digital Analyzer and 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 the IP Address settings Logged inas _ Test User Prosigna NanoString Diagnostics gm mm Dashboard Runs Reports 2 Admin My Profile Logout System Settings TYPE Dynamic IP Address IP ADDRESS 0 0 0 0 SUBNET GATEWAY DNS 1 DNS 2 WARNING TAKE CAUTION IN MAKING CHANGES HERE THE INSTRUMENTS WILL LOSE CONNECTIVITY WHICH MAY RESULT IN SAMPLE LOSS MAKE SURE INSTRUMENTS ARE NOT RUNNING AND NOTIFY ALL USERS PRIOR TO MAKING ANY CHANGES FIGURE 4 40 The IP Address tab The following fields are available e Type The following options are available to choose between e Static IP address This requires the network administrator to set an address that will never change e Dynamic IP address default Known as DHCP this option allows the local network to automatically find and assign an IP address This address is subject to change e IP Address IP address provided by
40. due to an error in the algorithm ReportCompleteWithError Report Complete with Error all processing for the Run Set is complete and a report generated but the assay failed 3 Created The date the Run Set was initially created using the web application 4 Created By The User ID that created the Run Set using the web application 5 Initiated By The User ID that started processing the Run Set on the Prep Station To view more details of the individual samples for a Run Set of interest click on the hyperlink for that Run Set FIGURE 4 15 The application will navigate to the Samples page and display sample information for the selected Run Set SO nanostring 2015 01 MAN C0034 02 USER MANUAL NanoString Technologies 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 Logged inas _ Test User Prosigna E SEL SEES OGGLGIAIALqG EP T Runs NanoString Diagnostics le Reports h Admin My Profile Run Sets 1 Samples Logout COMMON TASKS Show All b View Run Sets gt Create New Run Set b Download Reports b Add New User RUN SET ID 20140912 20140912GH 20140912EF 20140912CD 20140812AB STATUS BatchRegistered BatchRegistered BatchRegistered BatchRegistered BatchRegistered CREATED 9 12 2014 1 19 40 PM 9 12 2014 1 18 56 PM 9 12 2014 1 1
41. e e IP address e SSH settings e E mail configuration All forms are designed with the expectation that users complete an action prior to moving to another area within the web application In order to navigate to another function after completing a form click Save to retain the information entered or Cancel to exit the form and discard any changes Logged inas _ Test User Prosigna NanoString Diagnostics t Dashboard Runs g Samples i Reports a Admin My Profile Logout Edit Run Set 2 Enter Run Set ID 20140912CD Every Run Set ID must be unique Example 20120701LB2 3 Test Configuration code 9 Lkyy59D2x0 4 CodeSet Kit Number 012345019 Scan or manually enter the barcode labeled Run Scan or manually enter the Kit Lot Number from the 5 Semple Dats Configuration Code that came in the CodeSet box sticker included in the CodeSet box Enter Sample Data WELL SAMPLE ID LABEL Sample12353 Zero Positive Nodes Sample24213 Zero Positive Nodes Sample32365 1 3 Positive Nodes Sample48456 1 3 Positive Nodes FIGURE 4 13 The menu bar is inaccessible while editing the contents of a form nanostring NOoutoGies 2015 01 MAN CO0034 02 27 USER MANUAL nCounter Dx Analysis System C Dashboard and Status Pages Dashboard The Dashboard is the landing page the first screen displayed after logging into the nCounter web application The Dashboard can be accessed from other pages by clicking on the Dashb
42. e mail notification that the scan has completed remove the completed cartridge In case of an instrument error or reports not being available store cartridge in an opaque box to protect from light at 4 C for up to one week Contact dxsupport nanostring com for assistance nCounter amp Analysis System Counting Cartridge NanoString Diagnostics Logged in Test User Current Time 9 15 01 15 58 PM 1 2 3 Time Left N venue Wu vue Time Left All Finish Time 9 15 01 15 PM Time Since Finished 00 00 22 Start Counting Main Menu FIGURE 6 8 The Counting Cartridge screen with six completed cartridges 8 Using the link attached to the notification e mail open the web interface and download all the diagnostic reports associated with the Run Set just completed as described in Chapter 4 Operating the Web Application nanostring te 2015 01 MAN C0034 02 TecHnNnoLOGIEs NanoString Technologies USER MANUAL 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 Suite 2000 Seattle WA 98109 U S A Phone 1 888 358 NANO 1 888 358 6266 Fax 1 206 578 6288 E mail dxsupport nanostring com Website www nanostring com nanostring T E C H NOLO GI E s 2015901 MAN C0034 02
43. ect the desired page size from the drop down menu nanostring 24 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL Run Sets r Run Setid match AB All Run Sets FIGURE 4 9 An example of filter settings on the Run Sets page Click Apply when finished Only relevant rows will be displayed in the table FIGURE 4 10 NOTE The presence or absence of a funnel icon next to the page title indicates whether or not filtering is applied oma Logged inas _ Test User Prosigna NanoString Diagnostics O AAA O OA Am l m 4 Dashboard Runs M Samples IE Reports id Admin My Profile Logout Run Sets v RunSetid match AB All Run Sets RUN SET ID INITIATED BY 20140912AB BatchRegistered 9 12 2014 1 13 56 PM Test User FIGURE 4 10 An example of the funnel icon and filtered results on the Run Sets page Different filters are available depending on the page displayed For example the Samples page provides the ability to hide the two reference samples required for every run Samples v None w Omit All Samples 40 5 FIGURE 4 11 Check the Omit box to show or hide the reference samples nanostring 2015 01 MAN C0034 02 25 USER MANUAL nCounter Dx Analysis System 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 To
44. ectrode 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 Touch Next gt gt gt The Align Electrodes Close Door screen will appear nCounter Analysis System Dx Align Electrodes Close Door NanoString Diagnostics Please close the instrument door Press Next to continue or Maintenance to return to the maintenance menu FIGURE 7 5 The Align Electrodes Close Door screen step 2 of 5 3 Close the door and touch Next gt gt gt While the door is closed the electrode fixture tilts towards the operator for easier access to the electrodes Two screens follow in succession FIGURE 7 6 nCounter Analysis System Dx nCounter Analysis System Align Electrodes Preparing Fixture Align Electrodes Perform Alignment NanoString Diagnostics NanoString Diagnostics Please wait while preparing for electrode alignment Open the instrument door and align the electrodes When the electrodes have been aligned press Next to continue FIGURE 7 6 The Align Electrodes progress screens steps 5 and 4 of 5 nanostring 2015 01 MAN C0034 02 77 USER MANUAL nCounter Dx Analysis System 4 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 ca
