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QuantStudio™ 6 and 7 Flex Real-Time PCR Systems Maintenance

1. 2 00 000 cc cece eee eee eee nena 17 Instrument hardware c fd cco a a a a Nea ORL E E tetera sr EE ty rare degen 18 Rron song cciatich aca aah on eg Wart Oe Nee Sat te arlene N 18 Reale gence aed aie ete a a A a ate ol a ee ae wi a ees 19 Barcode Scanine s 2 c chiere oii a ae i a een cabins wna TE eaaa gals eile are E n ee 20 Twister Robot components 0 00 c cece cnn nen een enn cence ne eas 21 Electrical protective devices reia in a eae bide AE a aS 23 Instrument software a snnaan nnn eee nee ee ee tne ene e ene nnn neeeees 23 Computer requirements 2 000 ccc eee eee eee e eee e eee eee 24 Software installation 222 ccs reset tte eee oe reese eA VE ae elie eee 24 Third party software 22 2 6 e eee eee eee eee e eee e ees 24 Instrumenticonstiia bles ripear tnor dag E aaa tia Paced ented a eed och Moga 25 Interchangeable sample blocks heated covers and plate retainers 0 0 005 26 E CHAPTER 2 Calibrate the Instrument 0c cece eee 27 Calibration overview x22 biscuits ce eens bee atte a ee nde eae hd 28 Calibration and maintenance schedule 0 cece eee eee n een e ees 28 Planned maintenance 2 603 salad eet Cote en bo SO et UN oad bd th eda atte ded 28 About maint nance remind rs 0204 04 64 sce cea sake Sead Meg eee ed Cae eee waded 29 Calibration Workflow oreren n vidi dee Heh aie Gnd i wie en end ote cad 29 View the calibration status of an in
2. 2 0000 e eee 131 Set account setup and security policies 0 cece eee eee eee 131 Set up messaging notifications u eee nett ene eens 132 User account management css 2 dcuceny eet ee vee ieee eee baie wee eee 133 Create or edit user accOUNtS eeen E a A N EEA EREE SA ER A Ea 133 Determine the name of the logged in user 0 000 cece cece cece eee ees 134 Cr ate or edita user role snc sea ce ck uie eae eee ee ee eg ee Ede ee 134 View or print a user report 2 2 0 cece eee tenet tenet rnrn 136 Audit trail management 0000 c cece cee ene eee tenet teen eee 137 Access the Audit screen and enable or disable auditing 0000eee ee eeee 137 Modify the auditing settings cc cece cece eee ENRE 137 Audit report generatlon cscs2 os dnne a a n eek le et Mae deeb tebe ea Ee gee ee 138 Viewing audit histories from the Security Settings dialog box 22220200 138 Viewing audit histories from an experiment template or study 141 Manage electronic signature 0 0 0 cece ccc ence eee aee 142 Access the e signature settings screen and enable or disable e sig 142 Configure the meanings of the electronic signatures 2000000 cece eee eee 142 Configure the e signature rights for user roles 00000 cece eee eee 143 Select the actions that require signature 00 ccc 143 How the softwar
3. To Action View and print audit reports 1 Select the System Configuration History tab 2 Display the records of interest 3 Filter the list to decrease the time required to generate reports IMPORTANT You cannot cancel a report after you click a view button 4 Click View Report Note From the audit report the Create action value is listed as Added Delete action value is displayed as Removed and Update action value is displayed as Updated 5 From the Report screen click tool bar options to manipulate the report as needed Place the mouse pointer over an item for a description of the item e To print the report click ch Print e To save the report electronically PDF click Save 6 Close the report Archive purge and restore audit records The audit archive function makes a copy of audit records Purge makes a copy of audit records and then deletes them You can use the Restore function to restore purged audit records Archive and purge To selectively archive or purge delete system configuration or action audit records 1 Select the System Configuration History tab 2 Select records in the appropriate screen 3 Click Archive or Purge 4 If you select Archive specify a location and name for the archive file asz Restore To restore system configuration or action audit records click Restore then select the asz file to restore
4. 2000 0 0 e cece e eee ee eee eee eens 96 Clean the sample block 2 000 e eee e eee e eens 97 Replace the halogen lamp 2 0cc cece ete e cent e eens 99 Materials required 2 0c e enna teen ees 99 Halogen lampi Warnings ee ds ncn eden ce id ec aor tren ea die aa 99 View theslamp Status sees s cge esa siden aa dpkg tbh tence gles Pee ee 4 Gadde 99 Replace the lamp y c0eveeec0e eee rahe ne Seve abe pane whiny dy Feed E A ee 100 Replace the instrument fuses 0000 0c cece eee eee eee etna 102 Materials required 0 ccc rnnr rnnr nrnna ranna 102 Replacethe Tuses 2 2212 Bit Abe bea dle Aten tel ite ie BME US Le tial Ge See ah Sete t 102 Install the QuantStudio 6 and 7 Flex Real Time PCR System Software 0 0 0055 103 Computer requirements 202 cece cece eee ence nent etna 103 IStALLTNe SoftWare 260 25 ct ete ait etal Sei ehe Seu etige eth Ata a En SR aE 103 Manage QuantStudio 6 and 7 Flex Real Time PCR System Software licenses 104 QuantStudio 6 and 7 Flex Real Time PCR System Software license keys and files 104 Activate a license Gs spec endos tanni nae Dadian Pe Salen ete base Penge ale es 104 Installa license file cenrrie sarder ved ete et eed ene od raed He oe Fe ee eee veneers g eee 104 Update the QuantStudio 6 and 7 Flex Real Time PCR System Software 05 105 Update the software 2 2 2 2 eee e eee eee eee
5. Export audit records You can export audit records to a txt file for additional manipulation and reporting outside the QuantStudio 6 and 7 Flex Real Time PCR System Software 1 Display the records of interest as described above 2 Click Export 3 Specify a name and location for the export txt file then click Save Note If you export audit records for samples that have been deleted or moved an error message is displayed Return sample data files to their original location then export again Review the system configuration history The System Configuration History lists security audit and electronic signature configuration records QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 139 Audit report generation Appendix E Security Audit and Electronic Signature Review the system configuration history The following table summarizes the actions that can be audited using the QuantStudio 6 and 7 Flex Real Time PCR System Software The System Configuration History lists security audit and electronic signature configuration records Note If you have installed additional modules to the QuantStudio 6 and 7 Flex Real Time PCR System Software then the list can contain additional auditable records Record type Action Corresponds to Security Settings Update D
6. and 7 Flex Systems Accessory Part no accessories 384 Well Plate Array Card Heated Cover 4454163 384 Well Plate Sample Block 4454165 96 Well Plate Heated Cover 4459841 96 Well Plate Sample Block 4459839 Array Card Bucket Clip Set 4452205 Array Card Sample Block 4454164 Fast 96 Well Plate Heated Cover 4459842 Fast 96 Well Plate Sample Block 4459840 Halogen lamp 12 V 75 W 4480914 Handheld Barcode Scanner 4453271 Life Technologies Array Card Staker Sealer 4456102 a TM E I eeaes Consumable Part no empty plates and 96 Well Fast Plate empty 10 pack 4346907 array cards 96 Well Fast Plate with Barcode empty 10 pack 4346906 96 Well Plate empty 10 pack N8010560 96 Well Plate with Barcode empty 10 pack 4306737 Adhesive Seal Applicator Kit 5 pack 4481196 Array Card Kit empty 1 packt 4445702 Array Card Kit empty 4 packt 4445701 Optical Adhesive Covers 25 pack 4481193 t QuantStudio 7 Flex System only 164 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix G Parts and Materials G General use materials and consumables General use materials and consumables The following general use materials and consumables are required to calibrate maintain and operate the QuantStudio 6 and 7 Flex Systems Unless indicated otherwise all materials shown below are available from major laboratory suppliers MLS Material consumable Sourc
7. 0 00 eee eect cee e eee teens 114 Example network layouts 00 00 e eee e eee e nena 115 Networking guidelines and best practices 00000 cece cece eee e eens 116 Network setup workflow 1 0 0 0 cece cece ene n ene e eet ete eeee 117 Collect the required network information 0 000c cece eect eee eeee 117 Connect the QuantStudio 6 or 7 Flex System to the network 0000000 eee eee eens 118 Materials required lt 2 60 044 seat ade eu ee hes ep are dil ay 118 Define the instrument internet protocol settings 0 0000 c cece cece eee eee 118 Connect the computer to the network 0 00 ccc cece c eee eet tee e eee eeeee 119 Materials required lt 2 seats ihe bette tb baat ee ee eek ed act antl 119 Computer requirement 0 00 cece cece eee eee t ee eeeees 119 Collect required information n sasssa ennnen rnrn rnrn rnnr rnrn naan 119 Set up th computer irrena Ena a E E ie eed aed A E A 119 Install the QuantStudio 6 and 7 Flex Real Time PCR System Software 120 Monitor the QuantStudio 6 or 7 Flex System 2 0 6 0 cece cece ete e eee e ees 120 About remote monitoring 0 000 e cece eee eee eee eee eee eee eeeees 120 Monitorthe Status of aTM pa seta beet Medd Sede deena dea 120 Download experiment files nna nuanua naaraana eee eee eee e eae 121 Enable or change the calibration reminders 0 00000 cece cece cece nena 1
8. 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide standard dilution series standard quantity starting quantity step system dye target target color task technical replicates temperature plot template experiment thermal profile Glossary See also standard and standard curve In standard curve and relative standard curve experiments a set of standards containing a range of known quantities The standard dilution series is prepared by serially diluting standards For example the standard stock is used to prepare the first dilution point the first dilution point is used to prepare the second dilution point and so on In the software the volumes needed to prepare a standard dilution series are calculated by the number of dilution points the number of standard replicates the starting quantity the serial factor and the standard concentration in the stock See also standard curve In the PCR reaction a known quantity In standard curve experiments the quantity of target in the standard From the software the units for standard quantity can be for mass copy number viral load or other units for measuring the quantity of target Standard quantity can also refer to dilution factor When defining a standard curve in the software the highest quantity A component of the thermal profile For each step in the thermal profile you can set the ramp rate ramp increment for melt curve step
9. 62 Array Card RNase P Kits The RNase P Kits include one empty array card and eight tubes of solution Each tube contains reaction mix PCR master mix RNase P primers and FAM MGB dye labeled probe and a known concentration of human genomic DNA template To perform an instrument verification run each solution is loaded into the empty array card in the arrangement shown right When complete the array card contains five replicate groups of standards 200 400 800 1600 and 3200 copies two of unknown populations 800 and 1600 copies and one that serves as a no template control NTC The software performs the same analysis of data from an instrument verification run regardless of the type of consumable used After the run the software 1 Generates a standard curve from the averaged threshold cycle Cy values of the replicate groups of standards Calculates the concentration of the two unknown populations using the standard curve Calculates the following to assess the QuantStudio 6 or 7 Flex System performance CopyUnk T 3 ScopyUnk2 a CopyUnk az 3 ScopyUnk1 where e CopyUnk Average copy number of unknown population A OCopyUnk1 Standard deviation of unknown population A e CopyUnk Average copy number of unknown population B OCopyUnk2 Standard deviation of unknown popul
10. 11 From the Uniformity Calibration screen click Finish to complete the calibration then click Yes when prompted to save the results 12 Optional Click Print Report in the upper right corner of the screen to print a summary of the calibration results for your records QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 51 Chapter 2 Calibrate the Instrument Dye calibration Dye calibration When to perform the calibration About the dye calibration data 52 The software uses the calibration data collected from the dye standards to characterize and distinguish the individual contribution of each dye in the total fluorescence collected by the instrument After each run the instrument software receives data in the form of a raw spectra signal for each reading The software determines the contribution of the fluorescent dyes used in each reaction by comparing the raw spectra to the pure spectra calibration data When you save an experiment after analysis the instrument software stores the pure spectra with the collected fluorescence data for that experiment Perform a dye calibration once every 6 months IMPORTANT Perform a background calibration before every series of dye calibrations Because the age and use of instrument components can affect spectra readings you must perform a dye calibration at least every 6 months The product of a dye calibration is a collection of spectral profil
11. 6 and 7 Flex Real Time PCR System Software some of the touchscreen functions are not part of the recommended maintenance schedule The frequency that you perform them depends on your laboratory policies m Back up and restore the instrument settings 6 cece eee eee 85 E Perform an instrument self test 0 00 cece eee eee eee 86 m Update the instrument firmware 0 6 6 eens 87 Note The touchscreen does not provide access to all instrument functions Features such as instrument calibration and remote notification are available only through the TM QuantStudio 6 and 7 Flex Real Time PCR System Software You can use the QuantStudio 6 or 7 Flex System touchscreen to back up the instrument settings icon standby time out and cover idle temperature and some network settings the Autodiscovery and Smart Monitoring options If the QuantStudio 6 or 7 Flex Instrument settings are reset you can restore the settings using the backup Note The backup feature can be used as an administrative tool to manage QuantStudio 6 and 7 Flex Systems You can use the feature to create a standard image for a QuantStudio 6 or 7 Flex Instrument that can then be restored on other instruments to bypass the manual setup process The QuantStudio 6 and 7 Flex Systems back up to and restores instrument settings from a USB flash drive Before backing up or restoring settings you must plug the drive into one of the USB po
12. Define the instrument settings 6 cece cece eee eee 88 E Define the maintenance reminders 00 c cece eee ete eee eee 90 m Define the network settings 0 6 ccc cee eens 90 E Define the system shortcuts 6 6 0 c cece eee teens 91 E Review the instrument statistics 0 0 cece cee eee e eens 91 E Review the instrument version information 0 00 cee eee ences 91 E Enable disable instrument security unesu sunsun eens 92 E View the instrument log 6 asas auia a a a e ai aiae aaa aa nees 92 Note The touchscreen does not provide access to all instrument functions Features such as instrument calibration and remote notification are available only through the QuantStudio 6 and 7 Flex Real Time PCR System Software IMPORTANT If your laboratory is subject to daylight savings time changes you must manually adjust the time settings during daylight savings to ensure that the internal clocks of your computer and instrument are synchronized 1 From the Main Menu of the instrument touchscreen touch Settings then touch Set Date amp Time 2 From the Set Date amp Time screen a Touch the Time zone field then touch the correct time zone from the list b Touch the Date field enter the current date then touch Done c Touch the Date Format drop down list then select the format for your region d Touch each Time field enter the appropriate time units then touc
13. b If the QuantStudio 6 and 7 Flex Real Time PCR System Software Login appears enter your user name and password then click Log In Enter your user name and password to log in User Name Password Exit Application Note Security is a separately licensed module If your system requires this module contact Life Technologies Note If the QuantStudio 6 and 7 Flex Real Time PCR System Software displays the License Central screen after you log into the software your license file may have become corrupt Contact Life Technologies support to obtain a replacement license file Power off the QuantStudio 6 or 7 Flex System The QuantStudio 6 or 7 Flex Systems operate in low power mode when not in use however the instrument can be powered off completely so that the components draw no power Note If the QuantStudio 6 and 7 Flex Systems are inactive for extended periods of time prepare them for storage as explained in Store the QuantStudio 6 or 7 Flex System on page 126 1 Power off the QuantStudio 6 or 7 Flex System a If the touchscreen is not blank touch 8 to place the QuantStudio 6 or 7 Flex System into stand by mode b Toggle the power button on the rear of the QuantStudio 6 or 7 Flex System 2 Power off the QuantStudio 6 or 7 Flex System computer a From the desktop select Start Shut Down b From the Shut Down Windows dialog box select Shut Down
14. is used to plot a melting curve Significant decrease of the fluorescent signal generates a positive peak on the derivative view of the melting curve See melt curve Type of calibration in which the software collects spectral data from a series of dye standards and stores the spectral information for the dye standards in a pure spectra calibration file This file is used during experiment runs to characterize and distinguish the individual contribution of each dye in the total fluorescence collected by the instrument See amplification efficiency EFF The standard error of the slope of the regression line in the standard curve The error can be used to calculate a confidence interval CI for the slope Because the amplification efficiency EFF is calculated from the slope knowing the error allows a CI for the amplification efficiency to be calculated Dye excitation and emission filter combination that is set for a experiment The QuantStudio 7 Flex System includes a decoupled six by six color filter set The QuantStudio 6 Flex System includes a coupled five color filter set The excitation and emission filter combinations are preset by the experiment document eds file for your experiment A quality control QC indicator which when applied by the software to a well during analysis indicates a possible issue with that reaction For example a flag may be issued if no amplification is detected in a well Flags indicat
15. 10 Check the calibration status of the QuantStudio 6 or 7 Flex System see View the calibration status of an instrument on page 29 If the calibrations for the new sample block heated cover have expired perform the following calibrations in the specified order a ROI calibration b Background calibration c Uniformity calibration d Dye calibration e Normalization calibration IMPORTANT If the calibrations for the new sample block heated cover are valid you do not need to recalibrate the QuantStudio 6 or 7 Flex System Change the heated cover When to change the heated cover Materials required How to handle the heated cover 108 WARNING PHYSICAL INJURY HAZARD During instrument operation the sample block and heated cover can reach 100 C Allow the heated cover to cool to room temperature before removing You can change the heated cover e To change the consumable format of the QuantStudio 6 or 7 Flex System e In the event of a hardware failure e Safety glasses e Powder free gloves e Heated cover To prevent damaging or contaminating the heated cover handle the assembly as shown below After the assembly has been removed from the QuantStudio 6 or 7 Flex System place the heated cover on a clean dry surface or in its shipping container QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix B Maintenance Change the heated cover Chan
16. 6 and 7 Flex Systems that do not match security settings Note Secure mode limits the number of features that are available from the QuantStudio 6 or 7 Flex System touchscreen it does not provide user authentication functionality through the instrument touchscreen 1 If the instrument is in standby touch the QuantStudio 6 or 7 Flex System touchscreen to activate it then press 0 2 In the Main Menu touch Settings then touch Set Administrator Options 3 In the Set Administrator Options screen touch Secure Environment to enable checked or disable unchecked system security 4 Optional To change the administrator password a Touch Change Password b Enter the current password then touch Done c Enter the new password then touch Done d Reenter the password when prompted e Touch OK when prompted Note The default password for the QuantStudio 6 or 7 Flex System touchscreen is password however the password can be changed during installation 5 Touch gg Save 6 Touch the Administrator Password field enter the administrator password then touch Done 7 Touch a to return to the Main Menu You can use the QuantStudio 6 or 7 Flex System touchscreen to view a log that summarizes instrument activity from the last 6 months For each recorded activity the activity log provides a description of the activity and the date time when it occurred 1 From the Main Menu of the instrument touchscreen
17. Array Cards Applied Biosystems Array Card Staker Sealer Centrifuge with array card buckets and array card carrier clips Permanent marker or pen Pipettor 200 uL with pipette tips Powder free gloves Safety glasses Deionized water Create a IMPORTANT Wear powder free gloves while creating the background plate background plate 150 Remove a MicroAmp 96 384 Well Optical Reaction Plate from its box and place it on a clean dry surface Aliquot 20 uL deionized water to each well of the reaction plate Seal the plate using an optical adhesive cover or optical flat caps Use the plate for background calibration as you would a background plate from the spectral calibration kit QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix F Calibration Consumable Preparation Create a background plate or array card Create a 1 Remove an array card from its box and place it on a clean dry surface background array card QuantStudio 7 Flex System only 2 Using a permanent marker write Background on the side of the empty card 3 Pipet 100 uL of deionized water into each of the eight reservoirs in the card a Place the array card on a lab bench with the foil side down b Load 100 uL of the solution into a pipette c Hold the pipette in an angled position 45 and place the tip into the fill port There is a fill port on the left arm of each fill reservoir t
18. Biological hazard safety 184 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Documentation and Support Obtaining information from the Help system The QuantStudio 6 and 7 Flex Systems have a Help system that describes how to use each feature of the user interface Access the Help system by doing one of the following e Click in the QuantStudio 6 and 7 Flex Real Time PCR System Software window e Select Help gt QuantStudio 6 and 7 Flex Real Time PCR System Software Help e Press F1 You can use the Help system to find topics of interest by e Reviewing the table of contents e Searching for a specific topic e Searching an alphabetized index Obtaining support For the latest services and support information for all locations go to www lifetechnologies com At the Life Technologies website you can e Access worldwide telephone and fax numbers to contact Life Technologies Technical Support and Sales facilities e Search through frequently asked questions FAQs e Submit a question directly to Technical Support e Order Life Technologies user documents SDSs certificates of analysis and other related documents e Download PDF documents e Obtain information about customer training e Download software updates and patches Limited product warranty Life Technologies Corporation and or its affiliate s warrant their products as set forth in the Life Technolog
19. Click Export or OK 4 When prompted specify the name and location for the exported file dat then click Save A message is displayed when the export completes Import 1 In any screen in the Security Settings dialog box click Import in the Experiment Menu 2 Select the dat file to import then click Open A message is displayed asking if you want to overwrite the current system configuration Click Yes If any imported user accounts already exist on the system you are prompted to overwrite or skip each account QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 145 Appendix E Security Audit and Electronic Signature User overview User overview User account permissions Account suspension Session time out 146 The Security Audit and Electronic Signature SAE module is a component of the QuantStudio 6 and 7 Flex Real Time PCR System Software that provides the following functionality e System security Controls user access to the software e Auditing Tracks changes made to library items actions performed by users and changes to the Security Audit and Electronic Signature settings e Electronic signature Requires users to provide a user name and password when performing certain functions Depending on the way that your administrator configures these features you may see the following dialog boxes and prompts when you use the software If your us
20. If you are installing the update to a computer that already contains the QuantStudio 6 and 7 Flex Real Time PCR System Software the update automatically acquires the software license from the existing installation If you are installing the QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 105 Appendix B Maintenance Update the Windows operating system QuantStudio 6 and 7 Flex Real Time PCR System Software to a computer that does not contain a previous installation you must have a license file supplied by Life Technologies If you do not have a license file obtain one as explained in Manage QuantStudio 6 and 7 Flex Real Time PCR System Software licenses on page 104 Update the Windows operating system Do not upgrade or update the Microsoft Windows operating system of the computer running the QuantStudio 6 and 7 Flex Real Time PCR System Software without first consulting the software release notes or the Life Technologies website Future versions and updates to the Windows operating system may conflict with the QuantStudio 6 and 7 Flex Real Time PCR System Software To determine compatibility of an upgrade or update 1 Open lt drive gt Program Files Applied Biosystems QuantStudio 6 and 7 Flex Software double click QuantStudio 6 and 7 Software README docx then read the QuantStudio 6 and 7 Flex Real Time PCR System Software Release Notes for the compatibi
21. Instrument malfunction Multiple possible causes Contact your local Life Technologies Field Service Office Z 6unooysayqnos juauunsjsu ay ayeuqneg za4ajydeyg Chapter 2 Calibrate the Instrument Troubleshooting How to identify Signals that exceed the limit of normal background fluorescence may indicate contamination fluorescent contaminants on the calibration plate or array card or the sample block Common contaminants include ink residue from permanent pens powder from disposable gloves and dust To identify and resolve a possible contamination problem 1 While viewing the background calibration data in the Analysis screen select the QC tab to review the list of wells that failed the quality check Eject the background plate or array card from the instrument rotate the plate 180 then perform the background calibration again Determine the location of the contaminated wells again as in step 1 If the position s of the contaminated well s in the steps above are e Identical The sample block is contaminated Decontaminate the sample block as explained in Decontaminate the sample block on page 96 e Reversed The background plate or array card is contaminated Discard it then perform the background calibration using a new background consumable If the calibration fails after you replace the background plate or array card and decontaminate the sample block contact Life Technologies for
22. communication Network service Action DHCP Touch Obtain an IP address automatically Static IP 1 Touch Use the following IP address 2 Touch the IP Address field enter the IP address using the keypad then touch Done 3 Assign the e P addresses for the DNS Servers primary and secondary e Subnet Mask setting e Default Gateway setting 7 Touch Save to save the settings then touch OK when prompted 8 Touch w to return to the Main Menu 118 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix C Networking C Connect the computer to the network Connect the computer to the network Materials required Computer requirement Collect required information Set up the computer Ethernet cable with RJ45 connectors If you are connecting a computer that you provided to a network confirm that the computer contains a free network port Obtain the following information from your network administrator e Network policy for obtaining IP addresses DHCP or static IP e Ifthe network requires static IP addresses obtain the IP address subnet mask and gateway address for the computer IMPORTANT We recommend that you arrange for a network administrator to connect your computer to the network The following procedure does not provide adequate detail for all network architectures Note The following procedure is valid for the Microsoft Windows 7 operating system 1 Use