45. ed to track sample statuses Finally test reports are available for download using the web application nanostring SL ere UIDI MEC E02 USER MANUAL nCounter Dx Analysis System D Manual Conventions The following conventions are used throughout this manual and are described for your reference Bold text is typically used to highlight a specific button keystroke or menu option Bold text may appear elsewhere to Bolg highlight important text or terms Italic text is typically used to highlight references to another section or chapter of the manual Italic text may also be Italic E used to highlight references to other manuals or instructional material Blue Blue text is typically used to highlight references to specific figures or tables Blue text may also be used to indicate active hyperlinks to online content or e mail addresses uz NOTE This symbol indicates general information that may be useful when performing assays These notes may clarify other instructions or provide guidance to improve the efficiency of the assay workflow e IMPORTANT This symbol indicates important information that is critical when performing an assay A CAUTION This symbol indicates the potential for bodily injury or damage to the instrument if the instructions are not followed correctly Always carefully read and follow the instructions accompanied by this symbol to avoid potential hazards E Instrument Specifications Test Samples per R
46. er BatchRegistered 9 12 2014 1 13 56 PM Test User FIGURE 4 27 Location of the Print Worksheet button on the Run Sets page gt gt gt The worksheet will appear in a new window Run Set ID 20140912AB CodeSet Kit Number 0123450199 Assay Prosigna RNA Isolation Kit Lot Date Time 9 12 2014 1 49 PM Email Status Updates Test User Created By Test User Email Report Notifications Test User Sample ID Label of Positive Nodes Sample34352 1 3 Positive Nodes Sample48724 Zero Positive Nodes Well 7 2 3 Sample14578 Zero Positive Nodes 4 5 y yY 6l Sample52968 Zero Positive Nodes lt Sample27456 Zero Positive Nodes lt 8 Sample65702 sd 1 3 Positive Nodes 2cm 9 Sample 2800 ZeroPosiive Nodes SCM 10 Sample amp 23880 1 1 3Positive Nodes Tf Sample91306 1 ZeroPosiive Nodes SCM 12 Sample 0400 jZeroPosiive Nodes 2cm FIGURE 4 28 An example worksheet Click the Print button to begin the printing process for the worksheet or the Close button to close the window nanostring Notocgies 2Q15 01 MAN C0034 02 59 USER MANUAL nCounter Dx Analysis System F Reports Users with the Access Diagnostic Reports privilege can select and download diagnostic reports from the Reports page Users chosen to receive a report notification when setting up the Run Set should receive an e mail stating that the
47. ety precautions including wearing safety glasses and gloves Some materials are required but not provided with the kit e Silicone grease provided during system installation e Lint free paper e g Kimwipe by Kimberly Clark e Gloves O IMPORTANT DO NOT USE ANYTHING OTHER THAN THE SUPPLIED SILICONE GREASE ON O RINGS nanostring 2015 01 MAN C0034 02 79 USER MANUAL 80 1 Select Lubricate O rings on the Maintenance Menu gt gt gt A series of Lubricate O rings maintenance screens will appear nCounter Analysis System i i Dx Lubricate O Rings Start NanoString Diagnostics This function allows the user to lubricate the o rings on the nozzle head unit Make sure the heater lid is closed Press Next to continue or Maintenance to return to the maintenance menu NanoString Diagnostics nCounter amp Analysis System Lubricate O Rings Close Door Please close the instrument door Press Next to continue or Maintenance to return to the maintenance menu Maintenance Next gt nCounter Analysis System Lubricate O Rings Perform Lubrication NanoString Diagnostics Open the instrument door and lubricate the O Rings When the O Rings have been lubricated press Next to continue nCounter Dx Analysis System nCounter Analysis System Lubricate O Rings Lower Electrode Fixture NanoString Diagnostics Lower the electrode fixture and lock in place Press Next
48. for up to one week with minimal degradation d Empty the waste containers 21 Touch Finish to return to the Main Menu nanostring FE C H N i e s 2015 01 MAN C0034 02 67 USER MANUAL nCounter Dx Analysis System 6 Operating the Digital Analyzer A Initiating a Run 1 To scan a cartridge using the Digital Analyzer a user must log on to the instrument In order to log on touch Main Menu on the Welcome screen nCounter amp Analysis System Dx Welcome Dx NanoString Diagnostics Select an option a d System Info FIGURE 6 1 The Digital Analyzer Welcome screen 2 Enter a valid user name and password and touch Sign In nCounter amp Analysis System Dx Please enter a user name and password NanoString Diagnostics User Name FEROS Password 3 FIGURE 6 2 The sign in screen nanostring 68 2015 01 MAN COQDJS4 07 T E C H NOLO G I E S NanoString Technologies USER MANUAL gt gt gt The Main Menu will appear nCounter amp Analysis System Dx Main Menu NanoString Diagnostics Start Counting Maintenance Loggedin Test User FIGURE 6 3 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 Q IMPORTANT If a laboratory has more than one Digital Analyzer the cartridge must be scanned on the
49. g Te ON 9 9 999 5015 01 MAN C0034 02 63 USER MANUAL nCounter Dx Analysis System nCounter amp Analysis System Dx Notification Options OO NanoString Diagnostics Select notification options Beep when post hybridization completed FIGURE 5 24 The Notification Options screen 16 Select whether the Prep Station should make an audible alarm when processing is finished Touch Next gt gt gt The Start Deck Validation screen will appear nCounter amp Analysis System Dx Start Deck Validation OO NanoString Diagnostics Please close the instrument door Select Next to start the deck layout validation process Once the deck layout validation is complete you will be prompted to start the post hybridization protocol FIGURE 5 25 The Start Deck Validation screen a Touch Next to begin validation nanostring 64 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL b The nCounter Prep Station will now check that all of the consumables and reagents have been placed properly on the deck FIGURE 5 26 To do this the Prep Station confirms that the sensors for the sample cartridge electrode fixture and heater lid are all in the correct state The pipette head then checks that tips tip sheaths strip tubes and reagent plates are all in place by touching them with a set of validation tips Do not be alarmed that the Prep Station is touching the consumables this is a part of normal operat