23. e Safety goggles Prepare the plate IMPORTANT When performing the RNase P instrument verification test e Perform all calibrations beforehand Run the RNase P plate soon after you allow the plate to thaw Minimizing the time that the prepared plate or array card sits on the bench ensures optimal performance Wear powder free gloves and safety glasses when you prepare plates 1 Obtain the RNase P Instrument Verification Plate from the freezer then allow the plate to warm to room temperature for approximately 5 minutes IMPORTANT Use the RNase P plate within 30 minutes of defrosting it Until you are ready to run the plate store it in the dark and at ambient temperature 15 30 C Do not remove the plate from its packaging until you are ready to run it 2 Remove the RNase P plate from its packaging 3 Briefly vortex and centrifuge the RNase P plate a Vortex the plate for 5 seconds QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 63 Chapter 2 Calibrate the Instrument Verify the instrument performance b Centrifuge the reaction plate for 2 minutes at lt 1500 rpm IMPORTANT The reaction plate must be well mixed and centrifuged c Confirm that the liquid is at the bottom of each well of the reaction plate If not centrifuge the reaction plate again at a greater rpm and for a longer period of time IMPORTANT Do not allow the bottom of the plate to become di
24. e abzence 2 Optional During the PCR The QuantStudio 6 and 7 Flex System can collect data during the run real time collecting data during the run can be helpful for troubleshooting 3 After the PCR The instrument collects raw fluorescence data following each extension step of the PCR A data collection point or read on the QuantStudio 6 and 7 Flex System consists of three phases 1 Excitation The instrument illuminates all wells of the plate or array card within the instrument exciting the fluorophores in each reaction 2 Emission The instrument optics collect the residual fluorescence emitted from the wells of the plate or array card The resulting image collected by the device consists only of light that corresponds to the range of emission wavelengths 3 Collection The instrument assembles a digital representation of the residual fluorescence collected over a fixed time interval The software stores the raw fluorescent image for analysis After a run the software uses calibration data ROI background uniformity dye and normalization to determine the location and intensity of the fluorescent signals in each read the dye associated with each fluorescent signal and the significance of the signal Instrument filters and supported dyes System dyes The QuantStudio 6 Flex System features a coupled five color filter set while the QuantStudio 7 Flex System features a decoupled six by
25. information If a product insert does not exist or if the product insert does not contain the symbol or the required information consult the user manual CONT CONTAINS DO NOT REUSE For one time use only LOWER LIMIT OF TEMPERATURE The lower limit of temperature is indicated adjacent to the symbol MANUFACTURER The name and the address of the manufacturer will appear next to this symbol SERIAL NUMBER The serial number will appear after or below this symbol TEMPERATURE LIMITATION The upper and lower limits of temperature are indicated adjacent to the upper and lower horizontal lines UPPER LIMIT OF TEMPERATURE The upper limit of temperature is indicated adjacent to the symbol ro F E 8 HE E USE BY This symbol is accompanied by a date to indicate that the device should not be used after the end of the date shown 176 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix Safety Locations of safety labels on instrument Locations of safety labels on instrument The QuantStudio 6 and 7 Flex Systems contain warnings at the following locations QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 177 Appendix Safety Safety alerts on this instrument Safety alerts on this instrument Additional text may be used with one of the symbols described above when more specific
26. service the instrument QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix A Manual Instrument Operation Maintain the instrument from the touchscreen b Touch gy Save IMPORTANT Do not remove the USB drive from the QuantStudio 6 or 7 Flex System until instructed c When the QuantStudio 6 or 7 Flex System finishes writing the results to the USB drive touch OK then remove the USB drive 4 Touch B to return to the Main Menu Update the You can download QuantStudio 6 and 7 Flex Systems firmware updates directly instrument from the service section of the Life Technologies website After obtaining a firmware firmware update transfer the update to the QuantStudio 6 or 7 Flex System using a USB drive 1 Download the firmware update a Go to www lifetechnologies com us en home technical resources software downloads b In the Software Downloads page select Applied Biosystems QuantStudio 6 and 7 Flex Real Time PCR Systems from the menu c In the Software Downloads page for your QuantStudio 6 or 7 Flex System click Updates Patches d Download the QuantStudio 6 and 7 Flex Systems firmware to a USB drive 2 Plug a USB drive into the USB port below the touchscreen IMPORTANT Do not use the USB ports on the rear panel of the QuantStudio 6 and 7 Flex Systems The rear USB ports are for use by Life Technologies personnel to service the
27. touch Tools then touch View Log 2 From the View Log screen configure the settings to display the records of interest e Select an option from the drop down menu to filter the log e Select Earliest First or Latest First to determine the order to sort the records QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix A Manual Instrument Operation Administrate the instrument from the touchscreen 3 Optional Plug the USB drive into the port below the touchscreen then touch Export to USB to save the log to the drive IMPORTANT Do not use the USB ports on the rear panel of the QuantStudio 6 and 7 Flex Systems The rear USB ports are for use by Life Technologies personnel to service the instrument 4 Touch B to return to the Main Menu QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 93 Administrate the instrument from the touchscreen Appendix A Manual Instrument Operation 94 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Maintenance Decontaminate the sample block 0 6 0 cece cee eee ee 96 Replace the halogen lamp 66 c cece eee eens 99 Replace the instrument fuses 0 6 e ccc eee eee 102 Install the QuantStudio 6 and 7 Flex Real Time PCR System Software 103 Manage QuantStudio 6 and 7 Flex Real Time PCR System Software licenses 104 Update the Quant
28. 2 Unload the QuantStudio 6 or 7 Flex System and view the wells of the plate or array card If the liquid in the wells of the consumable is not e At the bottom of the wells centrifuge the plate or array card for a longer time then repeat the calibration e Equivalent in volume the plate or array card is not sealed and the reagents have evaporated Discard the consumable and run another 3 If the calibration plate or array card appears to be normal discard it and run another 4 f the calibration fails again contact Life Technologies One or more wells produced spectra that deviate significantly from the rest of the plate or array card 1 While viewing the calibration data in the Analysis screen locate the well s with abnormal signal in the Plate Layout tab 2 Rotate the plate or array card 180 then perform the calibration again 3 Determine the location of the contaminated wells again If the position s of the well s identified in the steps above are e Identical The sample block is contaminated Decontaminate the sample block e Reversed The ROI plate or array card is contaminated Discard the consumable then perform the uniformity calibration using a new ROI plate or array card 4 lf the calibration fails again contact Life Technologies Instrument does not eject the ROI plate or array card the consumable is stuck within the instrument The adhesive cover may have adhered the plate or array
29. 22 4 in 21 6 cm 8 5 in 10 kg 22 0 lbs Monitor 38 0 cm 15 0in 13 7 cm 5 4in 37 4 cm 14 7in 3 0 kg 6 7 lbs Keyboard 2 75 cm 1 1 in 44 5cm 17 8 in 13 75 cm 5 5in 0 75 kg 1 65 lbs t Weight varies depending on the sample block installed E 15 2cm 6in ul g ge wo Z7 Gg 53 0 cm 20 9 in 233 0 cm 91 in Ul G 6Z WO O GZ Required The QuantStudio 6 and 7 Flex Systems require the following additional clearances clearances Component Top Front Sides Back Instrument 30 5 cm 12 0 in 122 cm 48 0 in 51 0 cm 20 0 in 15 2 cm 6 0 in Computer 30 5 cm 12 0 in 15 2 cm 6 0 in 168 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Electrical requirements Environmental requirements Appendix H Instrument Specification and Layout QuantStudio 6 and 7 Flex Systems specifications WARNING For safety the power outlet used for powering the instrument must be accessible at all times See Required clearances on page 168 for information about the space needed between the wall and the instrument In case of emergency you must be able to immediately disconnect the main power supply to all the equipment Allow adequate space between the wall and the equipment so that the power cords can be disconnected in case of emergency Note Place the QuantStudio 6
30. 6 or 7 Flex System IMPORTANT After installing the sample block confirm that the indicator on the left side of the sample block is positioned behind the red line on the instrument rail If not push the sample block into the QuantStudio 6 or 7 Flex System until it is seated correctly If you are installing a sample block of a different consumable format replace the heated cover and plate adapter if necessary Close the access door IMPORTANT Confirm that the access door is completely closed The QuantStudio 6 and 7 Flex Real Time PCR System Software displays an error message if the door is not completely closed and latched or if the sample block is not seated correctly Plug in and power on the QuantStudio 6 or 7 Flex System From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab click Instrument Console QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 107 Appendix B Maintenance Change the heated cover 9 From the Instrument Console select your QuantStudio 6 or 7 Flex System from the list of instruments then review the Block Type field in the Instrument Properties pane The installation is successful if the QuantStudio 6 or 7 Flex System powers on and if the Block Type field displays the correct type of sample block Note The Block Type field displays the type of sample block installed to the QuantStudio 6 or 7 Flex System
31. 7 Flex System m Prepare the normalization calibration plates 0 0 eee ee eee 57 E Preparing array cards for instrument calibration 00058 36 Materials required e Normalization Plate with FAM ROX dyes e Normalization Plate with VIC ROX dyes e Centrifuge with plate adapter e Powder free gloves e Safety goggles Prepare the plate IMPORTANT Before performing a normalization calibration you must perform an ROI calibration a background calibration a uniformity calibration and a dye calibration IMPORTANT Wear powder free gloves and safety glasses when you prepare the plate 1 Remove the normalization calibration plates from the freezer then allow them to warm to room temperature approximately 30 minutes IMPORTANT Use the calibration plates within 2 hours of defrosting them Until you are ready to run the plates store them in the dark and at ambient temperature 15 30 C Do not remove the plates from their packaging until you are ready to run them QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 57 2 Chapter 2 Calibrate the Instrument Normalization calibration Perform the normalization calibration 58 Go to Perform the normalization calibration on page 58 Before using each normalization plate vortex the plate for 5 seconds centrifuge it for 2 minutes at lt 1500 rpm then confirm that the liquid in each
32. 85 F Thermal output During operation the net thermal output based on the actual current draw of the QuantStudio 6 and 7 Flex Instrument and computer is expected to be approximately 2731 Btu h 800 W Vibration Ensure that the instrument is not adjacent to strong vibration sources such as a centrifuge pump or compressor Excessive vibration will affect instrument performance Other conditions Ensure the room is away from any vents that could expel particulate material on the instrument components Avoid placing the instrument and computer adjacent to heaters cooling ducts or in direct sunlight QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 169 Appendix H Instrument Specification and Layout QuantStudio 6 and 7 Flex Systems specifications Network The computer is factory configured for the TCP IP protocol The product includes a requirements fast Ethernet adapter 10 100 Mbps with an RJ45 type connector and one 3 m 9 8 ft crossover Ethernet cable that connects the computer and the instrument If the instrument will be connected to a LAN an active tested LAN connection must be in place before the scheduled installation date Due to differences in network connections the Life Technologies service representative cannot configure the instrument to access a specific network You must supply a standard Category 5 Ethernet cable of the required length to conn
33. Administration Guide 27 Chapter 2 Calibrate the Instrument Calibration overview Calibration overview Calibration and maintenance schedule Planned maintenance 28 The QuantStudio 6 and 7 Flex Systems require regular calibration and maintenance for proper operation To ensure proper operation of your instrument perform weekly monthly and semiannual maintenance as indicated in the following table IMPORTANT Perform calibrations and run experiments under the environmental conditions specified in Appendix H Instrument Specification and Layout Exposure to extreme temperatures can have adverse effects on the run results as well as shortening the life span of the instrument components IMPORTANT Do not use organic solvents to clean the QuantStudio 6 and 7 Flex Systems Frequency User performed maintenance task Check the computer disk space If necessary archive or back up your experiment files and instrument settings Weekly Power off the computer that controls the instrument then power on the computer after 30 seconds Clean the surface of the instrument with a lint free cloth Perform a background calibration Monthly Run disk cleanup and disk defragmentation Perform an instrument self test Perform an ROI calibration Perform a background calibration Semi annually every 6 months Perform a uniformity calibration Perform a dye calibra
34. Do not remove the plate from its packaging until you are ready to run it 2 Remove the background calibration plate from its packaging Do not remove the optical film 3 Vortex and centrifuge the plate a Vortex the background calibration plate for 5 seconds b Centrifuge the plate for 2 minutes at lt 1500 rpm IMPORTANT The background calibration plate must be well mixed and centrifuged c Confirm that the liquid in each well of the background calibration plate is at the bottom of the well If not centrifuge the plate again at a higher rpm and for a longer period of time IMPORTANT Do not allow the bottom of the plate to become dirty Fluids and other contaminants that adhere to the plate bottom can contaminate the sample block and cause an abnormally high background signal Correct Incorrect bottom of well Liquid is at e Not centrifuged with enough force or e Not centrifuged for enough time QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 45 Chapter 2 Calibrate the Instrument Background calibration Perform the 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab background click Instrument Console calibration 2 From the Instrument Console select the icon for your instrument then click Manage Instrument Note If the Manage Instrument button is inactive add your QuantStudio 6 or 7 Flex System to the My
35. Instrument Specification and Layout Describes the QuantStudio 6 and 7 Flex System specifications requirements layout and connections QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 13 About This Guide Contents of this manual 14 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Getting Started E Differences between the QuantStudio 6 and 7 Flex Real Time PCR Systems 16 m About the QuantStudio 6 and 7 Flex Real Time PCR Systems 16 E Instrument hardware 0 ccc ccc eect nen n een eens 18 E Instrument software 0 6 ccc eee e errereen 23 E Instrument consumables 0 00 c cece cece nent eee n eens 25 m Interchangeable sample blocks heated covers and plate retainers 26 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 15 1 Chapter 1 Getting Started Differences between the QuantStudio 6 and 7 Flex Real Time PCR Systems Differences between the QuantStudio 6 and 7 Flex Real Time PCR Systems The following table displays the differences between the QuantStudio 6 Flex System and the QuantStudio 7 Flex System QuantStudio 6 Flex System QuantStudio 7 Flex System Does not support the Twister Robot Supports the Twister Robot Does not support the Array Card block Supports the Array Card block Features a coupled fiv
36. Ne es ane ees Re ee Re 181 EMG preteen Packet get ok ote or PCIE rant Per GE ea gt Be hed eee eee ae Pe ae fet RE ote 181 Environmental desig i issii bate g bie ny eather boll cle cg leet dae deans week 38 181 Chemicalsatety srs ci2 ae2 savheg eared pee baw Ga Ree weg peek 4 il gs weer eee 182 Biological hazard safety annann nnne eee e eee eeeees 183 Documentation and Support 0 ccc eee e cee eee eee 185 Obtaining information from the Help system 0000 cee eee ee enna 185 Obtadining support secera eerren n ere bess t ewe hee tee by ieb eee pees vewderes 185 Limited product warranty s sssusa cece eee eee eee naear 185 LO SSOP Y enea a a aan bccn en ome cna ee aesenn mace ane 187 Dde ee ee cen mee iin eua eee a eM eh dew ee 197 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 9 Contents 10 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Purpose Audience Assumptions About This Guide This user guide provides provides reference information for the QuantStudio 6 and 7 Flex Real Time PCR Systems and describes how to prepare maintain and troubleshoot the systems A N WARNING The protection provided by the equipment may be impaired if the instrument is operated outside the environment and use specifications the user provides inadequate maintenance or the equipment is used in a manner not specified by the manuf
37. QuantStudio 6 and 7 Flex Real Time PCR System Software is configured for password expiration you are periodically prompted to change your password Note If the QuantStudio 6 and 7 Flex Real Time PCR System Software is configured to monitor failed log in attempts you will be locked out of the software if you repeatedly enter an incorrect user name and or password Change your password when it expires When your password is about to expire a message is displayed when you log in To change your password select Tools Change Password Enter your current password then enter the new password two times then click OK Enter a reason for change If the QuantStudio 6 and 7 Flex Real Time PCR System Software is configured for auditing you may be prompted to specify a reason when you make certain changes in the software Depending on your QuantStudio 6 and 7 Flex Real Time PCR System Software configuration you can either select a reason from the list or enter a reason for change Perform an electronic signature If your system is configured for electronic signature you may be required to have the experiment signed by other users before you can print a report or start a run If an item is set to require multiple signatures all approvers must sign the associated data before the action can be completed If electronic signature is enabled for experiments any of the following may apply e The Tools gt S
38. RNase P Kit for the QuantStudio 7 Flex System with array card sample blocks RNase P Instrument Verification Plates The RNase P plate is preloaded with the reagents necessary for the detection and quantitation of genomic copies of the human RNase P gene a single copy gene encoding the RNase moiety of the RNase P enzyme Each well contains PCR master mix RNase P primers FAM dye labeled probe and a known concentration of human genomic DNA template The figure to the right illustrates the arrangement of the standard and unknown populations on a 96 well and Uikg wi A Fast 96 well RNase P plate The RNase P tanon plate contains five replicate groups of NTC STD 1250 STD 2500 standards 1250 2500 5000 10000 and 20000 copies two unknown populations 5 000 and 10 000 copies and a no Unknown B template control NTC 10000 The figure to the right illustrates the arrangement of the standard and unknown populations on a 384 well RNase P plate The RNase P plate contains five replicate groups of standards 1250 2500 5000 10000 and 20000 copies two unknown populations 5 000 and 10 000 copies and a no template control NTC Unknown A Unknown B 5000 10000 Si Standard 10000 e Standard 20000 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 61 Chapter 2 Calibrate the Instrument Verify the instrument performance Analytical performance
39. Time PCR System Software select Tools gt Security gt Settings 2 From the Security Settings dialog box select the e Signature tab 3 Select or deselect Enable e Signature IMPORTANT Enabling the electronic signature feature can substantially increase the size of experiment template and study files IMPORTANT If you disable security you inactivate audit and electronic signature functions No audit record is generated for the disabling of audit and electronic signature functions when you disable security 4 Click Apply Settings The e signature meanings are the text that a user can select to describe a reason for an TM electronic signature The QuantStudio 6 and 7 Flex Real Time PCR System Software is installed with the following default meanings Default data types E Signature definition Plate Thermocylcer Analysis Analysis setup protocol protocol results Reviewed and Approved Plate Set Up Yes Yes No No Reviewed and Approved Results No No Yes Yes Reviewed and Approved Template No No Yes Yes Use the Security Settings dialog box to add or remove electronic signature meanings and to determine the data types to which they apply To Action Add a meaning 1 From the e Signature tab of the Security Settings dialog box click Add in the e Signature Meanings settings 2 From the Create Meaning dialog box enter a description of the e Signature meaning then click OK 3 S
40. Yes Import the system preferences Yes No Yes Calibrations Perform calibrations Yes Yes Yes RNaseP Perform an RNase P run Yes Yes Yes Instrument Add and remove instruments from monitoring Yes No Yes Conhgupation Upgrade and downgrade instrument firmware Yes No Yes Security Configure the security and audit feature No No Yes Configuration Log in to user sessions that have timed out No No Yes Perform E Signing Yes No Yes Export Export primary and secondary analysis results Yes Yes Yes View or printa user Note The landscape and portrait functions are not available for the User or Roles report reports To print either report in landscape save the report electronically pdf then print the file in the desired orientation 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Security gt Settings 2 From the Security Settings dialog box select the Users or Roles tab 3 Click View Report 4 From the Report screen click tool bar options to manipulate the report as needed Place the mouse pointer over an item for a description of the item 5 Click Print to print the report or click A Save to save the report electronically pdf Close the report 136 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix E Security Audit and Electronic Signature Audit trail management Audit trail management Access the Audit Use the Audit screen
41. and the sample block D Lamp Illuminates the plate or array card during a run Heated cover Covers the plate or array card during a run to prevent condensation and leakage through the cover F Sample block Heats the plate or array card during a run G Side door Opens to allow extension of the tray arm H Plate adapter Secures the plate or array card to the tray arm Tray arm Conveys the plate or array card to and from the sample block in the interior of the instrument Ethernet Component Description Ethernet port An RJ45 port that provides Ethernet gigabit communication with the instrument 19 1 Chapter 1 Getting Started Instrument hardware Barcode scanner 20 Component Description B USB ports Provide USB communication with the instrument USB ports can be used to transfer data from the instrument Note If multiple USB drives are plugged into the instrument the instrument mounts only the first drive that is installed regardless of the USB port used C RS232 port Provides serial communication between the instrument and the computer IMPORTANT The serial port is for Life Technologies use only D Instrument Cool the interior of the instrument lane IMPORTANT The fans must be unobstructed to ensure adequate cooling and proper function of the instrument E On Off switch
42. describe how to troubleshoot failed calibrations and RNase P instrument verification tests ROI calibration troubleshooting 0 eee eens 70 Background calibration troubleshooting 6 6 66 c cece eee eee ee 71 Uniformity calibration troubleshooting 6 c cece eee eee 72 Dye calibration troubleshooting 0 0 6 c cece eee een ee 73 Normalization calibration troubleshooting 006 e cece eee eee 74 RNase P test troubleshooting 06 ee 75 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 69 aping UONENSIUIUPY pUe aoueuajuleW SWAaISAS Yd WIL JE Y X 4 Pue 9 olpnsiueng OL Table 1 ROI calibration troubleshooting Problem symptom Possible cause Action ROI calibration failed e ROI image is blurry e ROI image is faint e Plate or array card was centrifuged insufficiently e Plate or array card contains old or insufficient reagents e The sample block or heated cover may not be seated correctly CAUTION PHYSICAL INJURY HAZARD During operation the sample block can reach 100 C Before removing the plate or array card wait until the block reaches room temperature 1 Unload the instrument and confirm that you loaded the correct plate or array card If not perform the calibration again using the correct type of consumable 2 View the wells of the plate or array card If the liquid in the wells is not e At the bottom o
43. do not go past the first stop of pipettor plunger or you may blow the solution out of the port IMPORTANT Do not allow the tip to contact and possibly damage the coated foil beneath the fill port 5 Repeat step 4 to fill the remaining array card with the appropriate calibration reagents 6 Centrifuge the array card s a Place the filled array card s into a centrifuge array card carrier clip and place empty array cards in the remaining slots Confirm that the labels on the buckets and clips are oriented in the same direction b Place the filled carrier clips into the centrifuge buckets Make sure that the array card fill reservoirs and bucket and clip labels face outward when loaded into the centrifuge IMPORTANT You must run the centrifuge with all four buckets in place and each of the two carriers filled with array cards Place empty array cards into unfilled slots IMPORTANT Balance the loads in opposite buckets in the centrifuge QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 37 Chapter 2 Calibrate the Instrument Preparing array cards for instrument calibration c Close the centrifuge cover then spin the array card s for 1 minute at 1200 rpm d When the run is finished stop the centrifuge then spin the array card s again for 1 minute at 1200 rpm IMPORTANT Do not try to save time by doing one spin for 2 minutes The two sets of ramps are imp
44. dye plate is at the bottom of the wells If not centrifuge the plate again at a higher rpm and for a longer period of time Correct Incorrect Liquid is at e Not centrifuged with enough force or bottom of well e Not centrifuged for enough time From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab click Instrument Console From the Instrument Console select the icon for your instrument then click Manage Instrument Note If the Manage Instrument button is inactive add your QuantStudio 6 or 7 Flex System to the My Instruments group From the Instrument Manager start the calibration a Click X Maintenance then click Normalization b From the Normalization Calibration screen click Start Calibration From the Normalization Calibration screen select the reporter passive dye combination that you want to calibrate then perform the calibration as instructed From the bottom of the Setup tab enter the reagent information for the normalization plate or array card that you are using Reagent Information Plate Barcode Reagent Name Reagent Part Number Reagent Lot Number Reagent Expiration Date Check the box when the normalization calibration plate has been loaded and when you have ensured you have entered all reagents information correctly Bm QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Cali
45. eee eee eee eens 82 Transfer experiments templates and results data 0020 cece eee eee 83 Maintain the instrument from the touchscreen 00020c rnrn eee rnrn eee e eens 85 Back up and restore the instrument settings 0000 cee cece cence eee eee 85 Perform an instrument self test 00000 c rnnr rnrn anaran 86 Update the instrument firmware 0 000 0c cece eee eee e eet e eae 87 Administrate the instrument from the touchscreen 000c cece cece eect eee eees 88 Define the date and time 060 e eee e eae 88 Define the instrument settings 0 000 e eee eee eee nent eee 88 Define the maintenance reminders 000 0c cece cece e ee eee eee eee eens 90 Define the network settingS 000 cece eee eee eee e eee e eens 90 Define the system shortcuts aeris ioen a a A e eens 91 Review the instrument statisticS saanunna nrn e rnrn rennarar 91 Review the instrument version information 20000 cece cece cece eee e eee 91 Enable disable instrument security 60 0 ce cee e eee tenet eens 92 View the instrument log 000 e cece eee eee nett eee ee eeees 92 APPENDIX B Maintenance 0 0 c eee e eee eee 95 Decontaminate the sample block 2 0000 e eee e eee eaee 96 Materials required one cet ninaa ei Sade aar el Pa eat EA ee tal Se pt holed colt 96 How to handle the sample block
46. free gloves e MicroAmp Optical 96 384 Well Reaction Plate e Optical Adhesive Cover e Pipettors and pipette tips 200 uL and 1000 uL e Tubes 2 mL and 10 mL e Deionized water Note Wear powder free gloves while creating the dye plate 1 Prepare and load the custom dye plate a In the center of a 96 384 well plate prepare a dilution series of the custom dye for example 25 50 100 200 400 800 1600 and 3200 nM using 20 uL volumes for a 96 384 well plate b Seal the reaction plate using an optical adhesive cover c Load the prepared reaction plate 2 Start the calibration wizard a Inthe Home screen of the QuantStudio 6 and 7 Flex Real Time PCR System Software click Instrument Console b In the Instrument Console select your QuantStudio 6 or 7 Flex System then click Add to My Instruments Select the QuantStudio 6 or 7 Flex System then click Manage Instrument 2 p In the Instrument Manager click Maintenance then click ROI In the ROI Calibration screen click Start Calibration In the ROI dialog box click Next until prompted to load the QuantStudio 6 or 7 Flex System When the side door opens load the sealed plate Ensure that the plate array card is properly aligned in the holder PR Oo QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix F Calibration Consumable Preparation Create a custom dye plate for calibration g In the
47. further support Remove a plate If the QuantStudio 6 or 7 Flex System does not eject a plate after you touch Mon the stuck within the touchscreen the adhesive cover of the plate may have adhered it to the heated cover instrument 78 within the instrument If so you can remove the plate from the instrument as follows 1 Power off the instrument Wait 15 minutes then power on the instrument and eject the plate If the plate does not eject power off and unplug the instrument then open the access door While wearing powder free gloves reach into the instrument and remove the plate from the heated cover then close the access door Perform a background calibration to confirm that the sample block has not been contaminated QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Manual Instrument Operation Overview of instrument touchscreen functions 000000005 Operate the instrument from the touchscreen 000 000s Maintain the instrument from the touchscreen 000000 eee Administrate the instrument from the touchscreen 005 Note This appendix describes how to operate the QuantStudio 6 and 7 Flex Systems manually using the touchscreen interface Although the QuantStudio 6 and 7 Flex Systems can be used without an Ethernet connection to a computer the touchscreen allows you to perform only a subset of the total instrument funct
48. information is needed to avoid exposure to a hazard See the following table for safety alerts found on the instrument English French translation ZN CAUTION Hazardous chemicals Read the Safety Data Sheets SDSs before handling ATTENTION Produits chimiques dangereux Lire les fiches signal tiques FS avant de manipuler les produits ZN CAUTION Hazardous waste Refer to SDS s and local regulations for handling and disposal ATTENTION D chets dangereux Lire les fiches signal tiques FS et la r glementation locale associ es a la manipulation et a l limination des d chets A CAUTION Class 2 II visible and or invisible laser radiation present when open Do not stare directly into the beam or view directly with optical instruments ATTENTION Rayonnement laser visible ou invisible de classe 2 II pr sent en position ouverte Ne pas regarder directement dans le faisceau ou avec des instruments optiques Instrument safety General CAUTION Do not remove instrument protective covers If you remove the protective instrument panels or disable interlock devices you may be exposed to serious hazards including but not limited to severe electrical shock laser exposure crushing or chemical exposure Physical injury AN CAUTION Moving and Lifting Injury The instrument is to be moved and positioned only by the personnel or vendor specified in the applicable site preparatio
49. instrument 3 If the instrument is in standby touch the QuantStudio 6 or 7 Flex System touchscreen to activate it then press 4 In the Main Menu touch Tools then touch g Upgrade Firmware 5 In the Upgrade Firmware screen select the update package then touch Upgrade Firmware Allow the QuantStudio 6 or 7 Flex System to complete the upgrade IMPORTANT Do not remove the USB drive from the QuantStudio 6 or 7 Flex System until you are instructed to do so 6 After the upgrade is complete and the QuantStudio 6 or 7 Flex System reboots confirm the upgrade success a Unplug the USB drive b Touch Settings then touch About this instrument to view the software version number to confirm that the firmware has been upgraded QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 87 Administrate the instrument from the touchscreen Appendix A Manual Instrument Operation Administrate the instrument from the touchscreen Define the date and time Define the instrument settings 88 The touchscreen provides access to several administrative functions that you can use to integrate the QuantStudio 6 and 7 Flex Systems into a laboratory workflow The following functions are available from the touchscreen and can be used after installation to customize the instrument settings and configure it for network use E Define the date and time 0 c ccc teen teens 88
50. instrument calibrations and lamp replacement reminders e Activate deactivate or change the frequency of the maintenance reminders displayed by the QuantStudio 6 or 7 Flex System To set the reminder 1 Define the network 1 settings 2 3 4 90 From the Main Menu of the instrument touchscreen touch Settings then touch Set Maintenance Reminders For each reminder a Touch the Calibration expires after field b Use the keypad to enter the number of days or for the lamp the number of hours that should elapse before expiration then touch Done c Optional Touch the checkbox to activate or deactivate an expiration reminder then go to step 3 Optional Configure the reminder a Touch the Display reminders before field b Enter the number of days or for the lamp the number of hours from 1 2000 before which the instrument should display warnings of the impending expiration then touch Done Touch Save to save the settings then touch OK when prompted Touch a to return to the Main Menu From the Main Menu of the instrument touchscreen touch Settings then touch Set Network Information Note The Set Network Information screen displays the Media Access Control MAC address of the QuantStudio 6 or 7 Flex System below the Autodiscovery and Smart Monitoring check boxes The MAC address can be used to uniquely identify the QuantStudio 6 or 7 Flex System on the network Touch Autodiscove
51. license key with the computer from which the key was activated After a key is activated and a license file is generated the file cannot be transferred to another computer To transfer a license between computers you must reactivate the license key using the QuantStudio 6 and 7 Flex Real Time PCR System Software on the target computer Note License keys are found on the QuantStudio 6 and 7 Flex Real Time PCR System Software CD packaging or they can be supplied by Life Technologies support If you have a valid license key for the QuantStudio 6 and 7 Flex Real Time PCR System Software or an associated module you can activate the license as explained below IMPORTANT An internet connection a web browser and a valid email account are required to activate a QuantStudio 6 and 7 Flex Real Time PCR System Software license If the computer that contains the QuantStudio 6 and 7 Flex Real Time PCR System Software is not connected to the internet or it lacks a web browser application contact Life Technologies support to request the license file 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab select Tools gt License Central 2 From the License Central dialog box select the license of interest from the table click Activate License then wait for the default web browser application to connect to the Life Technologies website 3 From the Life Technologies Software License Activation
52. normalization calibration plates 0 annarrar nenene 57 Perform the normalization calibration 0 0 ccc eee eee aranaren 58 Verify the instrument performance 0000 cee eee eee ence eee rrr 61 When to perform the test i aot teaa cere ouea i iee biaa inie eee eee eee eee e eee eens 61 About the RNase P KIS 2 3 22 cccse sear eee es Send eed Saat Ween edhe eee 61 Analytical performance n nannu nunan rrna n rnrn rrna nnana 62 Installation specification s an 00 4 pele unnur nnna 63 Prepare the RNase P plate 0 0 00 eee 63 Preparing an array card for instrument verification s s s assunse rnrn errre 64 Run the RNase P plate or array card 2 2 2 cee eee eee eee aes 66 Troubleshooting sierras ieii ee bee ey e ne hdeye nd bee DOAN d eE ENOAR A vaayea dae saavdews 69 How to identify contamination 2000 cece eee eee eee e eens 78 Remove a plate stuck within the instrument 0000 00 0c cece cece eee eee es 78 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Contents APPENDIX A Manual Instrument Operation 05 79 Overview of instrument touchscreen functionS 2 2000 cece cece eee eee eee aes 80 Operate the instrument from the touchscreen 00000 eee eee eee e eens 81 Create an experiment from a template 000 ccc eee eee eee eee eee ee ee 81 Run an experiment 0000 cece eee
53. of the calibration where passed indicates that the run produced viable calibration data and failed indicates that the run did not produce data or that the data it collected is unusable QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 55 Chapter 2 Calibrate the Instrument Dye calibration Analysis status Action Passed 1 Click Next 2 Enter comments in the Comments field click Finish then click Yes when prompted to save the results Failed Troubleshoot the failed calibration as described in Dye calibration troubleshooting on page 73 10 Select the QC tab to review the quality check summary The QC status indicates 56 the quality of the calibration data where passed indicates that all wells produced data that passed the quality check and failed indicates that one or more wells produced dye spectra that differ significantly from the other wells on the plate or array card Note If the calibration failed the QC tab can provide information regarding the cause of the failure Unload the calibration plate or array card a After the calibration touch on the touchscreen to eject the plate or array card Note If the instrument does not eject the plate or array card remove it as explained in Dye calibration troubleshooting on page 73 b Remove the calibration plate or array card from the instrument tray and discard it A WARNING PHYSICAL INJU
54. or 7 Flex System and computer power receptacle on an electrical circuit that is not shared with electrically noisy devices or devices that can cause power surges such as refrigeration units The following table provides electrical specifications for the instrument and associated devices For all indicated input voltages a 15 A circuit is required Device Rated current Rated power Rated voltage Rated frequency Instrument 12 5A 950 VA 100 240 Computer 2 1A 125 VA 10 VAC 50 60 Hz Monitor 1 5A 65 VA Note The instrument monitor and computer self adjust for 100 240 V input voltages of 50 60 Hz Condition Description Altitude Located between sea level and 6000 ft 1800 m above sea level Electromagnetic Do not use this device in close proximity to sources of strong interference electromagnetic radiation for example unshielded intentional RF sources Strong electromagnetic radiation may interfere with the proper operation of the device Humidity 15 80 noncondensing Installation site For indoor use only Pollution The instrument has a Pollution Degree rating of II The instrument may only be installed in an environment that has nonconductive pollutants such as dust particles or wood chips Typical environments with a Pollution Degree II rating are laboratories and sales and commercial areas The noise output of the instrument is lt 60 dB at idle Temperature 15 30 C 60
55. or array card from the instrument as explained in Remove a plate stuck within the instrument on page 78 Instrument malfunction Multiple possible causes Contact your local Life Technologies Field Service Office juawnujsu ay ayeuqneg Zz 4ajdeyg 6unooysayqnos E N ol aping UONENSIUIUPY pUe aaueuajulew SW IS S Yd WIL JE Y X 4 PUL 9 olpnisjueng Table 6 RNase P test troubleshooting Problem symptom Possible cause Action RNase P plate or array card verification run failed e Contamination e Defective seal e Inaccurate fluid transfer during plate or array card manufacturing e Insufficient centrifugation CAUTION PHYSICAL INJURY HAZARD During operation the sample block can reach 100 C Before removing the plate or array card wait until the block reaches room temperature 1 Unload the RNase P plate or array card from the instrument 2 Hold the plate or array card up to a light source and confirm that all wells contain the same volume of fluid If there are differences in fluid volumes check the heat seal of the wells with lower volumes for signs of damage or evaporation Compare the position of the wells that have lower volumes with the outliers that you have removed from the plate or array card If the well positions coincide the heat seal on the consumable may be defective resulting in the evaporation of the associated samples 3 Contact Life Technologies t
56. properties and excitation energy between the individual wells QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Preparing the calibration plate or array card Prepare the dye calibration plates Chapter 2 Calibrate the Instrument Dye calibration IMPORTANT Wear powder free gloves and safety glasses when you prepare plates or array cards Prepare the calibration consumable appropriate for your QuantStudio 6 or 7 Flex System m Prepare the dye calibration plates 0 ees 53 E Preparing array cards for instrument calibration 000 36 Materials required e Spectral calibration plates Spectral Calibration Plate with FAM Dye Spectral Calibration Plate with VIC Dye Spectral Calibration Plate with ROX Dye Spectral Calibration Plate with NED Dye Spectral Calibration Plate with TAMRA Dye Spectral Calibration Plates as required by the experiment that you intend to run e Centrifuge with plate adapter e Powder free gloves e Safety goggles Prepare the plate IMPORTANT Before performing a dye calibration you must perform an ROI calibration a background calibration and a uniformity calibration IMPORTANT Wear powder free gloves and safety glasses when you prepare the plate 1 Remove the dye calibration plate from the freezer then thaw it at room temperature for approximately 30 minutes IMPORTANT Use t
57. reach the required temperature 8 When the run is complete and the Analysis screen displays confirm the status of the calibration The analysis status indicates the success of the calibration where passed indicates that the run produced viable calibration data and failed indicates that the run did not produce data or that the data it collected is unusable Analysis status Action Passed Click Next Failed Troubleshoot the failed calibration as described in Uniformity calibration troubleshooting on page 72 9 Select the QC tab to review the quality check summary Note The QC tab can provide information on the cause of a failed calibration 50 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Uniformity calibration 10 Unload the calibration plate or array card a After the calibration touch z on the touchscreen to eject the plate or array card Note If the instrument does not eject the plate or array card remove it as explained in Uniformity calibration troubleshooting on page 72 b Remove the calibration plate or array card from the instrument tray and discard it A WARNING PHYSICAL INJURY HAZARD During instrument operation the plate or array card temperature can reach 100 C Allow the consumable to cool to room temperature before removing c Touch on the instrument touchscreen to close the instrument tray
58. signature File Name Update Update the file name File Version Update Update the file version 140 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix E Security Audit and Electronic Signature Audit report generation t Creates one role assignment record for each permission in a role Viewing audit 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software open an histories from an experiment eds template edt or study edm file experiment 2 From the open file click Audit then click Audit Records template or study Studies only Select the audit records of interest e Study to view the audit records for the study e The name of an experiment to view the audit records for the experiment From the Audit Records screen of the open file you can perform the actions in the following table To Action Display the audit Optional Filter the table history 1 Check the Filter by check box 2 Enter criteria for the records of interest such as a date range a user name or a type of action 3 Click Refresh To view details for a specific record 1 Click the row in the list on the left to view the details of the record in the table on the upper right 2 Click any row to view details for individual records in the table on the bottom right Export audit records 1 From the table on the left select the records to be exported e Click in the tabl
59. that anyone using this product has received instructions in general safety practices for laboratories and the safety information provided in this document Before using an instrument or device read and understand the safety information provided in the user documentation provided by the manufacturer of the instrument or device Before handling chemicals read and understand all applicable Safety Data Sheets SDSs and use appropriate personal protective equipment gloves gowns eye protection etc To obtain SDSs see the Documentation and Support section in this document QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 173 Appendix Safety Symbols on this instrument Symbols on this instrument Symbols may be found on the instrument to warn against potential hazards or convey important safety information In this document the symbol is used along with user attention words described in the About This Guide section to highlight important safety information The following table gives the meaning of these symbols English Francais Caution risk of danger Consult the manual for further safety information Attention risque de danger Consulter le manuel pour d autres renseignements de s curit Caution hot surface Attention surface chaude Caution risk of electrical shock Attention risque de choc lectrique Laser radiation Rayonne
60. the Ethernet cable to connect the computer to the nearest network port 2 Power on the computer then log in using a user account that belongs to the Administrators user group From the desktop right click My Network Places then select Properties Right click Local Area Connection then select Properties Select Internet Protocol TCP IP then click Properties On OY ae Set the Internet Protocol TCP IP Properties for either DHCP or Static IP communication Network configuration DHCP Action Select Obtain an IP address automatically 2 Set the DNS address If the computer obtains DNS addresses e Automatically Select Obtain DNS server address automatically e Statically Select Use the following DNS address enter the address of the preferred and alternate DNS servers if available Static IP 1 Select Use the following IP address 2 In the IP Address field enter the static IP address 3 If necessary enter a subnet mask 4 If necessary enter a static gateway address in the Default Gateway field QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 119 Appendix C Networking Monitor the QuantStudio 6 or 7 Flex System Install the QuantStudio 6 and 7 Flex Real Time PCR System Software 7 If your network requires advanced TCP IP setup such as WINS define the settings a Click Advanced in the Internet Protocol TCP IP Propert
61. the endogenous control Comparative Cy experiments or the Q Avg of the target divided by the Q Avg of the endogenous control Relative Standard Curve experiments The relative standard curve equivalent of the ACy mean value found in Comparative Cy experiments computed as the geometric mean The relative standard curve equivalent of the ACy SE value found in Comparative Cr experiments computed as the geometric standard error of the mean Fluorescence signal from the reporter dye normalized to the fluorescence signal of the passive reference dye usually ROX dye on Life Technologies instruments A measurement such as a Cy that deviates significantly from the measurement of the other replicates for that same sample A dye that produces fluorescence signal independent of PCR amplification and that is added to each reaction at a constant concentration Because the passive reference signal should be consistent across all wells it is used to normalize the reporter dye signal to account for non PCR related fluorescence fluctuations caused by minor well to well differences in volume Normalization to the passive reference signal generally results in data with noticeably high precision among technical replicates An illustration of the grid of wells and assigned content in the plate or array card The number of rows and columns in the grid depends on the sample block that you use From the software you can use the plate layout as a s
62. the fuse voltage matches the supply voltage Replace fuses only with the type and rating specified for the unit Improper fuses can damage the instrument wiring system and cause a fire WARNING Ensure appropriate electrical supply For safe operation of the instrument Plug the instrument into a properly grounded receptacle with adequate current capacity Ensure the electrical supply is of suitable voltage Never operate the instrument with the ground disconnected Grounding continuity is required for safe operation of the instrument WARNING Power Supply Line Cords Use properly configured and approved line cords for the power supply in your facility WARNING Disconnecting Power To fully disconnect power either detach or unplug the power cord positioning the instrument such that the power cord is accessible Cleaning and A N CAUTION Cleaning and decontamination decontamination Ifhazardous materials are spilled onto the instrument the instrument should be appropriately decontaminated Using cleaning or decontamination methods other than those recommended by the manufacturer may compromise the safety or quality of the instrument Care should be taken to not use decontamination or cleaning agents which would cause a hazard as a result of a reaction with parts of the equipment or with material contained in it For the protection of others ensure the instrument is properly decontaminated prior t
63. the software connection to the QuantStudio 6 or 7 Flex System if you TM e Change the QuantStudio 6 or 7 Flex System that is connected directly to your computer e Use the touchscreen to change the instrument name or IP address Note To reestablish the connection restart the QuantStudio 6 and 7 Flex Real Time PCR System Software See Transfer experiments templates and results data on page 83 for more information on using QuantStudio 6 and 7 Flex Real Time PCR System Software to transfer experiment results from the QuantStudio 6 or 7 Flex System The calibration reminder settings allow you to configure the QuantStudio 6 and 7 Flex Real Time PCR System Software to alert you by email when the QuantStudio 6 or 7 Flex System requires calibration The notifications settings feature is optional and it does not affect performance IMPORTANT The QuantStudio 6 and 7 Flex Real Time PCR System Software transmits email only while the QuantStudio 6 or 7 Flex System is monitored If the network connection is interrupted the software stops transmitting updates Collect the required information The QuantStudio 6 and 7 Flex Real Time PCR System Software requires access to a Simple Mail Transfer Protocol SMTP server to email calibration reminders Contact your systems administrator or information technology department for the following information e Network address of a SMTP server e A username and passw
64. touch Save amp Start Run to start the experiment In the Start Run screen touch each field as needed to modify the associated parameter then touch Start Run Now to start the experiment Note When the run is complete touch to unload the plate You can download the experiment results to a computer if the QuantStudio 6 or 7 Flex System is connected to a network or you can copy the data to a USB device see Transfer experiments templates and results data on page 83 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Transfer You can transfer experiments templates and results experiments data to from the QuantStudio 6 and 7 Flex Systems using a USB flash drive Before transferring data you must plug the drive into the USB port below the touchscreen templates and results data IMPORTANT Do not use the USB ports on the rear panel of the QuantStudio 6 and 7 Flex Systems The rear USB ports are only for use by Life Appendix A Manual Instrument Operation Operate the instrument from the touchscreen Technologies personnel to service the instrument Transfer templates from a USB drive 1 2 Plug a USB drive into the USB port below the touchscreen If the instrument is in standby touch the QuantStudio 6 or 7 Flex System touchscreen to activate it then press In the Main Menu touch View Templates In the Browse Experiments scree
65. trim the fill reservoirs from the array card assembly using scissors Trim the foil array card so that the edge is even with the plastic carrier IMPORTANT Completely remove the fill reservoirs from the array card so that the edge is free of residual plastic The plastic from the fill reservoirs that extends beyond the edge of the card can prevent the array card from seating properly on the sample block and can affect amplification Correct trim Incorrect trim Sry aa f A i 9 Repeat step 8 to seal the remaining array cards IMPORTANT If an array card is sealed improperly the it can leak and contaminate the sample block and or it can cause the associated calibration or RNase P test to fail IMPORTANT As you seal the remaining filled array cards store them in a dark place Do not expose the array cards to light until you are ready to use them The dyes in the array cards are photosensitive Prolonged exposure to light can diminish the fluorescence of the dye QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 39 2 Chapter 2 Calibrate the Instrument ROI calibration ROI calibration A region of interest ROI calibration maps the positions of the wells on the sample block of the instrument The software uses the ROI calibration data to associate increases in fluorescence during a run with the wells on the plate or array card Th
66. used as the quencher Regression coefficient calculated from the regression line in the standard curve An important quality value the R value indicates the closeness of fit between the standard curve regression line and the individual Cy data points from the standard reactions A value of 1 00 indicates a perfect fit between the regression line and the data points A plot of raw fluorescent signal as detected through each emission filter used to view raw data for individual wells and at individual cycles A solution that contains all components to run the PCR reaction except for the template sample standard or control Also called a PCR cocktail The PCR reaction components used to amplify the target and to detect amplification Process of collecting fluorescence data during PCR Data from the real time PCR are used to calculate results for quantification experiments or to troubleshoot results for genotyping or presence absence experiments In relative standard curve and Comparative Cy AAC experiments the sample used as the basis for relative quantification results Also called the calibrator Type of calibration in which the software maps the positions of the wells on the sample block of the instrument The software uses the ROI calibration data to associate increases in fluorescence during a run with specific wells of the plate or array card A calibration image for each individual filter must be generated to account for
67. y intercept 196 The Life Technologies name for the electronic records that comprise all information about a particular plate or array card including metadata name barcode comments plate setup well contents assay definitions run method thermal cycling protocol run results analysis protocol analysis results audit records and other consumable specific data Experiment document files have the eds suffix In Amplification Plots the level of fluorescence above the baseline and within the exponential growth region The PCR cycle number at which the fluorescence meets the threshold in the Amplification Plot See melting temperature Tm Instrument display that you touch to control the instrument Type of calibration in which the software measures sample block uniformity The calibration generates data that compensate for the physical effects of the QuantStudio 6 and 7 Flex Systems filters on data collected during a experiment From the software the task for the target in wells that contain the sample being tested In quantification experiments the task for the target in wells that contain a sample with unknown target quantities In genotyping experiments the task for the SNP assay in wells that contain a sample with an unknown genotype In presence absence experiments the task for the target in wells that contain a sample in which the presence of the target is not known In melt curve experiments the task for the target