50. g alignment If the electrode is so severely bent that it cannot be inserted into a cartridge the process outlined below may need to be repeated twice once without a cartridge present to get the electrodes into roughly the right position so that they can be inserted into a cartridge and a second time with a cartridge present for fine tuning the placement of electrodes within the cartridge wells b NOTE The Prep Station checks electrode function during the validation steps of the process before any processing occurs to the samples 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 1 Select Align Electrodes from the Maintenance Menu gt gt gt The Align Electrodes Start screen will appear nCounter Analysis System Dx Align Electrodes Start NanoString Diagnostics This function allows the user to align a bent electrode in the electrode fixture Lower the electrode fixture and lock in place Press Next to continue or Maintenance to return to the maintenance menu FIGURE 7 4 The Align Electrodes Start screen step 1 of 5 nanostring 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL 2 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 el
51. he worksheet and then close the worksheet The application will return to the Run Sets page nanostring 56 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL 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 To edit a Run Set select the appropriate Run Set from the list on the Run Sets page and click the Edit button FIGURE 4 23 a Logged inas _ Test User Prosigna NanoString Diagnostics gt Dashboard Runs le Reports 2 Admin My Profile Logout NNLLA es a NCLCN Run Sets 201408121 J BatchRegistered 9 12 2014 1 19 40 PM Test User 20140912GH BatchRegistered 9 12 2014 1 18 56 PM Test User 2014091 2EF BatchRegistered 9 12 2014 1 17 51 PM Test User BatchRegistered 9 12 2014 1 16 52 PM Test User 20140912AB BatchRegistered 9 12 2014 1 13 56 PM Test User FIGURE 4 23 Location of the Edit button on the Run Sets page gt gt gt The Edit Run Set page will appear Logged inas _ Test User Prosigna NanoString Diagnostics t Dashboard mb Runs Na I amp Admin My Profile Logout mammasini maian Edit Run Set 2 Enter Run Set ID 20140912CD very Run Set ID must be unique Example E 20120701LB2 3 Test Configuration
52. iagnostics mode The system will load the application and present the Welcome screen FIGURE 3 2 Before operating the Prep Station a user must log on by selecting the Main Menu button nCounter amp Analysis System Dx Welcome NanoString Diagnostics Select an option System Registration a System Info _ FIGURE 3 2 The Welcome screen gt gt gt The sign in screen will appear FIGURE 3 3 nanostring 14 2015 01 MAN C0034 02 NanoString Technologies Enter a valid user name and password and touch the Sign In button nCounter amp Analysis System Dx Please enter a user name and password NanoString Diagnostics FIGURE 3 3 The sign in screen gt gt gt The Main Menu will appear FIGURE 3 4 nCounter Analysis System Main Menu NanoString Diagnostics LoggedIn Test User FIGURE 3 4 The Prep Station Main Menu in Diagnostics mode nanostring Loro Gies 2015 01 MAN C0034 02 USER MANUAL 15 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 gt gt gt The Exit Diagnostics Mode confirmation screen will appear nCounter Analysis System Dx Exit Diagnostics Mode NanoString Diagnostics This option will exit Diagnostics mode and return to the ma
53. in select instrument mode screen Press OK to continue and exit Diagnostics mode or Cancel to return to the main menu FIGURE 3 5 The Prep Station Exit Diagnostics Mode confirmation screen Touch OK to exit Diagnostics mode and return to the Select Instrument Mode screen FIGURE 3 1 Touch Cancel to return to the Main Menu nanostring 16 2015 01 MAN C0034 02 teEcHNOLOGIEsS USER MANUAL NanoString Technologies 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 nCounter amp Analysis System Select Instrument Mode Please select the appropriate instrument mode to begin NanoString Diagnostics NanoString Life Sciences FIGURE 3 6 The Digital Analyzer Select Instrument Mode screen Touch the blue icon labeled NanoString Diagnostics to enter Diagnostics mode The system will load the application and present the Welcome screen FIGURE 3 7 Before operating the Digital Analyzer a user must log on by selecting the Main Menu button nCounter amp Analysis System Dx Welcome NanoString Diagnostics Select an option System Info FIGURE 3 7 The Welcome screen gt gt gt The sign in screen will appear FIGURE 3 8 nanostring 2015 01 MAN C0034 02 17 USER MANUAL nCounter Dx Analysis System
54. ion FIGURE 4 5 See Section G Manage Users for more information about user types and privileges amp My Profile USER ID Test User PASSWORD CONFIRM PASSWORD E MAIL ADDRESS testuser nanostring com USER TYPE 4 Administrator General no admin privileges PERMISSIONS RUN POST HYBRIDIZATION x Prosigna Assay 2 ACCESS DATA x Prosigna Assay 2 CREATE RUNSET x Prosigna xX Assay2 FIGURE 4 5 The My Profile page To accept any changes made to a profile click the Save button To discard any changes and return to the previous page click the Cancel button nanostring 22 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL 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 FIGURE 4 6 The menu items separate the application into five sections Dashboard Common tasks and statuses of recent activities e Runs Create a Run Set and view run statuses a Run Set consists of 1 10 diagnostic samples and two mandatory reference samples processed at the same time e Samples View sample status Reports Download reports e Admin Manage users and other system settings Logged inas _ Test User NanoString Diagnostics M Samples IE Reports sh Admin My Profile Logout COMMON TASKS ue Run Sets Show AII b View Run Sets gt Create New Run Se
55. ion If the Prep Station determines that a consumable is misplaced it will instruct the user to fix the configuration nCounter Analysis System l Post Hybridization Validating Deck Layout OO NanoString Diagnostics Logged in Test User Current Time 9 15 12 19 42 PM Finish Time 9 15 02 45 PM P PY 096 Please wait while the deck layout is being validated FIGURE 5 26 The Post Hybridization Validating Deck Layout screen c After deck validation is complete FIGURE 5 27 a new screen containing the Start Processing button will appear Touch Start Processing to initiate the run nCounter Analysis System Dx Post Hybridization Deck Layout Validated OO NanoString Diagnostics The deck layout validation is complete Press Start Processing to start the post hybridization protocol Start Processing FIGURE 5 27 The Post Hybridization Deck Layout Validated screen O IMPORTANT If a run is paused resume the run as quickly as possible The system should not be in a paused state for more than 15 minutes or the test must be repeated for the affected samples Q IMPORTANT If a run is aborted the run cannot be restarted and the test must be repeated for the affected samples See the assay package insert for more information regarding repeat testing nanostring 2015 01 MAN C0034 02 65 USER MAN