68. 2 When you are finished touch EY to return to the Main Menu You can use the QuantStudio 6 or 7 Flex System touchscreen to view instrument version data such as instrument serial number and version numbers for most instrument components and firmware 1 From the Main Menu of the instrument touchscreen touch Tools then touch About the Instrument 2 When you are finished touch EY to return to the Main Menu QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 91 Appendix A Manual Instrument Operation Administrate the instrument from the touchscreen Enable disable instrument security View the instrument log 92 The QuantStudio 6 and 7 Flex Systems feature a secure mode that can be enabled to restrict local instrument functionality When security is enabled use of the touchscreen is restricted to administrative functions that change the instrument settings After the QuantStudio 6 or 7 Flex System is secured you must enter an administrator password to modify the instrument settings use the firmware tools or deactivate the secure mode IMPORTANT If you enable or disable the QuantStudio 6 and 7 Flex Systems security auditing and electronic signature feature you must similarly enable or disable the QuantStudio 6 and 7 Flex Real Time PCR System Software security see page 131 The QuantStudio 6 and 7 Flex Real Time PCR System Software cannot connect to QuantStudio
69. 21 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Contents APPENDIX D Power On or Off Store and Move 123 Place the QuantStudio 6 or 7 Flex System on standby 0 0 000 c eee cece eee eens 124 Power on the QuantStudio 6 or 7 Flex System 0 00 c cece teen eects 124 Power off the QuantStudio 6 or 7 Flex System 00 0 c cece cece eee eee renee ees 125 Store the QuantStudio 6 or 7 Flex System 0 00 e cece cece ete eee rrr 126 Materials required 0 ccc cee eee ee eee eee e eee e tees 126 Prepare the QuantStudio 6 or 7 Flex System n n nuanua nnan cece cence eee eens 126 Move the QuantStudio 6 or 7 Flex System 0 2 0 6 cece cnn een nett eens 127 How to handle the sample block and heated cover 00000e eee cece eeeeeeees 127 Prepare the QuantStudio 6 or 7 Flex System components 0 00eeeeeeeee 127 Move the QuantStudio 6 or 7 Flex System 0 0 cece cece eee eee eee ences 128 Reinstall the QuantStudio 6 or 7 Flex System 00000 cece eee een eee eee 128 APPENDIX E Security Audit and Electronic Signature 129 Administrator overview 0 cee cent enn teen ene e teen e teens 130 Example applications aseessa gran cetlee ated a da leduedth ed cera gee 130 Configure the security system 002 e eens 131 Access the Security screen and enable or disable security
70. 37 audited objects and actions 137 enable or disable 137 export records 139 export settings 145 import settings 145 object audit history 138 141 144 overview 130 purge records 139 restore records 139 system configuration history 138 139 140 141 144 when security is disabled 137 audit users enter reason for change 147 overview 146 Autodiscovery instrument 90 automatic baseline 188 automatic threshold 188 background calibration about 44 188 about the data 44 performing 46 plate preparation 45 troubleshooting 69 background fluorescence 44 backing up instrument settings 85 BADROX quality flag 66 barcode readers 21 barcode scanner 20 171 baseline 188 baseline corrected normalized reporter AR 188 biohazard safety 183 BLFAIL quality flag 66 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 197 Index blocked IPC 188 0 calibration array cards 25 36 background 44 consumables 25 custom dye 152 data 40 44 52 57 dye 52 instrument status viewing 29 kits 160 normalization 57 plates 25 35 reminders 31 33 90 121 ROI 40 schedule 28 uniformity 48 workflow 29 calibration plate background 45 dye 53 normalization 57 ROI 41 48 CE mark 188 chemical safety 182 cleaning safety 179 clearance requirements for instrument components 168 compatibility operating system 24 compatibility third party software 24 computer electrical requirements 169 layout 171 remote m
71. 39 39 PoT 09 01 2013 11 39 39 PST 02 01 2013 11 39 39 PS 09 01 2013 11 50 46 PST 02 01 2013 11 50 46 PS 13 07 2012 11 50 46 ror 13 07 2012 12 05 52 PDT 09 01 2013 12 05 52 PST 02 01 2013 12 05 52 PST ROI 09 01 2013 12 17 14 PST 02 01 2013 12 17 14 PST Background E Normalization 13 07 2012 12 17 14 roy 13 07 2012 13 51 56 PDT 09 01 2013 13 51 56 PST 02 01 2013 13 51 56 PST Normalzation FAM ROY 3 07 2012 12 28 14 PDT 09 01 2013 12 28 14 PST 02 01 2013 12 28 14 PST Uniformity Normalization VIC ROX 13 07 2012 12 38 04 PD 09 01 2013 12 38 04 PST 02 01 2013 12 38 04 PS 13 07 2012 14 27 41 PDT 09 01 2013 14 27 41 PST 02 01 2013 14 27 41 PST Dye Normalization HRM Reminders Separate e mail addresses with Email Addresses Settings Enter e mail addresses for notifications For example john email com Kevin email com 287880008 x QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Guidelines for preparing calibration plates and array cards Guidelines for preparing calibration plates and array cards Observe the following guidelines when preparing calibration plates and array cards e Wear appropriate protective eyewear clothing a
72. 4 If the calibration fails again determine the source of the contamination as explained in How to identify contamination on page 78 Instrument does not eject the background plate or array card it is stuck within the instrument The adhesive cover may have adhered the plate or array card to the heated cover within the instrument Remove the plate or array card from the instrument as explained in Remove a plate stuck within the instrument on page 78 Instrument malfunction Multiple possible causes Contact your local Life Technologies Field Service Office B 6unooysayqnos juauunsjsu ay ayeuqneg za4ajydeyg apIng UONENSIUIUPY pUe aaueualUleW SWAaISAS Yd awl jeay X 4 pue 9 olpnisiueng cL Table 3 Uniformity calibration troubleshooting Problem symptom Possible cause Action Uniformity calibration failed e Plate or array card was centrifuged insufficiently e Plate or array card contains old or insufficient reagents e Abnormally low spectra across all wells of the plate or array card CAUTION PHYSICAL INJURY HAZARD During operation the sample block can reach 100 C Before removing the plate or array card wait until the block reaches room temperature 1 Unload the QuantStudio 6 or 7 Flex System and confirm that you loaded the correct plate or array card into the instrument If not perform the calibration again using the correct type of consumable
73. 6 and 7 Flex Systems that do not match security settings 4 Click Apply Settings Note Security policies apply to all user accounts 1 In the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Security gt Settings In Account Setup specify User Name limits IMPORTANT The software allows spaces in user names Use spaces in user names with caution For information see Spaces in user names and or passwords on page 132 Specify User Password limits a Specify the passwords length limits b Specify password reuse You cannot disable the password reuse restriction QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 131 Appendix E Security Audit and Electronic Signature Configure the security system Set up messaging notifications 132 4 7 c Specify the allowed characters in user passwords spaces and alphabetical numeric uppercase lowercase and special characters commas periods semicolons dashes underscores and tildes In Security Policies specify Password Expiration Account Suspension and Session Timeout settings Note A session times out while a run is in progress if the time out period is exceeded and there is no other user activity In the Open Non Secure Data option select Yes or No to determine whether users can open experiments and templates that were created without security settings Click Set Up Messagin
74. 7 Flex System place them on a clean dry surface or in its shipping container heated cover Prepare the 1 Power off the QuantStudio 6 or 7 Flex System and computer TM QuantStudio 6 or 2 When the QuantStudio 6 or 7 Flex System and computer are powered off 7 Flex System disconnect all QuantStudio 6 or 7 Flex System components and package the components cabling for the move 3 Prepare the QuantStudio 6 or 7 Flex System for the move a Open the QuantStudio 6 or 7 Flex System access door b Firmly press down on the sample block handle pull the sample block from the QuantStudio 6 or 7 Flex System then place it on a clean dry surface c Pinch the handle of the heated cover together then pull the assembly from the QuantStudio 6 or 7 Flex System and place it on a clean dry surface QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 127 Appendix D Power On or Off Store and Move Move the QuantStudio 6 or 7 Flex System d Package the sample block and heated cover assemblies in a clean dust free container Move the Move the QuantStudio 6 or 7 Flex System according to the following guidelines QuantStudio 6 or 7 Flex System Reinstall the 1 QuantStudio 6 or 7 Flex System 128 Ensure that the surface on which you will place the QuantStudio 6 or 7 Flex System can support at least 77 9 0 6 kg 171 5 0 13 Ibs Ensure that the path to
75. 7 Flex Systems Note The QuantStudio 6 Flex System does not support the Array Card block WARNING Use the flat caps for 0 2 mL tubes and 0 1 mL tubes Rounded caps can damage the heated cover Sample block Consumable Reaction volume 96 well plate 0 2 mL MicroAmp Optical 8 Cap Strip MicroAmp 8 Tube Strips 0 2 mL MicroAmp Reaction Tubes without Caps 0 2 mL MicroAmp 96 Well Tray Retainer Set 100 pL MicroAmp Optical Adhesive Film MicroAmp Optical 96 Well Reaction Plate with Bar Code 100 pL 96 well plate 0 1 mL MicroAmp Optical Adhesive Film MicroAmp Optical 96 Well Fast Reaction Plate with Bar Code 50 uL QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 25 1 Chapter 1 Getting Started Interchangeable sample blocks heated covers and plate retainers Sample Concumable Reaction block volume 384 well Notched corner e MicroAmp Optical Adhesive 20 uL Film e MicroAmp Optical 384 Well Reaction Plate with Bar Code plate Array cardt Life Technologies Array Card Tul t QuantStudio 7 Flex System only Interchangeable sample blocks heated covers and plate retainers The QuantStudio 6 and 7 Flex Systems feature a set of interchangeable sample blocks heated covers and plate retainers that allow the instruments to support multiple consumable formats All of the
76. 81 Appendix Safety Chemical safety Chemical safety WARNING GENERAL CHEMICAL HANDLING To minimize hazards ensure laboratory personnel read and practice the general safety guidelines for chemical usage storage and waste provided below and consult the relevant SDS for specific precautions and instructions Read and understand the Safety Data Sheets SDSs provided by the chemical manufacturer before you store handle or work with any chemicals or hazardous materials To obtain SDSs see the Documentation and Support section in this document Minimize contact with chemicals Wear appropriate personal protective equipment when handling chemicals for example safety glasses gloves or protective clothing Minimize the inhalation of chemicals Do not leave chemical containers open Use only with adequate ventilation for example fume hood Check regularly for chemical leaks or spills If a leak or spill occurs follow the manufacturer s cleanup procedures as recommended in the SDS Handle chemical wastes in a fume hood Ensure use of primary and secondary waste containers A primary waste container holds the immediate waste A secondary container contains spills or leaks from the primary container Both containers must be compatible with the waste material and meet federal state and local requirements for container storage After emptying a waste container seal it with the cap provided Characterize by analysis i
77. Analysis screen confirm the status of the calibration The analysis status indicates the success of the calibration where passed indicates that the run produced viable calibration data and failed indicates that the run did not produce data or that the data it collected is unusable Analysis status Action Passed Enter comments in the Comments field click Next Failed Troubleshoot the failed calibration as described in the Normalization calibration troubleshooting on page 74 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 59 60 Chapter 2 Calibrate the Instrument Normalization calibration 10 11 12 13 Select the QC tab to review the quality check summary The QC status indicates the quality of the calibration data where passed indicates that all wells produced data that passed the quality check and failed indicates that one or more wells produced unusable data Note If the calibration failed the QC tab can provide information regarding the cause of the failure Unload the calibration plate or array card a After the calibration touch z on the touchscreen to eject the plate or array card Note If the instrument does not eject the plate or array card remove it as explained in Normalization calibration troubleshooting on page 74 b Remove the calibration plate or array card from the instrument tray and discard it A WARNING PHYSICAL IN
78. B Wrist Rotates materials to either the portrait or landscape positions where mechanism the range of motion is 135 270 total C Grip Consists of two sets of fingers that grip the consumable The fingers close to grasp a consumable and open to release it Robot tower Moves the arm up and down 21 5 in 54 6 cm from 6 5 in 16 5 cm to vertical axis 28 in 71 1 cm above the table Rotary axis Rotates the arm 340 around the base of the Twister Robot Mechanical stops prevent continuous rotation Bar code Scans the bar codes of consumables as they are loaded into the reader QuantStudio 7 Flex System Base cover Removable cover that contains four access bolts which secure the Twister Robot to the Sciclone ALH 3000 base Racks Provide storage for PCR consumables before and after they are run by the QuantStudio 7 Flex System one of three shown Power LED When lit indicates the Twister Robot is powered on QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 21 1 Chapter 1 Getting Started Instrument hardware 22 Rear view Component Description A On Off switch Power switch for the Twister Robot where the states are on or off 0 B Power port 100 240V port that provides power to the Twister Robot RS232 port Provides serial communication with the computer Fuse cover Two T1 6A 250VAC 5 x 20 mm
79. C 61010 2 010 EN 61010 2 010 Safety requirements for electrical equipment for measurement control and laboratory use Part 2 010 Particular requirements for laboratory equipment for the heating of materials IEC 61010 2 081 EN 61010 2 081 Safety requirements for electrical equipment for measurement control and laboratory use Part 2 081 Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes EMC Reference Description Directive 2004 108 EC European Union EMC Directive EN 61326 1 Electrical Equipment for Measurement Control and Laboratory Use EMC Requirements Part 1 General Requirements FCC Part 18 47 CFR U S Standard Industrial Scientific and Medical Equipment AS NZS 2064 Limits and Methods of Measurement of Electromagnetic Disturbance Characteristics of Industrial Scientific and Medical ISM Radiofrequency Equipment ICES 001 Issue 3 Industrial Scientific and Medical ISM Radio Frequency Generators Environmental Reference design Description Directive 2002 96 EC European Union WEEE Directive Waste electrical and electronic equipment Directive 2002 95 EC European Union RoHS Directive Restriction of hazardous substances in electrical and electronic equipment QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 1
80. Calibration then click Start Calibration From the Dye Calibration screen select the dye to calibrate from the Dye Name drop down list then perform the calibration as instructed From the bottom of the Setup tab enter the reagent information for the dye plate or array card that you are using Reagent Information Plate Barcode Reagent Name Reagent Part Number Reagent Lot Number Reagent Expiration Date Check the box when the dye calibration plate has been loaded and when you have ensured you have entered all reagents information correctly am Instrument Con 287880008 x Load the dye plate or array card into the instrument a From the instrument touchscreen touch B to eject the instrument tray b Confirm that the dye plate or array card matches the dye selected in the software then load it into the plate holder Load the plate or array card so that e Well A1 of the plate or array card is in the top left corner of the plate adapter e The barcode faces the front of the instrument QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Dye calibration 00000256 N ININIMNINIIUINNN Note The name of the dye contained by the plate or array card is next to the barcode on the front of it IMPORTANT Plates or array cards should be loaded and unloaded by operators who have been warned of the moving parts hazard and have been ad
81. E LL aping UONENSIUIUPY pUe aaueuajulew SWAaISKS Yq WIL JE Y X 4 PUL 9 olpnisjueng Problem symptom Possible cause Action Well displays the NOSIGNAL flag indicating that the well Missing reaction mix resulting from pipetting error If a well is flagged confirm the results 1 Consider omitting the well from the analysis produced very low or no fluorescence signal 2 Note the location for each flagged well and check each corresponding well in the plate or array card for evaporation or low reaction volume 3 Contact Life Technologies to order a replacement RNase P plate or array card If the replacement RNase P consumable fails contact Life Technologies for assistance Well displays the OFFSCALE e Fluorescent contaminant on 1 Perform a background calibration If you detect fluorescent contamination flag indicating that the the plate or array card or decontaminate the sample block fluorescence signal for one or sample block 2 Contact Life Technologies to order a replacement RNase P plate or array card If the more dyes in the well exceeds e Fluorescent contaminant in replacement consumable fails contact Life Technologies for assistance the instrument s maximum the reaction detectable range for one or more cycles Well displays the OUTLIERRG e Contamination 1 Decontaminate the work area and pipettors flag indicating that the C of the e Improper sealing or seal 2 Contact Life Technologies to order a r
82. Instruments group 3 From the Instrument Manager start the calibration a Click XK Maintenance then click Background b From the Background Calibration screen click Start Calibration 4 Click Next then prepare for the calibration as instructed 5 From the bottom of the Setup tab enter the reagent information for the background plate or array card that you are using Reagent Information Plate Barcode Reagent Name Reagent Part Number Reagent Lot Number Reagent Expiration Date E Check the box when the background calibration plate has been loaded and when you have ensured you have entered all reagents information correctly Bm 6 Load the calibration plate or array card into the instrument a From the instrument touchscreen touch B to eject the instrument tray b Load the calibration plate or array card into the plate holder so that e Well A1 of the plate or array card is in the top left corner of the plate adapter e The barcode faces the front of the instrument A 0000256 MINIMUM IMPORTANT Plates or array cards should be loaded and unloaded by operators who have been warned of the moving parts hazard and have been adequately trained c From the instrument touchscreen touch B to close the instrument tray 7 After loading the plate or array card start the calibration a From the Setup tab select Check the box when the background calibration plate has been loaded then
83. JURY HAZARD During instrument operation the plate or array card temperature can reach 100 C Allow the consumable to cool to room temperature before removing c Touch B on the instrument touchscreen to close the instrument tray From the Normalization Calibration screen click Finish to complete the calibration then click Yes when prompted to save the results Repeat the calibration procedure to perform the remaining normalization calibration Optional Click Print Report in the upper right corner of the screen to print a summary of the calibration results for your records QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Verify the instrument performance Verify the instrument performance When necessary you can perform the RNase P instrument verification test to confirm the performance of the QuantStudio 6 and 7 Flex Systems When to perform We recommend performing an RNase P instrument verification test the test e After moving the instrument to another location e As needed to confirm the function of the instrument About the RNase P The RNase P instrument verification test uses instrument verification kits available kits from Life Technologies The kits differ only in the consumable format for which they are designed an RNase P Instrument Verification Plate for QuantStudio 6 and 7 Flex Systems with 96 384 well sample blocks and an Array Card
84. Plate 61 RNase P test about 61 kits 61 order 160 performing 66 202 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide plate preparation 63 troubleshooting 69 robot 21 components 21 22 racks 22 ROI calibration about 40 about the data 40 performing 42 plate preparation 41 48 preparation 41 44 48 53 57 troubleshooting 69 ROX dye 193 RS232 port 22 run method 193 run experiments 82 S safety alerts on instrument 178 Array Card Staker Sealer 36 barcode scanner 180 biohazard 183 chemical 182 cleaning and decontamination 179 electrical 179 ergonomic 180 instrument 178 labels on instruments 177 lamp replacement 99 laser 180 moving and lifting 128 physical injury 178 repetitive motion 180 standards 181 symbols on instrument 174 workstation 180 sample 193 sample block decontamination 96 handling 96 106 installation 106 location 18 sample definition file about 193 SDSs obtaining 185 Index seal array cards 36 security enable disable 131 instrument setup 92 policies 131 software setup 131 security and auditing 194 security administrator about 130 account setup 131 disable effect on audit and e sig 131 enable disable 131 export settings 145 export user account settings 145 import settings 145 import user account settings 145 notification 131 132 overview 130 security policies 131 spaces in user names 132 user accounts 133 user name restrictions 131 use
85. Power switch for the instrument where the states are on or off 0 F Fuse cover Dual 12 5A Time Lag T 250 VAC 5 x 20 mm electrical fuses that protect the instrument from excessive electrical current For AU NZ only 6 3A Time Lag 250VAC 5 x 20 mm G Power port The 100 240 VAC port that provides power to the instrument Use the Ethernet cable supplied with the instrument to connect the instrument Ethernet port to the network interface card in the computer The QuantStudio 6 and 7 Flex Systems include an optional Handheld Barcode Scanner Part no 4453271 that you can purchase to assist you with data entry The barcode scanner uses a 670 nm Class II laser to scan plates or array cards for only the QuantStudio 7 Flex System and it is capable of reading Code 128 alphanumeric which supports 128 ASCII character barcodes AN WARNING LASER Exposure to direct or reflected laser light can burn the retina and leave permanent blind spots Never look into the laser beam Remove jewelry and anything else that can reflect the beam into your eyes Protect others from exposure to the beam The optional hand held barcode scanner functions as an extension of the keyboard You can use the scanner to scan barcodes into the instrument software To scan a barcode using the hand held barcode scanner 1 Select the field in the instrument software where you want to enter the barcode 2 Hold the hand held barco
86. ROI dialog box select Check the box when the ROI calibration plate has been loaded click Next twice then click START RUN to start the calibration 3 When the run is complete inspect the ROI images a Select the first filter from the Filter drop down list b Record the coordinate of the well that contains the lowest concentration of dye and that is encircled by a ring This well contains the optimal concentration of the custom dye at the given filter c Repeat steps a and b for the remaining filters d After you determine the optimum concentration for each filter determine the optimum concentration for the custom dye Compare the results from all filters then select the concentration that yields the highest possible signal in all filters 4 Discard the plate WARNING PHYSICAL INJURY HAZARD During instrument operation the plate can reach 100 C Allow the plate to reach room temperature before removing 5 In the ROI dialog box click Finish to complete the calibration then click No when prompted to save the results Create a custom IMPORTANT Wear powder free gloves while creating the dye plate dye plate 1 Prepare 2 mL of the custom dye at the concentration determined in Determine optimum dye concentration on page 152 2 Pipet 20 uL of the diluted custom dye to all wells of an optical reaction plate 3 Seal the wells of the reaction plate using an optical adhesive cover 4 Centrifuge the plate for 2 min
87. RY HAZARD During instrument operation the plate or array card temperature can reach 100 C Allow the consumable to cool to room temperature before removing c Touch z on the instrument touchscreen to close the instrument tray Repeat the calibration to calibrate the instrument for the remaining dyes that are present in the experiments that you will be running Optional Click Print Report in the upper right corner of the screen to print a summary of the calibration results for your records QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Normalization calibration Chapter 2 Calibrate the Instrument Normalization calibration When to perform the calibration About the calibration data Preparing the calibration plate or array card Prepare the normalization calibration plates During the normalization calibration the instrument collects and stores the data from the normalization standards Perform a normalization calibration once every 6 months During the normalization calibration the software captures a series of images of each normalization plate or array card using each instrument filter The normalization calibration yields a Pass or Fail result for each normalization consumable used IMPORTANT Wear powder free gloves and safety glasses when you prepare plates or array cards Prepare the calibration consumable appropriate for your QuantStudio 6 or
88. Reagent Lot Number Reagent Expiration Date Check the box when the ROI calibration plate has been loaded and when you have ensured you have entered all reagents information correctly eax reo 287880008 x QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 49 Chapter 2 Calibrate the Instrument Uniformity calibration 6 Load the calibration plate or array card into the instrument a From the instrument touchscreen touch B to eject the instrument tray b Load the calibration plate or array card into the plate holder so that e Well A1 of the plate or array card is in the top left corner of the plate adapter e The barcode faces the front of the instrument 00000256 MIIMINININIMINMNMIN IMPORTANT Plates or array cards should be loaded and unloaded by operators who have been warned of the moving parts hazard and have been adequately trained c From the instrument touchscreen touch to close the instrument tray 7 After loading the plate or array card start the calibration a From the Setup tab select Check the box when the ROI calibration plate has been loaded then click Next b From the Run screen click START RUN IMPORTANT Do not attempt to open the access door during the run The door is locked while the instrument is in operation Note Before starting the calibration the instrument may pause up to 10 minutes to allow the heated cover to
89. Start Collect the required network information Connect the QuantStudio 6 or 7 Flex System to the network Connect the computer to the network Monitor the QuantStudio 6 or 7 Flex System to test the network connection v Finish Collect the required network information Obtain the following information from your network administrator e Network policy for obtaining IP addresses DHCP or static IP IMPORTANT When the QuantStudio 6 or 7 Flex System is set for DHCP APIPA is automatically enabled and the QuantStudio 6 or 7 Flex System self assigns an IP address when no address is supplied by a DHCP server e Ifthe network requires static IP addresses obtain the IP address subnet mask TM and gateway address for the QuantStudio 6 or 7 Flex System QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 117 Appendix C Networking Connect the QuantStudio 6 or 7 Flex System to the network Connect the QuantStudio 6 or 7 Flex System to the network After deciding how to connect the QuantStudio 6 or 7 Flex System to a network set up the QuantStudio 6 or 7 Flex System according to your network policies Materials required Ethernet cable with RJ45 connectors a CAT6 Ethernet cable for a 1000Mbit s network connection or a CAT5 for 100Mbit s connection Define the 1 Use the Ethernet cable to connect the Ethernet port of the QuantStudio 6 or 7 instrument Flex System
90. Studio 6 and 7 Flex Real Time PCR System Software 105 Update the Windows operating system 0 6 6 cee eee 106 Change the sample block 6 cece eens 106 Change the heated Cover 2 ccc enn nee es 108 Change the plate adapter cos iiine i E E EE E E eens 111 IMPORTANT This chapter contains all user service procedures for the QuantStudio 6 and 7 Flex Systems Procedures other than those described in this document must be performed by a qualified Life Technologies Service Engineer QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 95 Appendix B Maintenance Decontaminate the sample block Decontaminate the sample block Materials required How to handle the sample block 96 Perform this procedure to eliminate fluorescent contaminants from the QuantStudio 6 or 7 Flex System sample block Contamination is generally evident in failed background calibrations where one or more wells consistently exhibit abnormally high signals CAUTION PHYSICAL INJURY HAZARD Do not remove the QuantStudio 6 or 7 Flex System cover There are no components inside the instrument that you can safely service yourself If you suspect a problem contact a Life Technologies Service Representative CAUTION PHYSICAL INJURY HAZARD During instrument operation the sample block can reach 100 C Allow the sample block to cool to room temperature before performing the procedure CAUTION B
91. The calibration reminders feature requires a connection between the QuantStudio 6 or 7 Flex System computer and a computer network If you choose to set up the feature as described below ensure that your network has appropriate security measures in place to protect data from threats such as computer viruses IMPORTANT The QuantStudio 6 and 7 Flex Real Time PCR System Software transmits emails only while the QuantStudio 6 or 7 Flex System is monitored If the network connection is interrupted the software will stop transmitting updates The QuantStudio 6 and 7 Flex Real Time PCR System Software requires access to a Simple Mail Transfer Protocol SMTP server to email calibration reminders Contact your systems administrator or information technology department for the following information e Network address of an SMTP server e A username and password for the server if required for access e The Secure Sockets Layer SSL setting of the server on or off 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Preferences 2 From the Preferences dialog box select the SMTP Settings tab 3 Define the settings for the SMTP server a From the Outgoing Mail Server SMTP field enter the network address of a Simple Mail Transfer Protocol SMTP server Optionally you can specify the transmission control protocol TCP port for the server by appending the port number to the server name s
92. Touch Upload Icon select the desired graphic file then touch Done Note The replacement graphic must be a maximum of 48 x 48 pixels and be stored in the portable net graphic PNG format 4 Define the standby time out setting a Select Standby Time out to activate the feature b Touch the Standby Time out field c Enter the number of minutes 1 300 that the QuantStudio 6 or 7 Flex System should remain idle until it enters standby mode then touch Done Note When in standby mode the QuantStudio 6 or 7 Flex System powers off the LCD screen backlight and enters low power mode 5 Define the heated cover temperature setting a Select Cover Idle Temperature to activate the feature b Touch the Cover Idle Temperature field c Enter the temperature 50 0 110 0 C that the heated cover should maintain when the QuantStudio 6 or 7 Flex System is idle then touch Done Note The recommended Cover Idle Temperature is 60 0 C for reaction plate formats and 85 0 C for the array card format 6 Touch Save to save the settings then touch OK when prompted 7 Unplug the USB drive 8 Touch to return to the Main Menu QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 89 Administrate the instrument from the touchscreen Appendix A Manual Instrument Operation Define the You can use the QuantStudio 6 or 7 Flex System touchscreen screen to maintenance e Set the expiration period for
93. USER GUIDE applied biosystems oy Life technologies QuantStudio 6 and 7 Flex Real Time PCR Systems MAINTENANCE AND ADMINISTRATION Publication Number 4489821 Revision A November 2013 ld technologies For Research Use Only Not for use in diagnostic procedures The information in this guide is subject to change without notice DISCLAIMER LIFE TECHNOLOGIES CORPORATION AND OR ITS AFFILIATE S DISC LAIM ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE OR NON INFRINGEMENT TO THE EXTENT ALLOWED BY LAW IN NO EVENT SHALL LIFE TECHNOLOGIES AND OR ITS AFFILIATE S BE LIABLE WHETHER IN CONTRACT TORT WARRANTY OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL INCIDENTAL INDIRECT PUNITIVE MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDI LIMITED USE LABEL LICENSE No 477 Real Time PCR System G BUT NOT LIMITED TO THE USE THEREOF Notice to Purchaser This product is licensed for use under certain pa ent claims owned by the University of Utah Research Foundation and licensed to BioFire Diagnostics Inc No right is conveyed expressly by implication or by estoppel under any other patent claim TRADEMARKS The trademarks mentioned herein are the property of Life Technologies Corporation and or its affiliate s or their respective owners Internet Explore
94. Well Region of Interest ROI and Background Plates Use the consumable e 96 Well Region of Interest ROI 4432626 lt 20 by the expiration date Calibration Plate on the packaging e 96 Well Background Plate 96 Well Normalization Plates with FAM ROX and VIC ROX Dyes e 96 Well Normalization Plate with FAM ROX Dye 4443661 e 96 Well Normalization Plate with VIC ROX Dye RNase P 96 Well Instrument Verification 4432593 Plate 96 Well Background Plate 4481309 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 161 G Appendix G Parts and Materials Kits consumables and accessories 384 well conc rables Conccmebls Pano Storage Shelf life at storage C temperature 384 Well Spectral Calibration Plate with FAM Dye 384 Well Spectral Calibration Plate with VIC Dye 384 Well Spectral Calibration Plate with ROX Dye 384 Well Spectral Calibration Plate with TAMRA Dye 384 Well Region of Interest ROI and Background Plates lt 20 e 384 Well Region of Interest ROI 4432482 Calibration Plate e 384 Well Background Plate 384 Well Normalization Plates with FAM ROX and VIC ROX Dyes e 384 Well Normalization Plate with FAM ROX Dye e 384 Well Normalization Plate with VIC ROX Dye RNase P 384 Well Instrument Verification Plate 384 Well Background Plate 4481310 4432445 4432452 4432458 4443619 Use
95. a Vortex the ROI calibration plate for 5 seconds b Centrifuge the plate for 2 minutes at lt 1500 rpm IMPORTANT The ROI calibration plate must be well mixed and centrifuged QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Perform the uniformity calibration Chapter 2 Calibrate the Instrument Uniformity calibration c Confirm that the liquid in each well of the ROI calibration plate is at the bottom of the well If not centrifuge the plate again at a higher rpm and for a longer period of time Correct Incorrect Liquid is at e Not centrifuged with enough force or bottom of well Not centrifuged for enough time From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab click Instrument Console From the Instrument Console select the icon for your instrument then click Manage Instrument Note If the Manage Instrument button is inactive add your QuantStudio 6 or 7 Flex System to the My Instruments group From the Instrument Manager start the calibration a Click XK Maintenance then click Uniformity b From the Uniformity Calibration screen click Start Calibration Click Next then prepare for the calibration as instructed From the bottom of the Setup tab enter the reagent information for the ROI plate or array card that you are using Reagent Information Plate Barcode Reagent Name Reagent Part Number
96. account settings 145 installation halogen lamp 99 heated cover 108 instrument fuses 102 license keys 104 network 114 operating system updates 106 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 199 Index plate adapter 106 111 software updates 105 third party software 24 instrument accessories 160 APIPA support 114 Autodiscovery 90 barcode scanner 20 171 calibration schedule 28 calibration workflow 29 control monitor over anetwork 114 data collection 16 data transfer 121 date time setting 88 DHCP support 114 dye calibration 152 electrical requirements 169 environmental requirements 169 Ethernet port 114 exhaust venting 169 filters 17 fuse replacement 102 heated cover temperature 88 icon 88 installation specification 63 IPV4LL 114 layout and connections 171 log 92 maintenance 85 mDNS DNS support 114 moving 127 name setting 88 network setting 90 networking 114 118 power line regulator 23 power on off 124 security 92 self test 86 settings 85 Smart Monitoring 90 specifications 168 standby 124 standby time out 88 static IP support 114 statistics 91 status viewing 29 storage 126 surge protector 23 system shortcuts 91 touchscreen 80 verification 36 64 Instrument Console 190 Instrument Manager 190 instrument safety 178 internal positive control IPC 190 IP settings Ethernet port 90 IPv4 link local IPV4LL 114 is sign
97. acturer Life Technologies Note For information and instructions on performing experiments on the QuantStudio 6 and 7 Flex Real Time PCR Systems refer to the QuantStudio 6 and 7 Flex Real Time PCR System Software Getting Started Guide Pub no 4489822 and the High Resolution Melt Module for QuantStudio 6 and 7 Flex Real Time PCR System Software Pub no 4489823 This user guide is written for laboratory staff who operate and maintain the QuantStudio 6 and 7 Flex Real Time PCR Systems TM This guide assumes that your QuantStudio 6 and or 7 Flex System has been installed by a Life Technologies service representative This guide also assumes that you have e Familiarity with Microsoft Windows operating system e Knowledge of techniques for handling and preparing nucleic acid samples for PCR e A general understanding of data storage file transfers and copying and pasting QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 11 About This Guide User attention words User attention words Four user attention words may appear in this document Each word implies a particular level of observation or action as described below Note Provides information that may be of interest or help but is not critical to the use of the product IMPORTANT Provides information that is necessary for proper instrument operation or accurate chemistry kit use CAUTION Indicates a pote
98. ad then touch Done 3 Assign the e P addresses for the DNS Servers primary and secondary e Subnet Mask setting e Default Gateway setting 5 Touch Save to save the settings then touch OK when prompted 6 Touch B to return to the Main Menu TM You can use the QuantStudio 6 or 7 Flex System touchscreen to map the shortcut buttons that appear in the Main Menu You can configure shortcuts to automatically open specific files and folders so that you can access data quickly and easily without having to navigate to it 1 Ifthe instrument is in standby touch the QuantStudio 6 or 7 Flex System touchscreen to activate it then press 2 In the Main Menu configure the shortcuts as desired To add a shortcut a Touch the shortcut of interest then touch gp Set Shortcut b Touch i From Templates to link to a specific template file or touch From Folders to link to a folder c Touch the desired template file or folder to configure the shortcut To delete a shortcut touch the shortcut of interest then touch ii Remove Shortcut or touch Remove All to delete all shortcuts 3 When you are finished configuring the shortcuts touch to return to the Main Menu You can use the QuantStudio 6 or 7 Flex System touchscreen to view usage statistics on the heated cover lamp and other instrument components 1 From the Main Menu of the instrument touchscreen touch Tools then touch Show Statistics
99. an reduce or prevent effects such as fatigue pain and strain Minimize or eliminate these effects by configuring your workstation to promote neutral or relaxed working positions CAUTION MUSCULOSKELETAL AND REPETITIVE MOTION HAZARD These hazards are caused by potential risk factors that include but are not limited to repetitive motion awkward posture forceful exertion holding static unhealthy positions contact pressure and other workstation environmental factors To minimize musculoskeletal and repetitive motion risks e Use equipment that comfortably supports you in neutral working positions and allows adequate accessibility to the keyboard monitor and mouse e Position the keyboard mouse and monitor to promote relaxed body and head postures QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix Safety Safety and electromagnetic compatibility EMC standards Safety and electromagnetic compatibility EMC standards The instrument design and manufacture complies with the standards and requirements for safety and electromagnetic compatibility as noted in the following table Safety Reference Description EU Directive 2006 95 EC European Union Low Voltage Directive IEC 61010 1 EN 61010 1 UL 61010 1 CSA C22 2 No 61010 1 Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements IE
100. anage electronic signature s s s usss rreren Generate e signature reports 6 eee Export and import user security audit and e signature settings User OVErvieW saien a e a a eect eee eee e eens QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Security Audit and Electronic Signature 129 Appendix E Security Audit and Electronic Signature Administrator overview Administrator overview Example applications 130 IMPORTANT Security Audit and Electronic Signature SAE is a separately licensed module available only on purchase If your system requires this module contact Life Technologies The feature is disabled by default even after the installation of the license and needs to be enabled The Security Audit and Electronic Signature SAE module is a component of the QuantStudio 6 and 7 Flex Real Time PCR System Software that allows you to configure the QuantStudio 6 and 7 Flex Systems to meet specific requirements The module provides the following functionality Security Controls user access to the software A default Administrator user account is provided and additional user accounts and permissions can be user defined Note You can enable or disable system security globally Note The default password for the Administrator user account is Administrator however the password can be changed during installation Auditing Tracks chang
101. ange the notification settings 122 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Power On or Off Store and Move Place the QuantStudio 6 or 7 Flex System on standby 64 124 Power on the QuantStudio 6 or 7 Flex System 6 66 eee eens 124 Power off the QuantStudio 6 or 7 Flex System 2 6 6 eee eee eee 125 Store the QuantStudio 6 or 7 Flex System 6 6 6 eee eee 126 Move the QuantStudio 6 or 7 Flex System 6 66 cece eee eee 127 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 123 Appendix D Power On or Off Store and Move Place the QuantStudio 6 or 7 Flex System on standby Place the QuantStudio 6 or 7 Flex System on standby If left unattended the QuantStudio 6 or 7 Flex System automatically enters standby mode to conserve power To enter standby mode manually touch 8J on the QuantStudio 6 or 7 Flex System touchscreen Power on the QuantStudio 6 or 7 Flex System To power on the QuantStudio 6 or 7 Flex System from a powered off state 1 124 Touch anywhere on the touchscreen to determine if the QuantStudio 6 or 7 Flex System is in standby mode Does the touchscreen display the Standby screen after you touch it e Yes The instrument is ready for use Go to step 4 e No Go to step 2 to power on the instrument TM Power on the QuantStudio 6 or 7 Flex System Togg
102. ata for each sample or set of replicates as follows target QAvg endogenous control QAvg A user defined biological grouping A replicate group may be a set of identical reactions in a experiment Total number of identical reactions containing identical components and identical volumes A fluorescent dye used to detect amplification With reagents the reporter dye is attached to the 5 end An oligonucleotide that flanks the 3 end of the amplicon The reverse primer and the forward primer are used together in PCR reactions to amplify the target An enzyme that converts RNA to cDNA See normalized reporter Rn A dye supplied by Life Technologies which is used as a passive reference in some experiments Definition of the reaction volume and the thermal profile for the instrument run The run method specifies the temperature time ramp and data collection points for all steps and stages of the instrument run The biological tissue or specimen that you are testing for a target gene A tab delimited file txt or Microsoft Excel file xls or xlsx that contains the sample name and custom sample properties for a single experiment 193 Glossary security auditing and e signature serial factor slope stage standard standard curve standard curve method 194 A separately licensed software module that provides e System Security Controls user access to the software Provides a default A
103. ate for calibration a In the plate layout select the wells of the plate b Inspect the raw data For each spectrum verify that the peak is e Within the detectable range for the QuantStudio 6 and 7 Flex Systems e Free of irregular spectral peaks e Present at the correct filter for the dye Note Among wells containing the same dye variations in spectral position and peak position are caused by minor differences in the optical properties and excitation energy between the individual wells 8 Verify the status of the calibration If the calibration Passed If all spectra are acceptable finish the calibration a Click Next b Enter any comments you have in the Comments field click Finish then click Yes when prompted to save the calibration results Failed Create another custom dye plate using the next dye concentration greater than the concentration determined in Determine optimum dye concentration on page 152 then perform the calibration again QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 155 Appendix F Calibration Consumable Preparation Create a custom dye plate for calibration 156 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Parts and Materials E Howto orders 34 tek cee ets bee ae nes Se oe Path one 158 E Kits consumables and accessories 0 0 eee cc raran 160 E General use materials and consumabl
104. ation B Note Unknown population A refers to the 5 000 copy population and unknown population B refers to the 10 000 copy population in the RNase P plate QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Installation specification Prepare the RNase P plate Chapter 2 Calibrate the Instrument Verify the instrument performance The QuantStudio 6 or 7 Flex System passes the installation specification if the inequality holds and the instrument successfully distinguishes between unknown populations A and B with a statistical confidence level of 99 7 As shown in the following table you can omit a limited number of outlier wells from the unknown populations to meet the installation specification Maximum number of outlier wells that can be removed Sample block Unknown Unknown Standards No template population At population Bt STD amp controls NTC 96 well platett 6 6 1 0 384 well plate 10 10 2 0 Array cardtt 4 4 4 0 t 5 000 copy population for 384 well plates 800 copy population for array cards t 10 000 copy population for 384 well plates 1 4600 copy population for array cards Maximum number of wells that can be removed from each standard population tt Standard 96 well plates or Fast 96 well plates tt QuantStudio 7 Flex System only Materials required e RNase P Instrument Verification Plate e Centrifuge with plate adapter e Powder free gloves
105. because some required signatures are missing The Following e Signatures must be collected before this operation can be performed Reviewed and Approved Plate Set Up by 2 Administrator s Before the run can start two administrators must sign If a user with an incorrect user role signs the message is displayed again Generate e signature reports You can use the QuantStudio 6 and 7 Flex Real Time PCR System Software to generate reports of e signature history from open experiment eds or template edt files Task Description Display the e sig records From the QuantStudio 6 and 7 Flex Real Time PCR System Software open an experiment or template file From the open experiment click Sp Audit then click E Signatures Optional Click any row to view details for individual signatures Save or print e sig records From the QuantStudio 6 and 7 Flex Real Time PCR System Software open an experiment or template file From the open experiment click Gp Audit then click E Signatures 3 From the table select the record to be saved or printed Save or print the record e Click H Save select a location for the export file enter a name for the file then click Save or e Click gh Print Click OK in the confirmation message Save or print the table of e signature events From the QuantStudio 6 and 7 Flex Real Time PCR System Software open an exper
106. box displayed when a user performs an audited action 1 To require users to select a pre defined reason in the Audit Reason dialog box displayed when a user performs an audited action enable Require users to select a reason to change from the list Users are not permitted to enter a reason 2 As needed click Create or select a reason from the list then click Edit or Delete QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 137 Appendix E Security Audit and Electronic Signature Audit report generation Audit report generation Viewing audit histories from the Security Settings dialog box You can use the QuantStudio 6 and 7 Flex Real Time PCR System Software to generate reports of audit history from both the Security Settings dialog box and from open experiments templates or studies m Viewing audit histories from the Security Settings dialog box 138 m Viewing audit histories from an experiment template or study 141 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Security gt Settings 2 From the Security Settings dialog box select the Audit tab then click View Reports Note To access the Audit Reports screen the user role for an account must have the Configure the security and audit feature permission Users without the permission can view object audit histories for individual entries i
107. brate the Instrument Normalization calibration 6 Load the calibration plate or array card into the instrument a From the instrument touchscreen touch to eject the instrument tray b Confirm that the normalization plate or array card matches the selection in the software then load it into the plate holder so that e Well A1 of the plate or array card is in the top left corner of the plate adapter e The barcode faces the front of the instrument 00000256 MMMM Mt Note The dyes contained in each plate or array card appear next to the barcode on the front of it IMPORTANT Plates or array cards should be loaded and unloaded by operators who have been warned of the moving parts hazard and have been adequately trained c From the instrument touchscreen touch z to close the instrument tray 7 After loading the plate or array card start the calibration a From the Normalization Calibration screen tab select Check the box when the normalization calibration plate has been loaded then click Next b From the Run screen click START RUN IMPORTANT Do not attempt to open the access door during the run The door is locked while the instrument is in operation Note Before starting the calibration the instrument may pause up to 10 minutes to allow the heated cover to reach the required temperature 8 When the run is complete and the QuantStudio 6 and 7 Flex Real Time PCR System Software displays the
108. card to the heated cover within the instrument Remove the plate or array card from the instrument as explained in Remove a plate stuck within the instrument on page 78 Instrument malfunction Multiple possible causes Contact your local Life Technologies Field Service Office juawnujsu ay ayeuqneg Zz 4ajdeyg 6unooysayqnos E N ow aping UONENSIUIUPY pUe aaueuajulew SWAaISKS Yq WIL JE Y X 4 PUL 9 olpnisjuenD Table 4 Dye calibration troubleshooting Problem symptom Possible cause Action Dye calibration failed One or more raw spectra are at or below the detectable threshold for the calibration e Dye plate or array card was centrifuged insufficiently e Dye plate or array card contains old or insufficient reagents CAUTION PHYSICAL INJURY HAZARD During operation the sample block can reach 100 C Before removing the plate or array card wait until the block reaches room temperature 1 Unload the QuantStudio 6 or 7 Flex System and view the wells of the plate or array card If the liquid in the wells of the consumable is not e At the bottom of the wells centrifuge the plate or array card for a longer time then repeat the calibration e Equivalent in volume the plate or array card is not sealed and the reagents have evaporated Discard the consumable and run another 2 If the dye calibration plate or array card appears to be normal discard it and run anothe
109. card is in the top left corner of the adapter e The barcode faces the front of the instrument 00000256 N INININNINIIONIMN IMPORTANT Plates and array cards should be loaded and unloaded by operators who have been warned of the moving parts hazard and have been adequately trained c From the instrument touchscreen touch B to close the instrument tray 66 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Verify the instrument performance 7 After loading the plate or array card start the instrument verification test a From the Overview screen select Check the box when the RNase P plate has been loaded then click Next b From the Run screen click START RUN to start the test IMPORTANT Do not attempt to open the access door during the run The door is locked while the instrument is in operation Note Before starting the instrument verification test the instrument may pause up to 10 minutes to allow the heated cover to reach the required temperature 8 When the run is complete and the software displays the Analysis screen confirm the status of the run Analysis status Action Passed The QuantStudio 6 or 7 Flex System passed the RNase P run Failed The QuantStudio 6 or 7 Flex System failed the RNase P run Review the data for outliers If the run fails the software may have included
110. click Next 46 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Background calibration b From the Run screen click START RUN IMPORTANT Do not attempt to open the access door during the run The door is locked while the instrument is in operation Note Before starting the calibration the instrument may pause up to 10 minutes to allow the heated cover to reach the required temperature 8 When the run is complete and the QuantStudio 6 and 7 Flex Real Time PCR System Software displays the Analysis screen confirm the status of the calibration The analysis status indicates the success of the calibration where passed indicates that the run produced viable calibration data and failed indicates that the run did not produce data or that the data it collected is unusable Analysis status Action Passed Click Next Failed Troubleshoot the failed calibration as described in Background calibration troubleshooting on page 71 Note Abnormal spectra or abnormally high background fluorescence can indicate the presence of contamination on the plate or array card or sample block which can cause the calibration to fail 9 Select the QC tab to review the quality check summary The QC status indicates the quality of the calibration data where Passed indicates that all wells produced data that passed the quality check and Failed i
111. d computer running the QuantStudio 6 and 7 Flex Real Time PCR System Software can transfer experiments to and from an instrument begin or stop a run and perform some maintenance functions During a run the Remote Monitoring feature of the software can be used to view the run status temperature and amplification data in real time Note Remote monitoring does not allow you to control the QuantStudio 6 or 7 Flex System The QuantStudio 6 or 7 Flex System features a Gigabit Ethernet port for direct communication with the QuantStudio 6 or 7 Flex System computer and for network communication When the QuantStudio 6 or 7 Flex System is connected to a network computers on the network that run the QuantStudio 6 and 7 Flex Real Time PCR System Software can e Send and download experiments to and from the QuantStudio 6 or 7 Flex System Run experiments on the QuantStudio 6 or 7 Flex System e Remote monitor the QuantStudio 6 or 7 Flex System as it performs runs The Ethernet port of the QuantStudio 6 or 7 Flex System supports e Static IP network service with subnet mask primary and secondary data network service DNS and default gateway settings or dynamic host configuration protocol DHCP network service e mDNS DNS for local domains Note Because mDNS is limited to direct network connections a QuantStudio 6 or 7 Flex System set for mDNS may not be visible to other nodes that are separated by a rout