56. iously selected during sign in FIGURE 4 1 To change this entry log out and sign in again while selecting a new assay type Run Set ID The Run Set ID must provide a unique name to identify the Run Set Test Configuration Code The Test Configuration Code is an alohanumeric barcode located inside the CodeSet box It determines the number of samples that can be processed CodeSet Kit Number The CodeSet Kit Number is a numeric barcode located inside the CodeSet box and Is also described as a CodeSet Barcode Sticker It determines the CodeSet expiration date Because there may be a delay between creating a Run Set and processing the samples a warning will be provided if the CodeSet is within two weeks of its expiration date when the Run Set is created Sample Data The reference samples are always located in wells 1 and 2 they do not require any input and cannot be edited Well numbers 3 12 are used for patient RNA samples Fields may vary for different assay types As an example Prosigna requires the following information a Sample ID Label required Sample IDs can be entered using barcoded sample tubes and a barcode scanner connected to the computer If a scanner is not available or if the barcodes are damaged sample IDs can be manually entered using a keyboard NanoString recommends using unique sample IDs to track samples b of Positive Nodes required Users can choose between zero positive nodes 1 5 positive nodes or gt 4
57. l Piercers screen will appear FIGURE 5 12 nCounter Analysis System d hc DX Tips And Foil Piercers Dx NanoString Diagnostics Confirm tips and foil piercers on deck Cancel FIGURE 5 12 The Tips And Foil Piercers screen 10 Instructions for the Tips and Foil Piercers screen a Remove the metal tip carrier from the Prep Station deck by lifting straight up b Place the tips and the foil piercers into the carrier Hold the plastic tip rack by the center tabs hold the tip rack over the metal holder and slowly lower the tips into the metal holder It is helpful to place the carrier at eye level to align the plastic tips FIGURE 5 13 FIGURE 5 15 Insert the tips and foil piercers into metal tip carrier NOTE There are two sets of tips nested in each box with each side of the box containing one set of tips Hold a hand firmly over the bottom of the box when opening to avoid accidentally spilling the second set of tips nanostring TECHNoOoOLoGcGi es 2015 01 MAN C0034 02 57 USER MANUAL nCounter Dx Analysis System e Replace the loaded metal tip carrier back onto the Prep Station deck with the foil piercers closest to the front of the deck FIGURE 5 14 FIGURE 5 14 Proper placement of rack containing pipette tips and foil piercers d Touch Next gt gt gt The Tip Sheaths screen will appear FIGURE 5 15 nCounter amp Analysis System Tip Sheaths NanoString Diagnosti
58. ls for status updates such as Prep Station run completion or diagnostic report notifications Logged inas _ Test User Prosigna NanoString Diagnostics C Dashboard Runs H Samples l Reports amp Admin My Profile Logout amp System Settings SMTP SERVER SMTP PORT FROM ADDRESS SMTP USERNAME PASSWORD CONFIRM PASSWORD ENCRYPTION PROTOCOL SSL3 TEST ADDRESS FIGURE 4 38 The E mail Settings tab The following fields are available e SMTP Server required Simple Mail Transfer Protocol E mail server name e SMTP Port required Port used for e mail server e SMTP Address required Address from which automated e mails are sent Enable SSL Check if using a secure e mail server e SMTP Username Account name for secure e mail server required if Enable SSL is checked Password Password for SMTP username required if Enable SSL is checked e Confirm Password Same password as above required if Enable SSL is checked Encryption Protocol These options effectively encrypt e mail data sent over the Internet between the client and e mail server The following are possible values for encryption protocol a selection is required if Enable SSL is checked e SSL3 Secure Socket Layer Widely used encryption protocol e TLS Transport Layer Security More secure encryption protocol than SSL e Test Address optional This can be use
59. n a server contained within the nCounter Digital Analyzer When the system is connected to a network the web application can be used to communicate with both the Prep Station and the Digital Analyzer Its primary functions are as follows e Create and edit Run Sets e View the statuses of Run Sets e Download reports e Perform administrative functions A Sign In and Profile Management 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 The sign in page will appear Enter the user ID and password provided by the administrator select the desired assay type and click Sign In ja NanoString Diagnostics Ea E DL MR dase Prosigna Forgot your password Click here Forgot your ID Please contact the system administrator The nCounter web application sign in page nanostring 20 2015 01 MAN C0034 02 USER MANUAL NanoString Technologies Forgot User ID Password If the user ID is forgotten contact the local nCounter system administrator to retrieve it If the password is forgotten the nCounter web application may be able to retrieve it Click the link next to Forgot your password to access the forgotten password submission page Ji NanoStri
60. n the Prep Station permission must still be assigned Administrators are able to assign permissions to their own accounts E NOTE Unique permission settings can be assigned for each assay type available on the system For example a user may be able to create a Run Set for all assays on their system initiate post hybridization for a single assay and be unable to access any reports The Manage Users function allows an administrator to edit or delete users To manage existing users select the Admin option from the menu bar at the top of the page and click on Manage Users gt gt gt The Manage Users screen will appear Logged inas _ Test User Prosigna NanoString Diagnostics 4 Dashboard Runs M Samples IE Reports l4 Admin My Profile Logout a Manage Users USER ID DATE ADDED LAST MODIFIED USER TYPE EMAIL Gamma 9 12 2014 1 55 01 PM 9 12 2014 1 55 01 PM General gamma nanostring com Beta 9 12 2014 1 54 47 PM 9 12 2014 1 54 47 PM General beta nanostring com 9 12 2014 1 54 28 PM 9 12 2014 1 54 28 PM General alpha nanostring com Test User 9 12 2014 12 29 00 PM 9 12 2014 12 29 00 PM Administrator smackenzie nanostring com FIGURE 4 32 The Manage Users page and the location of the Edit button nanostring 42 2015 01 MAN C0034 02 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 gt gt gt The Edit User Da