112. dd the custom dye to the software 0 cece eect ene eee e eae 154 APPENDIX G Parts and Materials 0 cece eee eee 157 PONTOD Sens aa a dan mand fog Olen ard dan aaa Shea DN goad end creel E E 158 How to order from the Life Technologies website 2 00000 cece cece eee eee 158 How to order from the QuantStudio 6 and 7 Flex Real Time PCR System Software 158 Kits consumables and acceSSOrieS 0 eee cece eee ene eee n eee e ne eneneaes 160 Fast 96 well consumables EERE ANARE AAS EER ENAERE RARR SEREAS 160 976 WellieConsUMables sei iai Tas Seed ieee aa Bee ee Aa e ee ee 161 384 well consumables soras tierna e aaa a GARA CRR Oa aa Ghee 162 Array card consumables 000 0c eee e eee ee eee eee eeeees 163 QuantStudio 6 and 7 Flex Systems accessories 0 02 cece eee eee eee ees 164 QuantStudio 6 and 7 Flex Systems empty plates and array cards 02005 164 General use materials and consumables 0 cece eee e eee eee eee e eens 165 APPENDIX H Instrument Specification and Layout 167 QuantStudio 6 and 7 Flex Systems specifications 0 0 0 cee cee eee eee ees 168 Required clearan s 0 70 74 oocegs oy 4 oo edge at AE eS eee ee 168 Electrical requirements n nannan annn cece cee eee earr 169 Environmental requirements 2 02 ce cece ccc e eee nena 169 Network requirementS 2 c eee n eee een E te
113. de scanner 20 30 cm away from a plate or array card and aim at the center of the barcode then press the trigger Slowly move the scanning beam across the barcode until the scanner emits a high pitched tone When the scanner scans a barcode it automatically e Transmits the alphanumeric equivalent of the barcode to the instrument software The software enters the barcode text wherever the cursor is active e Transmits a carriage return character the equivalent of pressing the Enter key QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Twister Robot components Chapter 1 Getting Started 1 Instrument hardware For more information on the hand held barcode scanner see the user documentation shipped with the barcode scanner IMPORTANT The Applied Biosystems Twister Robot component is supported only by the QuantStudio 7 Flex System The QuantStudio 7 Flex System supports the use of the Applied Biosystems Twister Robot an optional QuantStudio 7 Flex System accessory that consists of the components shown below Note See the Applied Biosystems Twister Robot Automation Accessory User Guide Pub no 4470693 for information on operating calibrating maintaining and integrating the Twister Robot Front view Component Description A Reach axis Moves the grip horizontally 11 25 in 28 5 cm to 19 75 in 50 1 cm from the center of the robot post
114. dministrator user account You can define additional user accounts and permissions e Auditing Tracks changes made to library items actions performed by users and changes to the Security and Audit settings The software automatically audits some actions silently You can select other items for auditing and specify the audit mode Provides reports for audited library items Security and Audit changes and actions e Electronic Signature e signature Controls whether users are permitted prompted or required to provide a user name and password when accessing certain software features You can select which features are controlled and the number of signatures required for access When authorized persons use this feature they are creating a legally binding signature In the software a numeric value that defines the sequence of quantities in the standard curve The serial factor and the starting quantity are used to calculate the standard quantity for each point in the standard curve For example if the standard curve is defined with a serial factor of 1 10 or 10X the difference between any two adjacent points in the curve is 10 fold Regression coefficient calculated from the regression line in the standard curve The slope indicates the PCR amplification efficiency for the assay A slope of 3 32 indicates 100 amplification efficiency See also amplification efficiency EFF and regression line In the thermal profile a group of o
115. e Bleach 10 solution MLS Centrifuge with 96 well plate buckets MLS Cotton or nylon swabs and lint free cloths MLS Ethanol 95 solution MLS Optical clear adhesive film for PCR MLS Pipettors 100 yL and 200 uL with pipette tips MLS Powder free gloves MLS Safety glasses MLS Screwdriver flathead MLS Tissue lint free MLS Deionized water MLS QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 165 G Appendix G Parts and Materials General use materials and consumables 166 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide H Instrument Specification and Layout QuantStudio 6 and 7 Flex Systems specifications s s s snese ran 168 QuantStudio 6 and 7 Flex Systems layout and connections 171 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 167 Appendix H Instrument Specification and Layout QuantStudio 6 and 7 Flex Systems specifications QuantStudio 6 and 7 Flex Systems specifications The figure below summarizes the specifications and requirements for the QuantStudio 6 and 7 Flex Systems For more information refer to the QuantStudio 6 and 7 Flex Systems Site Preparation Guide Component Height Depth Width Weight Instrument 75 0 cm 29 5 in 70 0 cm 27 6 in 53 0 cm 20 9 in 70 kg 154 3 lbs Computer 56 5 cm 22 3 in 54 7 cm
116. e instrument uses a set of optical filters to distinguish the fluorescence emissions gathered during runs The software generates a calibration image for each filter to account for minor differences in the optical path When to perform Perform the ROI calibration once every 6 months the calibration D IMPORTANT After every ROI calibration you must perform in order a background calibration uniformity calibration dye calibration and a normalization calibration About the During the ROI calibration the instrument software captures images of the ROI calibration data calibration plate or array card at each instrument filter An ROI calibration passes if the collected image for each filter distinguishes all wells of the ROI plate or array card Each well in the image must be distinct and visible at the same luminosity relative to the other wells in the image Note You can review the ROI calibration image for each filter set by selecting the desired filter combination from the Filter Set menu of the ROI tab in the Instrument Manager Passing image Failing image EIXE EEIEIE ae 0 0o DOO D000 2 eee e008 SRaERERE RE SR EE EE 9 6 8 Green circles around all wells indicate that Red circles around some of the wells the wells calibrated successfully Each green indicate that the wells did not calibrate The circle indicates that the region of intere
117. e then press Ctrl A to select all the records in the table e Click and drag or press Shift to select continuous rows e Press Ctrl to select discontinuous rows 2 Export the records e Click Export Summary to export only the records in the left table e Click Export Details to export the records in the left table and the associated details 3 Select a location for the export file enter a name for the file then click Save 4 Click OK in the confirmation message Print audit records 1 Click View Report to open the Print Preview dialog box 2 Preview save or print the report e Click Save to save the report as a pdf or html file Enter the file name select a location select the file type then click Save e Click H5 Print to send the report to the printer From the Print dialog box select the printer and print options then click OK 3 Click to close the Print Preview dialog box QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 141 Appendix E Security Audit and Electronic Signature Manage electronic signature Manage electronic signature Access the e signature settings screen and enable or disable e sig Configure the meanings of the electronic signatures 142 Use the Security screen to disable and enable electronic signature Note Electronic signature is disabled by default To enable or disable electronic signature 1 From the QuantStudio 6 and 7 Flex Real
118. e block on a clean dry surface 5 Clean the contaminated wells of the sample block using deionized water Pipet a small volume of deionized water into each contaminated well a b In each well pipet the water up and down several times to rinse the well A Pipet the water to a waste beaker d Use a cotton swab to scrub inside of each contaminated well e Use a lint free cloth to absorb the excess deionized water QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 97 98 Appendix B Maintenance Decontaminate the sample block 6 Load the sample block into the QuantStudio 6 or 7 Flex System then close the access door IMPORTANT After installing the sample block confirm that the indicator on the left side of the sample block is positioned behind the red line on the instrument rail If the indicator is forward of the red line push the sample block into the QuantStudio 6 or 7 Flex Instrument until it is seated correctly Close the access door IMPORTANT Confirm that the access door is completely closed The QuantStudio 6 and 7 Flex Real Time PCR System Software displays an error message if the door is not completely closed and latched or if the sample block is not seated correctly Plug in then power on the QuantStudio 6 or 7 Flex System Perform a background calibration to confirm that you have eliminated the contamination If the contamination r
119. e calibration the instrument may pause up to 10 minutes to allow the heated cover to reach the required temperature 8 When the run is complete and the software displays the Analysis screen select each filter from the Filter Set drop down list then confirm that the corresponding ROI Image displays a green circle around each well area 9 After you inspect all ROI images confirm the status of the calibration where passed indicates that the run produced viable calibration data and failed indicates that the run did not produce data or that the data it collected is unusable Analysis status Action Passed Click Next Failed Troubleshoot the failed calibration as described in ROI calibration troubleshooting on page 70 10 Unload the calibration plate or array card a After the calibration touch z on the touchscreen to eject the plate or array card Note If the instrument does not eject the plate or array card remove it as explained in ROI calibration troubleshooting on page 70 b Remove the ROI calibration plate or array card from the instrument tray and store it in the dark at room temperature until you are ready to perform the uniformity calibration A WARNING PHYSICAL INJURY HAZARD During instrument operation the plate or array card temperature can reach 100 C Allow the consumable to cool to room temperature before removing c Touch z on the instrument touchscreen to close the instrumen
120. e color filter set Features a decoupled six by six color filter set About the QuantStudio 6 and 7 Flex Real Time PCR Systems The QuantStudio 6 and 7 Flex Systems use fluorescent based polymerase chain reaction PCR reagents to provide e Quantitative research detection of target nucleic acid sequences targets using real time analysis e Qualitative research detection of targets using post PCR endpoint analysis e Qualitative analysis of the PCR product achieved by melt curve analysis that occurs post PCR Data collection The QuantStudio 6 and 7 Flex Systems collect raw fluorescence data at different points during a PCR depending on the type of run that the QuantStudio 6 and 7 Flex Systems perform Run type Data collection point Real time Standard curve The QuantStudio 6 and 7 Flex Systems collect data runs following each extension step of the PCR Relative standard curve Comparative Cy AAC7 Melting curve 16 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide About the QuantStudio 6 and 7 Flex Real Time PCR Systems Chapter 1 Getting Started Run type Data collection point Post PCR Genotyping The QuantStudio 6 and 7 Flex Systems collect data endpoint 1 Before the PCR For presence absence PUNS experiments data collection before the PCR is optional but recommended Prese
121. e detail to integrate the QuantStudio 6 or 7 Flex Systems into all possible network architectures Because your network may contain advanced features such as a firewall or network domains Life Technologies recommends that you consult a network administrator before connecting the QuantStudio 6 or 7 Flex Systems to your laboratory network QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 113 C Appendix C Networking Networking overview Networking overview Controlling and monitoring networked QuantStudio 6 and 7 Flex Systems About the Ethernet port 114 TM After installing the QuantStudio 6 or 7 Flex System you can connect the QuantStudio 6 or 7 Flex System to a local area network to enhance its functionality This appendix describes how to e Set up the QuantStudio 6 or 7 Flex System for use on a network e Set up a computer for remote monitoring e Test the network connection by engaging the remote monitoring feature When the QuantStudio 6 or 7 Flex System is connected to a network computers on the network that are running the QuantStudio 6 and 7 Flex Real Time PCR System Software can control or monitor it The QuantStudio 6 and 7 Flex Real Time PCR System Software can control up to 4 instruments and monitor up to 10 instruments simultaneously A networked QuantStudio 6 or 7 Flex System can be controlled by only one computer at a time A networke
122. e product of interest Instrument parts 1 Go to www lifetechnologies com quantstudio flex or and accessories www lifetechnologies com quantstudio7flex Calibration kits 2 Click Parts and accessories 3 Select the desired components the complete the order as instructed See Kits consumables and accessories on page 160 for a complete list of compatible instrument parts accessories and kits 1 To find your assay on the Life Technologies Store complete the Find Assay pane in the QuantStudio 6 and 7 Flex Real Time PCR System Software a Enter a gene name in the Enter Gene Name field then click Find Assay b In the Find Assay Results dialog box select your assay c Click Apply Assay Selection The selected assay gets added to your shopping list 2 Check that the Experiment Shopping List contains the desired materials other than the assay selected in the previous step and that the quantities are correct then click Order Materials in List QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix G Parts and Materials G How to order 3 In the Order Materials Login dialog box enter your user name and password for the Life Technologies Store then click Log In and Submit Order Materials Log In xj Log into the Applied Biosystems Store to place the selected items in your shopping basket If you do not have a user name and password click Register Now
123. e prompts electronic signature 2000 eee eee eee eee eee 143 Generate e signature reportS 0000 e neces 144 Export and import user security audit and e signature settings 2000 00005 145 WS ER OVERVICW re raa A canter s AR Sa Anca ce Ne oh tna ulcer e ah ana aged ai A a aia A suman 146 User account permissions ssn cyte ee ng Dita de wand Gabriel eet bees 146 Account SUSPENSION oreet see ee ede ees gation es gating ee Paes ean eee a de eclegs 146 SESSION tIME OUL see es eei a eed eE Saeco dala E EE EE EAE Hae Ee ane data oe ae eet 146 User Security tasks osre a sag Seed ov de eet ei ake See ta Seek ee 147 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 7 Contents APPENDIX F Calibration Consumable Preparation 149 Create a background plate or array card 0c cece eee nrnna 150 Required materials nsanra ccc ccc eee eee eee eens 150 Create a background plate annarrar eect tte eee 150 Create a background array card QuantStudio 7 Flex System only 6 0 00 e cence 151 Create a custom dye plate for calibration 0 0c cece eee eee 152 Before you use custom dyes 00 0c eee ee eee eens 152 Required materials nnana ccc cece eee e eee e eee aee 152 Determine optimum dye concentration 0 cee eee nett eens 152 Create a custom dye plate 0 0 ieee ene etna 153 A
124. e the QuantStudio 7 Flex System but not all of them are required for a monthly maintenance Before preparing array cards for calibration see Calibration and maintenance schedule on page 28 to determine which calibrations are required Note For more information on the array card loading procedure contact Life Technologies 1 Remove the tubes of calibration solutions from the freezer allow them to thaw then vortex the tubes to mix the contents well 2 Remove the array cards from their box and place them on a clean dry surface 3 Mark the side of the empty array cards with Background FAM ROI ROX VIC FAM ROX and VIC ROX 4 For each array card pipet 100 uL of the appropriate calibration solution into each of the eight reservoirs in the array card a Place the array card on a lab bench with the foil side down b Load 100 uL of the calibration solution into a pipette 36 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Preparing array cards for instrument calibration c Hold the pipette in an angled position 45 degrees and place the tip into the fill port The fill port is the larger of the two holes on the left side of the fill reservoir Fill Vent port port UVVU d Dispense the fluid so that it sweeps in and around the fill reservoir toward the vent port Pipet the entire 100 uL into the fill reservoir but
125. eaches room temperature 1 Unload the QuantStudio 6 or 7 Flex System and confirm that you loaded the correct plate or array card into the instrument If not perform the calibration again using the correct consumable 2 If you are using the correct plate or array card perform the calibration again using a different normalization consumable 3 If the calibration fails again contact Life Technologies Field Service Office One or more wells produced spectra that deviate significantly from the rest of the plate or array card 1 While viewing the calibration data in the Analysis screen locate the well s with abnormal signal in the Plate Layout tab 2 Rotate the plate or array card 180 then perform the calibration again 3 Determine the location of the contaminated wells again If the position s of the well s identified in the steps above are e Identical The sample block is contaminated Decontaminate the sample block e Reversed The normalization plate or array card is contaminated Discard the consumable then perform the normalization calibration using a new normalization plate or array card 4 If the calibration fails again contact your local Life Technologies Field Service Office Instrument does not eject the normalization plate or array card it is stuck within the instrument The adhesive cover may have adhered the plate or array card to the heated cover within the instrument Remove the plate
126. ect the computer to your LAN 170 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix H Instrument Specification and Layout QuantStudio 6 and 7 Flex Systems layout and connections QuantStudio 6 and 7 Flex Systems layout and connections The QuantStudio 6 and 7 Flex Systems consist of the components in the following figure Component Description QuantStudio 6 or 7 Performs fluorescence detection and data collection of experiment and calibration plates or array cards Run the QuantStudio 6 and 7 Flex Real Time PCR System Software that is used to e Calibrate the QuantStudio 6 and 7 Flex Systems e Set up experiments e Optional Run experiments e Analyze experiments Scans the barcodes of plates and array cards Description Supply power to the computer and the QuantStudio 6 and 7 Flex Systems t Connects the QuantStudio 6 and 7 Flex Systems Ethernet port to the Ethernet port on the network interface card in the computer The components can be connected over a local area network or a via a direct physical connection Connects the monitor to the computer DVI port Connects the optional barcode scanner to the computer USB port Connects the keyboard to the computer USB port Ei F
127. ectronic signature users is signed field 147 signing 147 enable security instrument 92 security software 131 enabling calibration reminders 31 90 121 electronic signature 142 environmental requirement 169 ergonomics safety 180 error 189 e sig See electronic signature Ethernet port about 114 defining instrument IP settings 90 118 location 19 experiment deleting from the instrument 84 transfer from the instrument 84 121 experiment document file 196 experiments create from touchscreen 81 run from touchscreen 82 transfer to from the instrument 83 EXPFAIL quality flag 66 export audit records 139 audit settings 145 e sig settings 145 security settings 145 user account settings 145 F feet 21 file experiment document file 196 fill array cards calibration 36 instrument verification 36 64 Index filter 189 filters supported 17 firmware update 87 flag 189 forward primer 189 fuse cover 22 fuses location 19 replacement 102 specification 102 G general use materials and consumables 165 guidelines calibration plate preparation 35 consumable preparation 25 networking 116 remote monitoring 120 H halogen lamp See lamp heated cover handling 108 installation 108 location 18 temperature setting 88 Help system accessing 185 heterozygote 189 HIGHSD quality flag 66 holding stage 189 homozygote 190 humidity requirement 169 icon instrument 88 import audit settings 145 security settings 145 user
128. ecurity Sign Data menu option is enabled e You are prompted to sign QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 147 User overview Appendix E Security Audit and Electronic Signature 148 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Calibration Consumable Preparation Create a background plate or array card 000 0 150 Create a custom dye plate for calibration 0 cece eee eee 152 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 149 Appendix F Calibration Consumable Preparation Create a background plate or array card Create a background plate or array card Whenever possible use a Background Plate or the TaqMan Array Background Buffer that is included with the spectral calibration kit The plates array cards supplied in the kit contain a buffer that accurately simulates the reagents used for PCR and therefore produces high quality calibration data If a background plate or array card froma spectral calibration kit is not available you can create one as described below Required materials 96 384 Well Plate Sample Block MicroAmp Optical 96 384 Well Reaction Plate Safety glasses Optical Adhesive Cover or Optical Flat Caps Pipettor 200 uL with pipette tips Powder free gloves Deionized water Array Card Sample Block QuantStudio 7 Flex System only
129. ed field 147 K keys software 104 L lab director user role 134 lamp location 18 99 replacement 99 laser classification 180 laser safety barcode scanner 180 requirements 180 layout instrument 171 network 115 License Central 104 licenses software 104 Life Technologies support 185 lifespan lamp 99 location requirement 169 log in user account 147 log instrument 92 logged in user name display 134 in user account 133 M mail server settings 31 maintenance instrument 85 instrument settings 85 planned maintenance 28 reminders 31 90 schedule 28 software licenses 104 materials accessories 160 200 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide general use 165 kits 160 mDNS support 114 melt curve 190 melting temperature Tm 190 monitor computer electrical requirements 169 layout 171 requirements 24 specifications 168 monitoring an instrument over a network 114 monthly maintenance 28 moving the instrument 127 N name instrument 88 negative control NC 190 negative control blocked IPC wells 190 negative control IPC wells 190 network computer setup 119 guidelines 116 instrument setup 118 layouts 115 overview 114 settings instrument 90 no template control 191 NOAMP quality flag 66 NOISE quality flag 66 nonfluorescent quencher minor groove binder 191 normalization calibration about 57 191 about the data 57 performing 58 plate preparation 57 t
130. eees 105 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 5 Contents Update the Windows operating system n nunnur cece cece eee rnrn e teens 106 Change the sample block 0 0 0 cece cece eee ett ear 106 When to change the sample block 000 cece cece cece cece eee eee eens 106 Materials required moye ina pe aaa cece eee eee AE EE aa a 106 How to handle the sample block 2 0 00 cece eect aena EEE enna 106 Change the sample block 0 cece INRE enn e enna 107 Change the heated cover 0 cece eee c cece eee eet eee tee aene 108 When to change the heated cover 0000 cece eee eee cece eee rnrn 108 Materials required 000 eee eee eee e nena 108 How to handle the heated cover 0 0 cece cence nett tenet eens 108 Change the heated cover si sce eines ee head eee aes PEE EN EAR LENI EERE 109 Change the plate adapter 0 cece cect ttt e eee eee 111 When to change the plate adapter 00 00 cece cece eee rarene 111 Materials required 020 e cece eee ence eens 111 Change the plateadaptelh ce cides aesideth eel eita ei a ada dain eee ee 111 APPENDIX C Networking 2c e ee eee eee eee eee 113 Networking overvieW 2 ccc eee ccc e eee teen ee ee eens 114 Controlling and monitoring networked QuantStudio 6 and 7 Flex Systems 114 About the Ethernet port
131. efore 2000 hours of life WARNING PHYSICAL INJURY HAZARD The QuantStudio 6 or 7 Flex System and lamp are hot The lamp can become very hot while in use Before handling the lamp allow it to cool for 15 minutes and put on protective powder free gloves CAUTION PHYSICAL INJURY HAZARD Wear disposable powder free gloves when handling the lamp to prevent burns and to prevent shortening the life of the replacement lamp WARNING This QuantStudio 6 or 7 Flex System is designed for 12 V 75 W halogen lamps only Replace with halogen bulbs supplied by Life Technologies Safety glasses Powder free gloves Halogen bulb 12 V 75 W The QuantStudio 6 and 7 Flex Real Time PCR System Software can display the following warnings before or during an experiment The lamp current is below the acceptable level at the start of the run Replace the halogen bulb as explained in Replace the lamp on page 100 The QuantStudio 6 and 7 Flex Real Time PCR System Software stopped the run because the lamp current decreased below the acceptable level during the run Replace the halogen bulb as explained in Replace the lamp on page 100 Click OK in the message box then replace the lamp bulb The lamp usage exceeds 2000 hours at the start of a run Click Cancel Run then replace the lamp before you perform another experiment From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab click Instrument Conso
132. efore using a cleaning or decontamination method other than those recommended by the Life Technologies confirm with Life Technologies that the proposed method will not damage the equipment e Bleach 10 solution e Tissue lint free e Cotton or nylon swabs and lint free cloths e Ethanol 95 solution e Safety glasses e Pipette 100 uL with pipette tips e Powder free gloves e Screwdriver e Deionized water To prevent damaging or contaminating the sample block handle the assembly as shown Also when the assembly has been removed from the QuantStudio 6 or 7 Flex System place the sample block on a clean dry surface or in its shipping container QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix B Maintenance Decontaminate the sample block Clean the WARNING PHYSICAL INJURY HAZARD During instrument operation the sample block sample block can reach 100 C Allow the sample block to cool to room temperature before performing the procedure IMPORTANT Wear powder free gloves when you perform this procedure 1 Identify the contaminated wells of the sample block see How to identify contamination on page 78 2 Power off and unplug the QuantStudio 6 or 7 Flex System then allow it to cool for 15 minutes 3 Open the access door 4 Firmly press down on the handle of the sample block then remove it from the QuantStudio 6 or 7 Flex System Place the sampl
133. elect what data is signed for the selected meaning 4 Click Apply Settings Delete a meaning 1 Select the meaning from the e Signature Meanings list then click Remove 2 Click Apply Settings QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Configure the e signature rights for user roles Select the actions that require signature How the software prompts electronic signature Appendix E Security Audit and Electronic Signature Manage electronic signature To determine the user roles that can perform an electronic signature 1 From the e Signature tab of the Security Settings dialog box select the check box next to the appropriate user roles in the User Role signature rights table 2 Click Apply Settings IMPORTANT Do not change electronic signature settings during calibration 1 In the Signature Required column select the check box next to each action for which you want to require electronic signatures see below This selection causes the software to present an e sig prompt if a user performs the action on a data file that does not have the required signatures The data must be signed before the user can perform the action Action The software requires e signatures when a user Print Report Prints a report from an experiment or study Start Run Initiates a run from the QuantStudio 6 and 7 Flex Real Time PCR System Software 2 F
134. election tool to assign well contents to view well assignments and to view results The plate layout can be printed included in a report exported and saved as a slide for a presentation One standard in a standard curve The standard quantity for each point in a standard curve is calculated based on the starting quantity and serial factor In genotyping and presence absence experiments a DNA sample with a known genotype homozygous or heterozygous In the software the task for the SNP assay in wells that contain a sample with a known genotype QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 191 Glossary pure dye quantity quencher R2 value Raw Data Plot reaction mix reagents real time PCR reference sample region of interest ROI calibration regression coefficients regression line 192 Fluorescent compound used to calibrate the instrument See system dye In quantification experiments the amount of target in the samples Absolute quantity can refer to copy number mass molarity or viral load Relative quantity refers to the fold difference between normalized quantity of target in the sample and normalized quantity of target in the reference sample A molecule attached to the 3 end of probes to prevent the reporter from emitting fluorescence signal while the probe is intact With reagents a nonfluorescent quencher minor groove binder NFQ MGB can be
135. electrical fuses that protect the Twister Robot from excessive electrical current Rack parts and functions Racks are removable aluminum frames used as input and output locations for PCR consumables Rack positions are numbered counter clockwise with position 1 closest to the front of the Twister Robot see below Each rack is labeled for a specific position and cannot be exchanged with the other racks Component Description A Handles For connecting or disconnecting racks from the pod B Rack locator notch Locks the rack onto the pod in the correct position Note Do not drop the racks If the rack is bent the Twister Robot cannot properly place the consumables QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Electrical protective devices Chapter 1 Getting Started 1 Instrument software We recommend several protective devices to protect the instrument in environments with large voltage and power fluctuations Power line regulator We recommend the use of a 1 5 kVA power line regulator in areas where the supplied power fluctuates in excess of 10 of the normal voltage Power fluctuations can adversely affect the function of the instrument Note A power line regulator monitors the input current and adjusts the power supplied to the instrument or computer It does not protect against a power surge or failure Uninterrupt
136. emains repeat steps 2 5 then clean the contaminated wells of the sample block using a 95 ethanol solution a Pipet a small volume of 95 ethanol solution into each contaminated well b In each contaminated well pipet the solution up and down several times to rinse the well c Pipet the ethanol solution to a waste beaker Repeat steps 5 9 to rinse the wells of the sample block and to ensure that you have eliminated the contamination IMPORTANT Always use deionized water to rinse wells after cleaning with bleach or ethanol solution If the contamination remains repeat steps 2 5 then clean the contaminated wells of the sample block using 10 bleach solution a Pipet a small volume of 10 bleach solution into each contaminated well b In each contaminated well pipet the solution up and down several times to rinse the well c Pipet the bleach solution to a waste beaker Repeat steps 5 9 to rinse the wells of the sample block and to confirm that you have eliminated the contamination IMPORTANT Always use deionized water to rinse wells after cleaning with bleach or ethanol solution If the contamination remains contact Life Technologies QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix B Maintenance Replace the halogen lamp Replace the halogen lamp Materials required Halogen lamp warnings View the lamp status Replace the halogen lamp at or b
137. en ERAS 170 QuantStudio 6 and 7 Flex Systems layout and connections 000 cece eee eee 171 APPENDIX Safety 0 2 cece eee eee 173 Symbols on this instrument 00000 c cece ee anneren rnrn ranean 174 Conformingisymibols lt 5222 bs E head Pik plates ib aegis oa eee bd 176 Locations of safety labels on instrument 00 000 eee eee eens 177 Safety alerts on this instrument 00000 rnrn eee eect eeee 178 IPStRUIMeNt Safety sce oct tiie Ot taht det Rik ede tae dale sheet A eh eel dd ech lel GNA 178 General EET Aisa ce eae erode eal ae ceil nee he telat ae T EESE 178 Physicals Urry ss sacs dich pve ad pied BSG ene a a Ace eee He ee og 178 Electrical Sue eewctea gusts tein ia putes oka hele t cha hard ace Sas genannten 179 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Contents Cleaning and decontamination n n s sssusa arer cece eee eee neta 179 Instrument component and accessory disposal 0000ce eee ee eee ee eeeee 179 Barcode scanner laser safety 0 000 eect nent eeees 180 LaserclassifiGatlon aa r weg bees PERE bees DEMERS TE eae Be ees Slee Gigs Se See ee 180 Laser safety requirements 00 0c cece eee nee eee e eee eens 180 Workstation Saf ty nye ceresna loses neti eked ete deed Wages adh a A 180 Safety and electromagnetic compatibility EMC standards 00 c cece eee eee 181 SeT rea CC
138. ence of the dyes 2 Remove the ROI plate from its packaging Do not remove the optical film 3 Vortex and centrifuge the plate a Vortex the ROI calibration plate for 5 seconds b Centrifuge the plate for 2 minutes at lt 1500 rpm IMPORTANT The ROI calibration plate must be well mixed and centrifuged c Confirm that the liquid in each well of the ROI calibration plate is at the bottom of the well If not centrifuge the plate again at a higher rpm and for a longer period of time Correct Incorrect Liquid is at e Not centrifuged with enough force or bottom of well Not centrifuged for enough time QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 41 2 Chapter 2 Calibrate the Instrument ROI calibration Perform the ROI 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab calibration click Instrument Console 2 From the Instrument Console select the icon for your instrument then click Manage Instrument Note If the Manage Instrument button is inactive add your QuantStudio 6 or 7 Flex System to the My Instruments group 3 From the Instrument Manager start the calibration a Click XK Maintenance then click ROI b From the ROI Calibration screen click Start Calibration 4 Click Next then prepare for the calibration as instructed 5 From the bottom of the Setup tab enter the reagent information for the ROI plate or a
139. enerates data that allows the software to compensate for the physical effects of the instrument filters Perform a uniformity calibration once every 6 months IMPORTANT Wear powder free gloves and safety glasses when you prepare plates or array cards Prepare the calibration consumable appropriate for your QuantStudio 6 or 7 Flex System E Prepare the ROI calibration plate 0 eee 48 E Preparing array cards for instrument calibration 0 0 cee eee eee 36 Materials required Note The uniformity calibration requires the same materials used to perform the ROI calibration e Region of Interest ROI Plate e Centrifuge with plate adapter e Powder free gloves e Safety goggles Prepare the plate IMPORTANT Wear powder free gloves and safety glasses when you prepare the plate If you have a prepared ROI calibration plate from a recent ROI calibration go to step 3b below otherwise prepare the ROI calibration plate as follows 1 Remove the ROI calibration plate from the freezer then thaw it at room temperature for approximately 30 minutes IMPORTANT Use the calibration plate within 2 hours of defrosting it Until you are ready to run the plate store it in the dark and at ambient temperature 15 30 C Do not remove the plate from its packaging until you are ready to run it 2 Remove the ROI plate from its packaging Do not remove the optical film 3 Vortex and centrifuge the plate
140. ent RNase P plate or array card Repeat the test and make sure to properly centrifuge the RNase P consumable If the replacement RNase P plate or array card fails contact Life Technologies for assistance B 6unooysayqnos juauunsjsu ay ayeuqneg za4ajydeyg apIng UONENSIUIUPY pUe aaueuajUleW SWAaISAS Yd awl jeay X 4 pue 9 olpnisiuenD 9L Problem symptom Possible cause Action Well displays the BLFAIL flag indicating that the software cannot calculate the best fit baseline for the data Amplification too late No amplification e Well displays the CTFAIL flag indicating that the software cannot calculate the threshold cycle C4 e Well displays the EXPFAIL flag indicating that the software cannot identify the exponential region of the amplification plot Amplification too early Amplification too late Low amplification No amplification If a well is flagged confirm the results 1 2 Select the flagged well s in the plate layout or well table View the amplification plot R vs Cycle and DR vs Cycle and check for early late low or no amplification Contact Life Technologies to order a replacement RNase P plate or array card Repeat the test making sure to properly seal and centrifuge the RNase P plate or array card If the replacement RNase P plate or array card fails contact Life Technologies for assistance Well displays the HIGHSD flag indicating that the C
141. eparating the two using a colon QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 31 Chapter 2 Calibrate the Instrument Enable or change the calibration reminders For example smtp mycompany com 2023 Note If a TCP port is not specified the QuantStudio 6 and 7 Flex Real Time PCR System Software uses the default port number 25 Select Encryption Required if the mail server has SSL enabled Select Authentication Required if the mail server requires a user name and password If the mail server requires authentication enter the user name and password provided by your systems administrator 42 Preferences Defaults Startup Experiment iL Print Export Display Format SMTP Settings Notification Settings GP Enter the SMTP server settings for email notifications Outgoing Mail Server SMTP Encryption Required Authentication Required User Name Password fon 4 Click OK 5 Test the mail server settings a From the Home tab of the QuantStudio 6 and 7 Flex Real Time PCR System Software select any experiment in the Set Up panel then click Set Up to create a new experiment From the experiment document click Run in the Experiment Menu then click Notification Setting to view the notification settings for the experiment From the Notification Settings of the experiment document select Yes to enable the E
142. eplacement RNase P plate or array card well deviates significantly from C values in the associated replicate group only the outlier is flagged leaks Repeat the test and make sure that the RNase P consumable is properly sealed If the replacement RNase P plate or array card fails contact Life Technologies for assistance Well displays the SPIKE flag indicating that the amplification curve contains one or more data points inconsistent with the other points in the curve e Bubbles in the reaction e Evaporation during the denaturation step because of improper sealing or seal leaks Contact Life Technologies to order a replacement RNase P plate or array card Repeat the test and make sure to properly centrifuge the RNase P consumable If the replacement RNase P plate or array card fails contact Life Technologies for assistance Well displays the THOLDFAIL flag indicating that the software cannot calculate the threshold e Amplification too early e Amplification too late e Low amplification e No amplification If a well is flagged confirm the results 1 2 Select the flagged well s in the plate layout or well table View the amplification plot Ra vs Cycle and DR vs Cycle and check for early late low or no amplification Contact Life Technologies to order a replacement RNase P plate or array card If the replacement RNase P consumable fails contact Life Technologies for assistance
143. equately trained c From the instrument touchscreen touch to close the instrument tray 7 After loading the plate or array card start the calibration a From the Dye Calibration screen select Check the box when the dye calibration plate has been loaded then click Next b From the Run screen click START RUN IMPORTANT Do not attempt to open the access door during the run The door is locked while the instrument is in operation Note Before starting the calibration the instrument may pause up to 10 minutes to allow the heated cover to reach the required temperature 8 When the run is complete and the software displays the Analysis screen confirm the grouping of the dye spectra a Select the Plate Layout tab then review the raw data For each spectrum confirm that the peak is e Within the detectable range for the QuantStudio 6 and 7 Flex Systems e Free of irregular spectral peaks e Present at the correct filter for the dye see Instrument filters and supported dyes on page 17 Note Among wells containing the same dye variations in spectral position and peak position are caused by minor differences in the optical properties and excitation energy between the individual wells b Select the QC tab then review the summary of wells that failed the quality check QC 9 After you inspect the dye spectra confirm the analysis status of the calibration The analysis status indicates the success
144. er hub or another network device e IPv4 link local IPV4LL in the RFC also known as Automatic Private IP Addressing APIPA or Internet Protocol Automatic Configuration IPAC Note When the QuantStudio 6 or 7 Flex System is set for DHCP APIPA is automatically enabled and the QuantStudio 6 or 7 Flex System provides an IP address when no address is supplied by the DHCP server QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Example network layouts Appendix C Networking C Networking overview Example 1 In the following example one or more QuantStudio 6 or 7 Flex Systems which have been configured for dynamic host configuration protocol DHCP operation are connected to a network by their Ethernet ports In this layout any computer on the network can monitor and control the QuantStudio 6 or 7 Flex Systems Note A networked computer running the QuantStudio 6 and 7 Flex Real Time PCR System Software can simultaneously control up to 4 instruments and monitor up to 10 instruments that have been connected to the network DHCP server Networked Networked computer instrument s Example 2 In the example shown below the QuantStudio 6 or 7 Flex System is connected directly to the QuantStudio 6 or 7 Flex System computer which is also connected to the local area network In
145. er account does not have permission to perform any function in the software menu commands are shaded If the QuantStudio 6 and 7 Flex Real Time PCR System Software is configured to suspend a user account for failed logins and if you repeatedly enter an incorrect user name and or password your user account is suspended and the Log In dialog box indicates that your account is inactive There are two ways to activate a suspended account e You can wait until the suspension period ends e An administrator can change the account status from Suspended to Active Note While a user is suspended another user can click Reset then log in and replace the suspended user If the QuantStudio 6 and 7 Flex Real Time PCR System Software is configured to time out and there is no user activity for the specified time the Log In dialog box indicates that your user session has timed out You must enter your user name and password to access the software The administrator or another user with permission to log in to timed out sessions can click Reset then log in QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide User overview Appendix E Security Audit and Electronic Signature User security tasks Description Log in Your access to functions in the software is based on the permissions associated with your user account Functions for which you do not have permissions are shaded Note If the
146. es 000 ce cece eee ee 165 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 157 G Appendix G Parts and Materials How to order How to order How to order from the Life Technologies website How to order from the QuantStudio 6 and 7 Flex Real Time PCR System Software 158 You can order materials and accessories directly from the Life Technologies store over the internet Note Product availability and pricing may vary according to your region or country Online ordering through the Life Technologies Store is not available in all countries Contact your local Life Technologies representative for help To order through the website or the QuantStudio 6 and 7 Flex Real Time PCR System Software e Confirm that your computer has an Internet connection e We recommend the following browsers and Adobe Acrobat Reader versions to use the Life Technologies website Microsoft Apple Mozilla Adobe 7 Operating system Internet 3 Acrobat Safari Firefox Explorer Reader Microsoft Windows v x or later Nonet v2 x or later v4 0 or later Macintosh Nonet v2 0 4 or later t Browser not available for this platform Note Confirm that cookies and Javascript are turned on for the website to function correctly To order Procedure Assays and 1 Go to www lifetechnologies com reagents 2 Under I Want to Buy select th
147. es Type Select e Reporter if the dye works in conjunction with a quencher dye to report an increase of PCR product e Quencher if the dye suppresses the fluorescence of a reporter dye until amplification of PCR product Both if the dye reports an increase of PCR product without the aid of a quencher dye d Click Close 3 In the Dye window enter a temperature setting for the calibration Set the temperature to match the temperature at which you intend to collect data For example the temperature for all Life Technologies system dyes is 60 C because data collection for TaqMan reagents occurs during the 60 C extension step of the PCR 4 Load the appropriate dye plate into the plate adapter select Please check the box when the dye calibration plate has been loaded click Next twice then click START RUN to start the calibration 5 When the run is complete and the QuantStudio 6 or 7 Flex System ejects the plate remove and discard the plate or array card WARNING PHYSICAL INJURY HAZARD During instrument operation the plate can reach 100 C Allow the plate to reach room temperature before removing 6 In the Dye dialog box of the QuantStudio 6 and 7 Flex Real Time PCR System Software click Next 7 Verify the grouping of the dye spectra 154 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix F Calibration Consumable Preparation Create a custom dye pl
148. es for the amplification plot See also baseline An analysis setting in which the software calculates the baseline start and end cycles and the threshold in the amplification plot The software uses the baseline and threshold to calculate the threshold cycle Cy See also threshold cycle CT Type of calibration in which the instrument performs reads of a background plate or array card averages the spectra recorded during the run and extracts the resulting spectral component to a calibration file The software then uses the calibration file during subsequent runs to remove the background fluorescence from the run data From the Amplification Plot a cycle to cycle range that defines background fluorescence The magnitude of normalized fluorescence signal generated by the reporter In experiments that contain data from real time PCR the magnitude of normalized fluorescence signal generated by the reporter at each cycle during the PCR amplification From the AR vs Cycle Amplification Plot AR is calculated at each cycle as AR cycle Rn cycle Rn baseliney Where R normalized reporter See also normalized reporter Rn In presence absence experiments a reaction that contains IPC blocking agent which blocks amplification of the internal positive control IPC In QuantStudio 6 and 7 Flex Real Time PCR System Software also the name of the task for the IPC target in wells that contain IPC blocking agent See also nega
149. es made to library items actions performed by users and changes to the Security Audit and Electronic Signature settings The software automatically audits some actions silently You can select other items for auditing and specify the audit mode The Auditing function provides reports for audited library items Security Audit and Electronic Signature changes and actions Note You can enable or disable auditing globally and by record type Electronic signature e sig Determines if users are required to provide a user name and password when performing certain functions You can configure e sig so that a user can print a report or start a run only if the associated data are signed You can also configure each e sig event to require multiple signatures and to require users with specific permissions to sign Note You can enable or disable electronic signature globally You can configure the Security Audit and Electronic Signature module in a variety of ways For example you can Require users to log in and leave audit disabled Allow only certain users to create or modify protocols Allow only certain users to approve reviewed samples Require experiments to be signed before users can run or print them QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix E Security Audit and Electronic Signature Configure the security system Configure the security system Access the Security
150. es that represent the fluorescence signature of each dye standard Each profile consists of a set of spectra that correspond to the fluorescence collected from the wells of the calibration plate or array card Following the calibration of each dye the software extracts a spectral profile for each dye The software plots the resulting data for each profile in a graph of fluorescence versus filter When the software extracts the dye calibration data it evaluates the fluorescence signal generated by each well in terms of the collective spectra for the entire calibration plate or array card Dye spectra are generally acceptable if they peak within the same filter as their group but diverge slightly at other wavelengths see below Acceptable spectra Unacceptable spectra Spectra peak at the same wavelength and do Spectra peak at the different wavelengths not diverge significantly 10 f M 10 A Normalized Fluorescence Normalized Fluorescence oo E ll n OL o o L a a x1 m21 81 4 rab MD 22 BO e ni2 rB MB v3 rneB MOA m m 4 m5 m5 m amp mM x1 ml m21 m81 m m51 mMR m22 m82 mME m52 m83 MB m43 m63 m m44 m t m85 m55 m m Filter Filter Note Because the wells of a calibration plate or array card contain identical concentrations of a dye the resulting signals for the wells should be similar Variations in spectral position and peak position are caused by minor differences in the optical
151. f necessary the waste generated by the particular applications reagents and substrates used in your laboratory Ensure that the waste is stored transferred transported and disposed of according to all local state provincial and or national regulations IMPORTANT Radioactive or biohazardous materials may require special handling and disposal limitations may apply WARNING HAZARDOUS WASTE from instruments Waste produced by the instrument is potentially hazardous Follow the guidelines noted in the preceding General Chemical Handling warning WARNING 4L Reagent and Waste Bottle Safety Four liter reagent and waste bottles can crack and leak Each 4 liter bottle should be secured in a low density polyethylene safety container with the cover fastened and the handles locked in the upright position 182 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix Safety Biological hazard safety Biological hazard safety A WARNING Potential Biohazard Depending on the samples used on this instrument the surface may be considered a biohazard Use appropriate decontamination methods when working with biohazards WARNING BIOHAZARD Biological samples such as tissues body fluids infectious agents and blood of humans and other animals have the potential to transmit infectious diseases Follow all applicable local state provincial and or national regulations Wear appropriate
152. f the wells centrifuge the plate or array card for a longer time then repeat the calibration e Equivalent in volume the plate or array card is not sealed properly and the reagents have evaporated Discard the consumable and run another 3 If the calibration plate or array card appears to be normal discard it and run another 4 If the calibration fails again check the sample block and heated cover positions a Power off and unplug the instrument Wait 15 minutes then open the access door b Firmly push the sample block and the heated cover toward the back of the instrument to confirm that they are seated correctly IMPORTANT Align the arrows on the front handle of the heated cover as shown If the arrows are not aligned push the heated cover into the instrument until the handle locks into place IMPORTANT Confirm that the indicator on the left side of the sample block is positioned behind the red line on the instrument rail If not push the sample block into the instrument until it is seated correctly c Repeat the calibration 5 If the calibration fails again contact Life Technologies Instrument does not eject the ROI plate or array card it is stuck within the instrument The adhesive cover may have adhered the plate or array card to the heated cover Remove the plate or array card from the instrument as explained in Remove a plate stuck within the instrument on page 78 Instrument malfunct
153. g Notification Settings to specify when and how the QuantStudio 6 and 7 Flex Real Time PCR System Software notifies the administrator of certain security events For information see Set up messaging notifications on page 132 Click Apply Settings The new settings are applied to the user account the next time that the user logs in Spaces in user names and or passwords If you allow spaces in user names and or passwords be aware of the following issues Leading and trailing spaces in user names are difficult to detect on the screen or in printed reports The number of consecutive spaces in a user name is difficult to determine on the screen or in printed reports Spaces in user names may cause confusion when a user searches for an audit record associated with a user name To find a record associated with a user name specify the user name exactly including leading consecutive and trailing spaces 1 In the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Security gt Settings In the Security screen click Set Up Messaging Notifications to display the Setup Notifications dialog box Select the events for notification e System security enabled or disabled Security has been enabled or disabled e User did not enter correct password A user attempts to log in with an incorrect password The message indicates the number of failed authentications e User account suspended The
154. ge the heated Note Confirm that the replacement heated cover supports the plate or array card format that you want to use Some heated covers support more than one consumable cover y PP type 1 Power off and unplug the QuantStudio 6 or 7 Flex System then allow it to cool for 15 minutes Open the access door Unlock the heated cover by pinching the handle together then pull the assembly from the QuantStudio 6 or 7 Flex System and place it on a clean dry surface N Install the new heated cover into the QuantStudio 6 or 7 Flex System IMPORTANT Align the arrows on the front handle as shown below If the arrows are not aligned push the heated cover into the QuantStudio 6 or 7 Flex System until the handle locks into place Correct Incorrect 5 Ifyou are installing a heated cover of a different consumable format replace the sample block and plate adapter if necessary QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 109 110 Appendix B Maintenance Change the heated cover Close the access door and ensure it is completely closed Note The QuantStudio 6 and 7 Flex Real Time PCR System Software displays an error message if the door is not completely closed and latched or if the sample block is not seated correctly Plug in and power on the QuantStudio 6 or 7 Flex System From the QuantStudio 6 and 7 Flex Real Time PCR System S
155. h Done e Touch 12 Hour or 24 Hour to select the appropriate time format f Touch Save to save the settings then touch OK when prompted 3 Touch ft to return to the Main Menu 1 From the Main Menu of the instrument touchscreen touch Settings then touch Configure the Instrument 2 Touch the Instrument Name field enter up to a 25 character name for the QuantStudio 6 or 7 Flex System then touch Done QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Administrate the instrument from the touchscreen Appendix A Manual Instrument Operation The instrument name is the alphanumeric string used to identify the QuantStudio 6 or 7 Flex Instrument on the network IMPORTANT To connect the QuantStudio 6 or 7 Flex System to a network the name must be unique IMPORTANT The instrument name cannot include spaces or special characters such as lt gt 1 3 Upload the instrument icon TM The instrument icon is the graphic used to represent the QuantStudio 6 or 7 Flex System in the QuantStudio 6 and 7 Flex Real Time PCR System Software Instrument Console a Save the replacement graphic to a USB drive then plug the drive into the USB port below the touchscreen IMPORTANT Do not use the USB ports on the rear panel of the QuantStudio 6 and 7 Flex Systems The rear USB ports are for use by Life Technologies personnel to service the instrument b
156. hardware is user installable Replacement can be done without the need for recalibration of the instrument provided that the calibrations for the new format have not expired See Appendix B Maintenance for more information about changing the sample block heated cover and plate retainer 26 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Calibrate the Instrument E Calibration overview 0 0 ccc cence cent e nee n eens 28 m Enable or change the calibration reminders 00 00 c eee eee eee 31 E Guidelines for preparing calibration plates and array cards 35 m Preparing array cards for instrument calibration 0008 36 Mf RO calibrating Scacchi lad weil Gat Sek isle alg le ase ne Aiea 40 m Background calibration 0 6 c ccc eens 44 Mm Uniformity calibration 0 eee es 48 E Dye calibratione actA eA eet PRCA Sell ates Satie BEN I a Bl ie 52 E Normalization calibration 0 e eens 57 m Verify the instrument performance 6666s 61 E Troubleshooting sohet ocoed ited adn a dead Rd Det Ld eda 69 IMPORTANT Perform the procedures for preparing array cards only if you are verifying the performance of a QuantStudio 7 Flex System with an array card sample block The QuantStudio 6 Flex System does not support the array card sample block QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and