61. ng Diagnostics Forgot Password To retrieve your password please enter your user ID sen 0 EITNEIEEENEEEEEEE Cancel Retrieve Did you forget your User ID Please contact the system administrator The forgotten password submission page Enter the user ID If the nCounter system finds a matching profile the password will be e mailed to the address on record Ifa matching profile is not found the user will be instructed to contact the nCounter system administrator in order to reset the password NanoString Diagnostics Forgot Password Thank you We have sent you your password Please check your email and try to sign in The forgotten password confirmation page nanostring 2015 01 MAN CO034 02 21 USER MANUAL nCounter Dx Analysis System Updating My Profile User information can be updated by selecting the My Profile button from the menu bar at the top of the page FIGURE 4 4 Logged inas _ Test User Prosigna NanoString Diagnostics Dashboard Runs Samples IE Reports amp Admin My Profile Logout COMMON TASKS ad Run Sets Show All gt View Run Sets b Create New Run Set RUN SET ID CREATED INITIATED BY P Download Reports No items b Add New User FIGURE 4 4 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 account informat
62. nload Logs Power Off FIGURE 7 12 Screens that appear during the Home Robot process nanostring 97 2015 01 MAN CO034 0272 TECHNOLOGIE NanoString Technologies USER MANUAL 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 Q IMPORTANT If the Digital Analyzer is shut down the web application will be unavailable and the Prep Station will be inoperable The Digital Analyzer has been designed to require no maintenance other than instrument power cycling see previous section However if any issues occur NanoString Support may request a download of the log files Downloading Log Files In the Maintenance Menu select the Download Logs button Log files are stored according to the date of each run Multiple dated folders may be selected for download by touching each one Selected folders will be highlighted in blue 1 Insert a USB flash drive into the Digital Analyzer s front USB port 2 When the correct folders have been selected touch Download to transfer them to the flash drive nCounter amp Analysis System nCounter amp Analysis System Download Logs Download Logs NanoString Diagnostics NanoString Diagnostics This function allows the user to selectively K 2014 07 download log files E 2014 08 Make
63. ntrifuge 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 c While the cartridges and plates come to room temperature continue setting up the Prep Station Touch Next gt gt gt The Waste Receptacles screen will appear nCounter Analysis System Waste Receptacles NanoString Diagnostics Confirm waste receptacles are empty Cancel FIGURE 5 9 The Waste Receptacles screen 8 Make sure the disposables from the previous run have been appropriately discarded Press Next gt gt gt The Scan Reagent Plate screen will appear nCounter Analysis System Scan Front Reagent Plate NanoString Diagnostics Please scan or manually enter 16 digit barcode Barcode FIGURE 5 10 The Scan Reagent Plate screen nanostring 2015 01 MAN C0034 02 55 USER MANUAL nCounter Dx Analysis System 9 Instructions for the Reagent Plate screen a 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 If there are problems scanning the barcode the number can be entered manually Touch Manual Entry a numeric keypad will
64. o delete User Alpha ELI NM FIGURE 4 55 The Delete User prompt Click OK to delete the user or click Cancel to return to the Manage Users page 44 2015 01 MAN C0034 02 a EMAIL gamma nanostring com beta nanostring com alpha nanostring com smackenzie nanostring com nanostring NanoString Technologies USER MANUAL System Settings System settings are available to users with the Administrative user type There are four main functions within the System Settings page e Date and Time e E mail Settings e SSH Settings e IP Address To access the System Settings page select the Admin option on the top menu bar and select System Settings FIGURE 4 36 Logged inas _ Test User Prosigna NanoString Diagnostics gm mm mm 4 Dashboard Runs M Samples li Reports hA Admin My Profile Logout IL BENED Run Sets Show All COMMON TASKS b View Run Sets gt Create New Run Set RUN SET ID STATUS CREATED CREATED BY gt Download Reports 20140912 BatchRegistered 9 12 2014 1 19 40 PM Test User gt Add New User 20140912GH BatchRegistered 9 12 2014 1 18 56 PM Test User 20140912EF BatchRegistered 9 12 2014 1 17 51 PM Test User 20140912CD BatchRegistered 9 12 2014 1 16 52 PM Test User 20140912AB BatchRegistered 9 12 2014 1 13 56 PM Test User FIGURE 4 36 Location of the System Settings option in the Admin sub menu gt gt gt The System Settings page will appear FIGURE 4 37
65. oard menu item but it will be unavailable when editing a form until that form has been saved or discarded me Logged inas _ Test User Prosigna NanoString Diagnostics et Fe Pa el cC ha cC d FCD N 4 Dashboard Runs M Samples IE Reports My Profile Logout COMMON TASKS E Run Sets Show AII b View Run Sets b Create New Run Set RUN SET ID STATUS CREATED CREATED BY gt Download Reports 201408121J BatchRegistered 9 12 2014 1 19 40 PM Test User b Add New User 20140812GH BatchRegistered 9 12 2014 1 18 56 PM Test User 20140912EF BatchRegistered 9 12 2014 1 17 51 PM Test User 20140812CD BatchRegistered 9 12 2014 1 16 52 PM Test User 20140812AB BatchRegistered 9 12 2014 1 13 56 PM Test User M EE gt Support Overview gt Contact Support Show All Ordering and Assay Info SAMPLE ID RUN SET ID STATUS LAST UPDATE CREATED BY Order Prosigna Kits Sample14578 20140912AB SampleRegistered 9 12 2014 1 36 07 PM Test User Sample27456 20140912AB SampleRegistered 9 12 2014 1 36 07 PM Test User Sample34352 20140912AB SampleRegistered 9 12 2014 1 36 07 PM Test User Sample48724 20140912AB SampleRegistered 9 12 2014 1 36 07 PM Test User News and Technology Info Sample52968 20140912AB SampleRegistered 9 12 2014 1 36 07 PM Test User gt Main Site and News SSS eee gt Prosigna Website Show All FIGURE 4 14 The Dashboard landing page and the location of the Dashboard menu option The Dashboard provides quick access to the stat
66. positive nodes where available c Tumor Size required Users can choose between lt 2 cm or gt 2 cm d Memo optional Any notes about the sample can be entered here There is a maximum limit of 32 characters NOTE Leave the remaining fields blank if any strip tube wells are not needed If additional fields are required for more samples use a different test configuration that accommodates more samples Q IMPORTANT Some handheld scanners can misinterpret barcodes if they are not properly configured It is essential that the Test B Configuration Code and CodeSet Kit Number be entered correctly If you encounter errors contact dxsupport nanostring com for assistance Set E mail Recipients If desired choose e mail recipients by selecting users from the contact list on the left side and clicking the Add gt gt button Conversely e mail recipients can be removed by selecting the users from the list on the right side and clicking the lt lt Remove button Press the Ctrl key or the Command key if using an Apple computer on the keyboard while selecting multiple addresses to add or remove multiple recipients at once a E mail Status Updates to Users assigned here will receive e mail updates anytime the Run Set status has changed b E mail Report Notifications to Users assigned here will receive an e mail when the sample reports for the Run Set are available for download E mails will include a link to log in and download
67. print the worksheet for the current run set EL NN FIGURE 4 21 The Print Worksheet prompt Select OK to print the Run Set Worksheet D NOTE Clicking the Cancel button will navigate the user to the Run Sets page E NOTE The Run Set will still be saved in the application if a worksheet is not printed but it is recommended that a printed worksheet be used in the laboratory when preparing samples The worksheet may also be printed at a later date nanostring 2015 01 MAN C0034 02 55 USER MANUAL nCounter Dx Analysis System gt gt gt The worksheet will appear in a new window FIGURE 4 22 Run Set ID 20140912AB CodeSet Kit Number 0123450199 Assay Prosigna RNA Isolation Kit Lot Date Time 9 12 2014 1 14 PM Email Status Updates Created By Test User Email Report Notifications Well amp Sample ID Label 1 sofPositive Nodes 1 TumorSize 1 Reference O JNA J NA 2 Reference2 2 NANA S Sampei jZeroPosiiveNods cm wi 8 6l 7 c Sampe2 Zeer Positive Nodes Sampe3 1 3 Positive Nodes Sampled 7 Sample5 ZeroPositive Nodes Sample6 1 3 Positive Nodes lt 8l 9 Sample7 Zero Positive Nodes 10 Sample8 1 3 Positive Nodes pT lt A Sample4 Zero Positive Nodes Sample9 Zero Positive Nodes Sample10 Zero Positive Nodes FIGURE 4 22 An example worksheet Select Print to print t
68. put on the European Market after August 15 2005 e The device is not to be disposed via the municipal waste collection system of any member state of the European Union 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 nanostring 84 2015 01 MAN C0034 02 NanoString Technologies Symbols and Definitions ud EC REP Manufacturer Authorized Representative in the European Community In vitro diagnostic medical device S Consult Instructinos for Use CE Mark CN PN Catalogue or Reference Number Batch code Lot number Serial number Contains sufficient for lt n gt tests Temperature range storage conditions Lower limit of temperature storage conditions Upper limit of temperature storage conditions For Use by Expiry Date Date of manufacture LEES as es a Room Temp Room Temperature HYB Hybridization Regulatory Disclaimer For in vitro diagnostic use nanostring T E C H NOLO GI E s 2015901 MAN C0034 02 USER MANUAL 85 USER MANUAL nCounter Dx Analysis System NanoString Technologies Inc 550 Fairview Ave N Suite 2000 Seattle Washington 98109 USA 2013 2015 NanoString Technologies In
69. re are several buttons that appear in the touchscreen user interface For example Next Proceeds to the next screen e Back Moves back to the previous screen e Cancel Returns to beginning of the current workflow or the main menu nanostring 10 2015 01 MAN C0034 02 T E C H N Co L O G I E s NanoString Technologies USER MANUAL B Prep Station The Prep Station is a multi channel pipetting robot configured specifically for use with NanoString nCounter Test Kits The instrument performs liquid transfers magnetic bead separations and immobilization of molecular labels on the sample cartridge surface FIGURE 2 1 FIGURE 2 1 The Prep Station The Prep Station deck must be loaded with the appropriate consumables prior to use FIGURE 2 2 FIGURE 2 2 The Prep Station Deck nanostring 11 T E C H NOLO G IE S 2015901 MAN C0034 02 USER MANUAL nCounter Dx Analysis System C Digital Analyzer The Digital Analyzer is a multi channel epifluorescence scanner configured specifically for use with NanoString s nCounter Test Kit Cartridges Up to six cartridges can be loaded into the instrument FIGURE 2 3 When one or more scans have been completed the instrument may be paused to allow new cartridges to be swapped in without disrupting the remaining cartridges nano rin TECHNOLOGIES FIGURE 2 3 The Digital Analyzer nanostring 12 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL Selecting
70. re sort the data in the reverse order click again on the same column heading FIGURE 4 12 Logged inas _ Test User Prosigna NanoString Diagnostics o Dashboard Runs lE Reports h Admin My Profile Logout 3 Samples v RUN SET ID Sample10410 20140912AB SampleRegistered 9 12 2014 1 36 07 PM Test User Sample12353 20140912CD SampleRegistered 9 12 2014 1 35 36 PM Test User Sample13910 201409121J SampleRegistered 9 12 2014 1 22 24 PM Test User Sample13950 20140912GH SampleRegistered 9 12 2014 1 22 35 PM Test User Sample14578 20140912AB SampleRegistered 9 12 2014 1 36 07 PM Test User Sample14820 20140912EF SampleRegistered 9 12 2014 1 22 48 PM Test User FIGURE 4 12 An example of alphabetically sorting samples by clicking on the SAMPLE ID column heading b NOTE Tables are typically displayed by default with the most recently added items at the top and the oldest items at the bottom nanostring 26 2015 01 MAN CO034 02 trecHnNotogcs NanoString Technologies USER MANUAL Forms Forms are defined in the nCounter web application as pages in which a user can make manual data entry changes General users with the Create Run Set account privilege have access to the Create Run Set and Edit Run Set forms Users that 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 e Add new user e Edit user e Date and tim
71. ring recommends that all users read and understand this manual prior to attempting to operate the system Keep this manual in close proximity to the instruments for easy access to instructions and safety information Failure to comply with the instructions in this manual may pose a dangerous risk to the operator and void the manufacturer s warranty B Product Components The nCounter Dx Analysis System consists of two instruments the Prep Station and the Digital Analyzer A power cable is included with each instrument The Prep Station also includes a pipette tip rack a liquid waste container a solid waste container and silicone grease In addition to instrument software a web based software application web application is provided to configure runs to observe sample statuses and to download sample reports C Overview of the Procedure 1 The web application is used to identify and annotate samples and define the test to be performed 2 After sample processing and hybridization has been completed according to the test kit instructions samples are inserted into the Prep Station for purification and immobilization onto the internal surface of a sample cartridge 2 3 hours depending on the number of samples 3 The sample cartridge is then transferred to the Digital Analyzer for imaging and analysis about 4 5 hours or 20 25 minutes per sample 4 During processing with the nCounter Dx Analysis System the web application may be us
72. rtridge well Touch Next gt gt gt The final screen will appear when the procedure is complete nCounter amp Analysis System Dx Align Electrodes Close Door NanoString Diagnostics Please close the instrument door Press Finish to complete the operation FIGURE 7 7 The Align Electrodes Close Door screen step 5 of 5 5 Close the door and touch Finish The electrode fixture will tilt back to its home position and then the Maintenance Menu will be displayed nanostring 78 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL 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 The Prep Station Maintenance Menu has an interface to facilitate O ring lubrication by bringing the pipetting head to the front of the deck for easy access b NOTE An icon will appear on the Main Menu and Maintenance Menu when it is necessary to lubricate the O rings FIGURE 7 8 nCounter amp Analysis System i Dx Maintenance NanoString Diagnostics Home Robot Align Electrodes A Lubricate O Rings Download Logs Power Off FIGURE 7 8 The yellow Lubricate O rings symbol CAUTION When performing maintenance functions always use appropriate saf
73. same instrument registered to the Prep Station that was used earlier to process the samples see Chapter 4 Operating the Web Application nanostring 2015 01 MAN C0034 02 69 USER MANUAL nCounter Dx Analysis System 3 Place the sample cartridge into an empty slot Make sure the cartridge is inserted in the correct orientation the slot and cartridge are keyed to help ensure the correct orientation and is completely flat in the slot The barcode will be facing up FIGURE 6 4 Close the magnetic holder over the cartridge in the slot and close the door to the Digital Analyzer FIGURE 6 4 Orient cartridges with the barcode toward the user when placing them into the Digital Analyzer Close the magnetic clips gently and be sure to push down on the metal plate above the cartridge after the lid is closed to ensure the cartridge lays flat a Select the Start Counting button gt gt gt The Checking Stage Configuration screen will appear nCounter Analysis System D Checking Stage Configuration NanoString Diagnostics Please wait while the Digital Analyzer identifies cartridges on the stage FIGURE 6 5 The Checking Stage Configuration screen NOTE The Digital Analyzer tracks which stage positions have already been scanned are currently in progress or are waiting to be scanned nanostring O 2015 01 MAN C0034 02 te NOLO Gi NanoString Technologies USER MANUAL 4 The scanner will use the bar
74. sample processing is complete and that the report is available for download 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 the samples to be downloaded and click the Download button FIGURE 4 29 Logged inas Test User NanoString Diagnostics My Profile Logout RUN SET ID REPORT DATE CREATED BY ASSAY STATUS Reference1 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Reference2 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample1 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample2 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample3 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample4 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample5 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample6 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample7 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample8 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample9 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete Sample10 20140912AB 9 13 2014 5 36 29 PM Test User ReportComplete FIGURE 4 29 The Reports page The reports will be compressed into a ZIP file zip This file can be opened immediately or saved
75. sure a USB flash drive is inserted 2014 09 Press Next to continue or Maintenance to return to the maintenance menu Maintenance Next gt Maintenance FIGURE 7 13 Screens that appear when downloading log files nanostring 2015 01 MAN C0034 02 85 USER MANUAL nCounter Dx Analysis System E Cleaning Instructions Follow all safety and operating instructions provided in this manual Use safe laboratory operating precautions including personal protective equipment such as safety glasses and gloves Prep Station After a completed run remove all consumables and waste Periodically clean the stage surface and waste receptacles of the Prep Station by wiping with a disinfectant followed by wiping with water or 70 ethanol Avoid the electrode fixture An RNase removal agent such as RNaseZap from Ambion may also be used Clean the exterior periodically using a diluted neutral soap followed by water Use a damp towel rather than spraying directly on the instrument Digital Analyzer Clean the exterior periodically using a diluted neutral soap followed by water Use a damp towel rather than spraying directly on the instrument 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 SS e The device was
76. t RUN SET ID STATUS CREATED CREATED BY INITIATED BY gt Download Reports No items b Add New User Sd Show All Support gt Support Overview gt Contact Support SAMPLE ID RUN SET ID STATUS LAST UPDATE CREATED BY No items Ordering and Assay Info gt Order Prosigna Kits Show All SAMPLE ID RUN SET ID REPORT DATE CREATED BY ASSAY STATUS News and Technology Info No items gt Main Site and News a a a a oo a b Prosigna Website FIGURE 4 6 The web application main menu Most of the menu options have sub menus that are available when a user hovers over the item FIGURE 4 7 If no sub menus are available the user may simply click on the menu item Logged inas _ Test User Prosigna NanoString Diagnostics fi i a ja Hn M ae Dashboard Runs Samples le Reports a Admin My Profile Logout View Run Sets Create New Run Set COMMON TASKS m Run Sets Show All b View Run Sets gt Create New Run Set RUN SET ID CREATED INITIATED BY b Download Reports No items gt Add New User I U FIGURE 4 7 Sub menus are avaialble for some menu options nanostring Ec ovtocicrtcs 2015 01 MAN C0034 02 25 USER MANUAL nCounter Dx Analysis System Tables The nCounter web application displays tables to quickly view Run Set statuses sample statuses users and reports Filter Tables can
77. ta form will appear Edit User Data USERID Test User PASSWORD eessssss CONFIRM PASSWORD mr E MAIL ADDRESS testuser nanostring com USER TYPE Administrator General no admin pnvileges PERMISSIONS RUN POST HYBRIDIZATION vw Prosigna Assay 2 ACCESS REPORTS w Prosigna Assay 2 CREATE RUN SET w Prosigna wv Assay2 FIGURE 4 33 The Edit User Data form Edit any of the following information and click the Save button to save any changes made e UserID e Password e Confirm Password e E mail Address e User Type e Assay Permissions e Run Post Hybridization e Access Reports e Create Run Set nanostring 2015 01 MAN CO034 02 43 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 34 Logged inas _ Test User Prosigna NanoString Diagnostics ee S ESE a zm ES Dashboard Runs 2 Admin My Profile Logout a Manage Users USER ID DATE ADDED LAST MODIFIED USER TYPE Gamma 9 12 2014 1 55 01 PM 9 12 2014 1 55 01 PM General Beta 9 12 2014 1 54 47 PM 9 12 2014 1 54 47 PM General 9 12 2014 1 54 28 PM 9 12 2014 1 54 28 PM General Test User 9 12 2014 12 29 00 PM 9 12 2014 12 29 00 PM Administrator FIGURE 4 34 Location of the Delete button on the Manage Users page gt gt gt A confirmation message will appear dh Delete User Are you sure you want t
78. the Instrument Mode Users who have the FLEX configuration are able to run their instruments in either Life Sciences or Diagnostics Dx application modes The FLEX configuration must be enabled by NanoString Support D NOTE If the FLEX configuration has not been enabled the instructions provided in this chapter will not apply only the Diagnostics application mode will be available Proceed to Chapter 4 AIl NanoString IVD assays must be performed using the Diagnostics mode on these instruments In Diagnostics mode there are procedures and controls in place that restrict access to data and some features to authorized users 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 nanostring 7 13 T E C H NOLO GIES 2015901 MAN C0034 02 USER MANUAL nCounter Dx Analysis System A Prep Station Select Instrument Mode After turning on the Prep Station 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 nCounter amp Analysis System Select Instrument Mode Please select the appropriate instrument mode to begin T NanoString Diagnostics NanoString Life Sciences FIGURE 3 1 The Prep Station Select Instrument Mode screen Touch the blue icon labeled NanoString Diagnostics to enter D
79. tring 74 2015901 MAN COO0584 02 T E C 1 N L E NanoString Technologies USER MANUAL 2 Select Confirm to continue the system shutdown nCounter Analysis System Dx nCounter Analysis System Dx Confirm Prep Station Shutdown System Shutdown NanoString Diagnostics NanoString Diagnostics Are you sure you wish to shut down this prep station Shutting down this digital analyzer will shut down this system and prevent cartridge preparation and analysis Press Confirm to continue with the shutdown or Please make sure that all prep stations connected to this Press Resume to return to the Maintenance screen IVD system are properly shut down before shutting down this digital analyzer When shutdown is complete flip the power button on the back of the digital analyzer for a full power off Press Confirm to continue with the shutdown or Press Resume to return to the Maintenance screen one oe FIGURE 7 3 System shutdown messages displayed by the Prep Station left and the Digital Analyzer right gt gt gt A confirmation message will appear 3 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 4 Wait an additional 30 seconds and then use the power switch to restore power to the instrument gt gt gt The system will initialize and display the Select Instrument Mode screen
80. un 1 10 Prep Station 5s 265 lbs 120 kg Weight Digital Analyzer 5s 150 lbs 68 kg Prep Station 5s 35 0 x 26 4 x 24 6 in 89 x 67 x 68 cm Dimensions W x D x H Digital Analyzer 5s 26 x 26 x 19 in 66 x 66 x 48 cm Power Requirements 100 240 VAC 610 VAC Fuse 8A 100 120 VAC or 4A 200 240 VAC nanostring 8 2015 01 MAN C0034 02 NanoString Technologies USER MANUAL F Additional Precautions e The Digital Analyzer is a Class 1 laser product and the instrument contains an internal Class 2 laser barcode reader Class 2 laser radiation exposure is possible while the Digital Analyzer cover is opened Do not stare into the barcode reader laser beam e The Prep Station contains high voltage and heater modules indicated by symbols on the deck Avoid contacting the heater module and electrodes The instrument is equipped with a safety interlock that will prevent voltage from being applied while the instrument door is open e Do not use this device in close proximity to sources of strong electromagnetic radiation or vibration which may interfere with proper operation e Do not attempt to install move or disassemble the instruments e Do not override the door sensors a pinch hazard exists e Ensure that all consumables are properly inserted into the system prior to starting a procedure e Operate the system using only NanoString nCounter test kits in accordance with their Intended Use e Wear gloves while operating or
81. ure in place over the cartridge FIGURE 5 20 The 24 electrodes should insert easily into the 24 wells Touch Next gt gt gt The Hybridized Samples screen will appear FIGURE 5 21 FIGURE 5 20 Carefully lower the electrode fixture into place over the cartridge Q IMPORTANT Do not use the release handle to lower the fixture Doing so will prevent the fixture from locking Instead press on the body of the fixture away from the release handle FIGURE 5 20 Q 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 re align the electrodes using the Align Electrodes workflow under the Maintenance Menu The Prep Station will not be able to process any of the samples if there are bent electrodes nanostring 2015 01 MAN C0034 02 6 USER MANUAL nCounter Dx Analysis System nCounter amp Analysis System y i Dx Hybridized Samples o NanoString Diagnostics Confirm sample strip tube loaded on deck with well position 1 on the left Confirm tube holder closed 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 Note that the strip tube is asymmetrically keyed and if the strip tube is placed incorrectly the lid will not close properly Hy
82. uses of Run Sets Samples and Reports assuming appropriate privileges have been applied to the user profile To view the complete status of any of these click on the Show All button shown on the right hand side of the title bar for each The Dashboard also provides quick access to common tasks located on the left side of the page Click on the appropriate link to navigate and perform the desired action All navigations provided on the Dashboard can be accessed individually by using the menu bar at the top FIGURE 4 14 The Dashboard provides a consolidated view of these to make it easy to perform any function quickly from one place nanoStri g 28 2015 01 MAN CO034 02 e D OUS E g NanoString Technologies USER MANUAL 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 The Run Sets page displays the statuses of all Run Sets that have been created Logged inas _ Test User NanoString Diagnostics ps a M Samples le Reports 2 Admin My Profile Logout Run Sets RUN SET ID INITIATED BY 201409121J BatchRegistered 9 12 2014 1 19 40 PM Test User 20140912GH BatchRegistered 9 12 2014 1 18 56 PM Test User 20140912EF BatchRegistered 9 12 2014 1 17 51 PM Test User 20140912CD BatchRegistered 9 12 2014 1 16 52 PM Test User 20140912AB BatchRegistered 9 12 2014 1 13 56 PM Test User FIGURE 4 15 Statuses of all Run Sets

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NanoString Technologies®: User Manual