157. hat can be removed Sample block Unknown Unknown Standards No template population At population Bt STD 8 controls NTC 96 well platett 6 6 1 0 384 well plate 10 10 2 0 Array cardtt 4 4 4 0 t 5 000 copy population for 384 well plates 800 copy population for array cards 10 000 copy population for 384 well plates 1 400 copy population for array cards Maximum number of wells that can be removed from each standard population tt Standard 96 well plates or Fast 96 well plates tt QuantStudio 7 Flex System only 11 Repeat step 10 for each replicate population unknowns standards and no template controls on the plate or array card 12 Review the Results Table for quality flags generated by the test a Select the Results Table tab b Review the Flag column for wells that generated quality flags c Troubleshoot each well that generated a flag as explained in RNase P test troubleshooting on page 75 AMPNC Amplification in negative control BADROxX Bad passive reference signal BLFAIL Baseline algorithm failed CTFAIL Cy algorithm failed EXPFAIL Exponential algorithm failed HIGHSD High standard deviation in replicate group NOAMP No amplification NOISE Noise higher than others on the consumable NOSIGNAL No signal in well OFFSCALE Fluorescence is offscale OUTLIERRG Outlier in replicate group SPIKE Noise spikes THOLDFAIL Thresholding algorithm failed 13 If you o
158. he calibration plates within 2 hours of defrosting them Until you are ready to run the plates store them in the dark and at ambient temperature 15 30 C Do not remove the plates from their packaging until you are ready to run them QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 53 Perform the dye Chapter 2 Calibrate the Instrument Dye calibration calibration 54 2 Before using each dye plate vortex the plate for 5 seconds centrifuge it for 2 minutes at lt 1500 rpm then confirm that the liquid in each dye plate is at the bottom of the wells If not centrifuge the plate again at a higher rpm and for a longer period of time Correct Incorrect Liquid is at e Not centrifuged with enough force or bottom of well e Not centrifuged for enough time IMPORTANT The software guides you through the calibration of each dye separately You must set up run and analyze each dye independently From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab click Instrument Console From the Instrument Console select the icon for your instrument then click Manage Instrument Note If the Manage Instrument button is inactive add your QuantStudio 6 or 7 Flex System to the My Instruments group From the Instrument Manager start the calibration a Click X Maintenance then click Dye b From the Dye Calibration screen select System Dye
159. he larger of the two holes Fill Vent A port port 1 2 3 4 5 6 ANANA AM C V C E d Dispense the fluid so that it sweeps in and around the fill reservoir toward the vent port When pipetting the reagents into the array card pipet the entire 100 uL volume into the fill reservoir but do not go past the first stop of pipettor plunger or you may blow the solution out of the port IMPORTANT Do not allow the tip to contact and possibly damage the coated foil beneath the fill port 4 Centrifuge and seal the array card as explained in Filling the calibration array cards on page 36 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 151 Appendix F Calibration Consumable Preparation Create a custom dye plate for calibration Create a custom dye plate for calibration Before you use custom dyes Required materials Determine optimum dye concentration 152 The QuantStudio 6 or 7 Flex System can be used to run assays designed with custom dyes dyes not manufactured by Life Technologies Custom dyes must excite between 455 and 672 nm and read between 505 and 723 nm Before using custom dyes with the QuantStudio 6 or 7 Flex System you must e Determine optimum dye concentration e Create a custom dye plate e Add the custom dye to the software e Perform a dye calibration e Centrifuge with plate adapter e Custom dye s e Safety glasses e Powder
160. ible after filling it IMPORTANT Store the array card in a dark place until you are ready to run it The fluorescent dyes in the array card are photosensitive Prolonged exposure to light can diminish the fluorescence of the dye Run the RNase P From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab plate or array card click Instrument Console 2 From the Instrument Console select your instrument icon then click Manage Instrument Note If the Manage Instrument button is inactive add your QuantStudio 6 and 7 Flex Instrument to the My Instruments group 3 From the Instrument Manager start the RNase P run a Click xX Maintenance then click RNase P Run b From the RNase P Run screen click Start RNase P Run 4 Click Next then prepare for the instrument verification test as instructed 5 From the bottom of the Setup tab enter the reagent information for the RNase P plate or array card that you are using Reagent Information Plate Barcode Reagent Name Reagent Part Number Reagent Lot Number Reagent Expiration Date E Check the box when the RNase P plate has been loaded and when you have ensured you have entered all reagents information correctly ease Peo 6 Load the RNase P plate or array card into the instrument a From the instrument touchscreen touch B to eject the instrument tray b Load the plate or array card into the plate holder so that e Well A1 of the plate or array
161. ible power supply UPS We recommend the use of a 1 5 kVA uninterruptible power supply UPS especially in areas prone to power failure Power failures and other events that abruptly terminate the function of the QuantStudio 12K Flex System can corrupt data and possibly damage the computer or the instrument IMPORTANT UPSs provide power for a limited time They are meant to delay the effects of a power outage not to serve as replacement power sources In the event of a power loss power off the instrument and the computer unless you expect to regain power within the battery life of the UPS Surge protector We recommend the use of a 10 kVA surge protector line conditioner in areas with frequent electrical storms or near devices that are electrically noisy such as refrigerators air conditioners or centrifuges Short duration high voltage power fluctuations can abruptly terminate the function of and thereby damage the components of the computer and the instrument Note A dedicated line and ground between the instrument computer and the building s main electrical service can also prevent problems caused by power fluctuations Instrument software The QuantStudio 6 and 7 Flex Systems include a suite of software applications that can be used to calibrate run and integrate the instrument into a laboratory workflow The installation of the software contains the components described below The QuantStudio 6 and 7 Flex S
162. ide the lamp release lever downward b Firmly grasp the lamp and lift it up and out of the slotted mount 5 Inspect the lamp for damage carbon usually coats the inside of a failed lamp If necessary dispose of the lamp and obtain a replacement IMPORTANT Dispose of the lamp in accordance with your local municipal waste ordinances Do not dispose of the lamp as unsorted municipal waste 6 Install the new lamp into the QuantStudio 6 or 7 Flex System a Slide the lamp release lever upward 100 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix B Maintenance Replace the halogen lamp b Firmly grasp the lamp place it into the slotted mount then carefully slide the lamp downward into place 7 Close the access door 8 Plug in and power on the QuantStudio 6 or 7 Flex System IMPORTANT Confirm that the access door is completely closed The QuantStudio 6 and 7 Flex Real Time PCR System Software displays an error message if the door is not completely closed and latched or if the lamp is not seated correctly 9 Start the QuantStudio 6 and 7 Flex Real Time PCR System Software then perform an ROI calibration While the QuantStudio 6 or 7 Flex System is running look through grating of the access door and confirm that the lamp is illuminated e Ifthe lamp is illuminated the lamp has been installed successfully e Ifthe lamp is not illuminated the
163. ies General Terms and Conditions of Sale found on Life Technologies website at www lifetechnologies com termsandconditions If you have any questions please contact Life Technologies at www lifetechnologies com support QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 185 Documentation and Support Limited product warranty 186 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide aligned melt curve plot allele amplicon amplification amplification efficiency EFF Amplification Plot amplification stage assay assay mix Glossary Plot of the re scaled melt curve In a diploid organism one of two DNA sequences found at the same locus for example a particular gene but located on homologous chromosomes Two corresponding alleles may have the identical sequence or they may differ somewhat often at one or more single base sites SNPs A segment of DNA amplified during PCR Part of the instrument run in which PCR amplifies the target Fluorescence data collected during amplification are displayed in an Amplification Plot and the data are used to calculate results Note Only quantitative real time PCR experiments not end point experiments take amplification data into account Calculation of the efficiency of the PCR amplification in an experiment EFF is calculated using the slope of the regression line in the standard curve A
164. ies dialog box b Define the IP Settings DNS and WINS tabs as instructed by your systems administrator then click OK 8 Close all dialog boxes by clicking OK 9 Restart the computer The computer is now visible to other computers on the network If you are using a computer that you have provided install the QuantStudio 6 and 7 Flex Real Time PCR System Software using the QuantStudio 6 and 7 Flex Real Time PCR System Software CD Note You must install the QuantStudio 6 and 7 Flex Real Time PCR System Software to monitor the QuantStudio 6 or 7 Flex System over the network Monitor the QuantStudio 6 or 7 Flex System About remote monitoring Monitor the status of arun 120 After connecting theQuantStudio 6 or 7 Flex System and a computer to the network you can enable remote monitoring in the QuantStudio 6 and 7 Flex Real Time PCR System Software to observe the instrument status remotely When the QuantStudio 6 or 7 Flex System is connected to the network any computer on the network that is running the QuantStudio 6 and 7 Flex Real Time PCR System Software can E Monitor the status of arun 0 cece eee eee eee see below m Download experiment files 0 eee ees 121 m Enable or change the calibration reminders 66 0 cece eens 121 Guidelines for remote monitoring To ensure optimal performance of the remote monitoring feature observe the following guideli
165. iment or template file From the open file click Audit then click Print E Signatures Save or print the record e Click H Save select a location for the export file enter a name for the file then click Save or e Click gh Print Click OK in the confirmation message 144 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix E Security Audit and Electronic Signature Export and import user security audit and e signature settings Export and import user security audit and e signature settings Note The export import feature can be used to replicate identical security audit and e signature settings across multiple computers The feature allows you to create a standard security audit and e signature settings image for the QuantStudio 6 and 7 Flex Real Time PCR System Software that can then be imported by other copies of the software to bypass manual setup Task Description Export 1 In any screen of the Security Settings dialog box click Export 2 Select the items to export All or Custom Custom contains select settings e Users amp Roles All user accounts with Active status and all user roles and associated permissions in case a user account specifies a user role that does not exist on the system into which you import the profiles e System amp Roles All system settings and all user roles and associated permissions 3
166. in wells that contain a sample with an unknown melt curve profile A sample or group of samples with a unique melt curve that is the melt curve is different from the melt curves of other samples or controls used in the experiment The software determines melt curve differences by the melting temperature Tn and the shape of the melt curve From the standard curve the value of y where the regression line crosses the y axis The y intercept indicates the expected threshold cycle Cy for a sample with quantity equal to 1 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide A accessories 160 account setup 131 suspended activate 133 suspension 131 146 user 133 action log contents 138 display 138 141 144 activation license keys 104 administrator auditing 137 password 130 security 130 user role 134 aligned melt curve plot 187 allele 187 altitude requirement 169 amplicon 187 amplification 187 amplification efficiency EFF 187 Amplification Plot 187 amplification stage 187 AMPNC quality flag 66 annual semi annual maintenance 28 APIPA support 114 archive audit records 139 instrument settings 85 array card background creating 150 calibration 25 prepare for calibration 36 prepare for verification 36 64 Array Card RNase P Kit 62 assay 187 audit administrators 137 Index action log 138 141 144 archive records 139 audit actions 138 audit mode 137 audit reason settings 1
167. ing potential problems are displayed in the Quality Control tab of the Plate Layout Well Table and QC Summary screens Oligonucleotide that flanks the 5 end of the amplicon The reverse primer and the forward primer are used together in PCR reactions to amplify the target Samples having both allele 1 and allele 2 In the thermal profile the stage that holds the temperature constant for a defined period of time QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 189 Glossary homozygote Instrument Console Instrument Manager internal positive control IPC IPC IPC melt curve melt curve characteristics melt curve stage melting temperature Tm melting transition region negative control NC negative control blocked IPC wells negative control IPC wells 190 Samples having only allele 1 or only allele 2 A software feature that allows you to monitor the status of any instrument on the network view calibration maintenance and instrument properties for a selected instrument and open and close the instrument drawer A software feature that allows you to monitor the status of an instrument monitor Amplification Plots and temperature plots in real time view the calibration status perform calibrations and manage files on the instrument including downloading completed experiments to your computer In presence absence experiments a short synthetic DNA tem
168. ings 2 From the Security Settings dialog box select the Users tab From the Users tab you can perform the actions in the following table To Action Create a user account 2 Click Create to display the New User dialog box Enter user name password first name middle initial optional and last name Click a field to display the field limits which are specified in Security settings Note First name MI middle initial and last name are used to create User Full Name which is displayed as the name of the logged in user Note You cannot change the user name after you save the user account 3 Select Password Expires at First Login to require the user account to specify a new password at first log in The Password Expires On date is specified in Security settings 4 Select the user role described in Create or edit a user role on page 134 and the electronic signature state determines if a user account has permission to electronically sign objects Leave the status set to ACTIVE 5 Optional Enter email for information only phone and comments 6 Click Save A shaded Save button indicates an invalid entry in a field Click a field to display the limits for the field then enter a valid entry QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 133 Appendix E Security Audit and Electronic Signature User account management Determine the
169. ion Multiple possible causes Contact your local Life Technologies Field Service Office juauUNsjsu ay ayeuqijeg Z4aydeyg Bunooysayqnos al LZ aping UONeENSIUIUPY pUe aaueuajulew SW IS S Yq WIL JE Y X 4 PUL 9 olpnisjueng Table 2 Background calibration troubleshooting Problem symptom Possible cause Action Background calibration failed e Plate or array card was centrifuged insufficiently e Plate or array card contains old or insufficient reagents e One or more wells of the background plate or array card produced spectra that exceed the maximum limit for the instrument CAUTION PHYSICAL INJURY HAZARD During operation the sample block can reach 100 C Before removing the plate or array card wait until the block reaches room temperature 1 Unload the QuantStudio 6 or 7 Flex System and confirm that you loaded the correct plate or array card into the instrument If not perform the calibration again using the correct type of consumable 2 View the wells of the plate or array card If the liquid in the wells of the consumable is not e At the bottom of the wells centrifuge the plate or array card for a longer time then repeat the calibration e Equivalent in volume the plate or array card is not sealed and the reagents have evaporated Discard the consumable and run another 3 If the calibration plate or array card appears to be normal discard it and run another
170. ions QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 79 Appendix A Manual Instrument Operation Overview of instrument touchscreen functions Overview of instrument touchscreen functions 80 The QuantStudio 6 and 7 Flex Systems feature a touchscreen interface that you can use to transfer data manage instrument settings and configure the instrument for network use The touchscreen does not provide access to all instrument functions Features such as analyzing experiments instrument calibration and remote notification are available only through the QuantStudio 6 and 7 Flex Real Time PCR System Software The following table summarizes the functions that are available from the QuantStudio 6 or 7 Flex System touchscreen Catego Function Available in mane secure mode t Operational Create experiments from templates No Run experiments Transfer and delete experiments templates and results to from a USB drive Maintenance Back up and restore the instrument settings Yes Perform an instrument self test Install and record a new lamp Update the instrument firmware Administration t Define the date and time Define the instrument settings Define the network settings Define the maintenance reminders Define the system shortcuts Enable or disable instrument security Review the instrument statistics Review the instrument ve
171. isable enable or modify security policies and session time out settings Account Settings Update Modify password settings security policies password expiration and account suspension or user name settings User Group Manager Update Create delete or modify reason for change User Role Create Create user role Delete Delete user role Update Modify user role User Account Create Create new user account Update Edit or suspend a user account Role Assignment Delete Assign a different user role to an existing user account Update Create a user account or assign a different user role to an existing account Audit Settings Update Enable or disable auditing Audit Type Update Modify audit settings Function Management Settings Update Update function management Function Access Manager Update Update function access management Function Create Create function Delete Delete function Update Update function Role Permissions Create Create a user rolet Delete Delete a user role Update Modify user role permissions Audit Reason for Change Delete Create reason for change Update Delete or modify reason for change Event Manager Update Update the event manager E signature Manager Update Enable or disable e signature E signature Type Create Create an e signature meaning Delete Delete an e signature meaning Update Edit an e signature meaning or an e signature action E signature Function Update Edit an action requiring e
172. ist user role 134 Temperature Plot about 195 temperature requirement 169 template 195 test RNase P 61 thermal output requirement 169 third party software 24 THOLDFAIL quality flag 66 threshold 196 threshold cycle 196 threshold cycle Cy 196 timeout session 131 146 touchscreen 18 touchscreen instrument 80 training information on 185 transfer data to from instrument 84 121 troubleshooting calibrations and RNase P test 69 identifying contamination 78 instrument fuses 102 lamp replacement 99 sample block decontamination 96 U uniformity calibration 196 about 48 performing 49 troubleshooting 69 unknown 196 update firmware 87 operating system 106 service packs 106 software 105 USB drive transfer data 83 USB ports 83 backup instrument settings 85 location 18 19 restore instrument settings 85 transferring experiments 84 transferring self test results 86 transferring the instrument log 92 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide uploading the instrument icon 88 user account activate suspended 133 create or edit 133 delete 133 inactivate 133 permissions 134 user role create 134 V variant 196 verification array cards 36 64 verification plate ordering 160 vibration requirement 169 W warnings lamp 99 weekly maintenance 28 weight instrument 168 Windows operating system compatibility 24 workflow calibration 29 workstation safety 180 Y y i
173. ked IPC wells because the reaction contains no sample and amplification of the IPC is blocked Previously called no amplification control NAC In presence absence experiments wells that contain IPC template and buffer or water instead of sample Only the IPC template should amplify in negative control IPC wells because the reaction contains no sample Previously called IPC QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide no template control NTC nonfluorescent quencher minor groove binder NFQ MGB normalization calibration normalized quantity normalized quantity mean normalized quantity SE normalized reporter Ry outlier passive reference plate layout point positive control Glossary See negative control NC Molecules that are attached to the 3 end of probes When the probe is intact the nonfluorescent quencher NFQ prevents the reporter dye from emitting fluorescence signal Because the NFQ does not fluoresce it produces lower background signals resulting in improved precision in quantification The minor groove binder MGB increases the melting temperature Tn of the probe without increasing its length allowing for the design of shorter probes Type of calibration in which the software collects data from the normalization standards then stores it in a normalization calibration file Either the Cy Avg of the target gene minus the Cy Avg of
174. late adapter to cool to room temperature before removing You can change the plate adapter To change the consumable format of the QuantStudio 6 or 7 Flex System In the event of a hardware failure Safety glasses Powder free gloves Plate adapter Touch the instrument touchscreen to activate it then press OF From the Main Menu touch gB When the tray arm opens pull the latch then lift and remove the plate adapter Attach the new adapter to the tray arm then pull the latch to allow the adapter to lower into place If necessary apply pressure as indicated until the adapter snaps into place From the Main Menu touch g If you are installing a tray adapter of a different consumable format replace the sample block and heated cover if necessary QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 111 Appendix B Maintenance Change the plate adapter 112 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Networking Networking Overview 0 eee eee Network setup workflow 0 cee eens Collect the required network information 0 cece cece eee eee Connect the QuantStudio 6 or 7 Flex System to the network Connect the computer to the network 0 eee eee ee Monitor the QuantStudio 6 or 7 Flex System 6 2 6c cece eee eee IMPORTANT This chapter does not provide adequat
175. le From the Instrument Console select your QuantStudio 6 or 7 Flex System from the list of instruments then review the Lamp Life and Last Serviced readings in the Maintenance Info pane If the lamp usage has reached 2000 hours replace the lamp see Replace the lamp below Note The Lamp Life report displays the total number of hours that the halogen lamp has been illuminated The Last Serviced report displays the date that the lamp was installed QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 99 Appendix B Maintenance Replace the halogen lamp Replace the lamp IMPORTANT Always wear powder free gloves when you handle the lamp Finger prints shorten the lamp life 1 Record the lamp installation a From the Main Menu of the touchscreen touch Tools then touch Record Lamp Installation b Touch the Name field enter any relevant information such as the make model or serial number of the lamp then touch Done c Touch the Comments field enter any additional information that you want to record then touch Done d Touch Save then touch OK e When asked to confirm lamp replacement touch OK Note The data that you enter for the new lamp appears in the instrument log 2 Power off and unplug the QuantStudio 6 or 7 Flex System then allow it to cool for 15 minutes 3 Open the access door 4 Remove the lamp from the QuantStudio 6 or 7 Flex System a Sl
176. le the power button on the rear of the QuantStudio 6 or 7 Flex System then wait for it to start The QuantStudio 6 or 7 Flex System is ready to use when the touchscreen displays the Main Menu QuantStudio 7 Flex System only If you have an Applied Biosystems Twister Robot toggle the power button on the rear of the Twister Robot Note The Twister Robot is ready to use when the power LED illuminates Power on the monitor Power on the computer a Press the computer power button then wait for it to start b When the Login screen appears enter your user name and password then click OK Start the QuantStudio 6 and 7 Flex Real Time PCR System Software a From the desktop double click QuantStudio 6 and 7 Flex System Software Note If the shortcut is not present on the desktop select Start All Programs gt Applied Biosystems gt QuantStudio 6 and 7 Flex Software gt QuantStudio 6 and 7 Flex Software to start the software QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix D Power On or Off Store and Move Power off the QuantStudio 6 or 7 Flex System IMPORTANT If the QuantStudio 6 and 7 Flex Real Time PCR System Software does not start confirm that no other instances of the instrument control software are open If any instance of the software is open close it before starting the QuantStudio 6 and 7 Flex Real Time PCR System Software
177. les e Administrator cannot be edited or deleted e Lab Director e Technologist You can modify the Lab Director and Technologist roles and you can create your own roles with customized settings as needed 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Security gt Settings 2 From the Security Settings dialog box select the Roles tab From the Roles tab you can perform the actions in the following table QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix E Security Audit and Electronic Signature User account management To Action Create a user role Click Create Enter a role name and optional description Select permissions see Permissions and default user roles on page 135 To select all permissions in a category select the check box next to the category Note Operations not shown in the following table are available to all user roles Click Save Role Edit a user role From the Roles screen select a user role then click Edit Edit settings as needed You cannot edit the Administrator user role Click Save Role Permissions and default user roles Note To determine the permissions for a default role or to edit it select the role then click Edit The following table shows all user configurable permissions and the settings for the default user accoun
178. lex System O Computer C Monitor c Keyboard af Mouse wl Barcode scanner 7 Connection A Power cables B LAN connection or Ethernet cablet DVI cable Barcode scanner cable E Keyboard cable F Mouse cable Connects the mouse to the computer USB port Supplies 115 230 V depending on the geographic location of the installation Supplied with the QuantStudio 6 and 7 Flex Systems QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 171 Appendix H Instrument Specification and Layout QuantStudio 6 and 7 Flex Systems layout and connections 172 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Symbols on this instrument 066 174 Locations of safety labels on instrument 0 00 cece eee eee eee 177 Safety alerts on this instrument 6 e ec nee ees 178 Instrument safety 2 66 66 dinadak ie baasai hah biaa nee aA 178 Barcode scanner laser safety n nunnu unnan ence cnn eee ees 180 Workstation safety 066 6 180 Safety and electromagnetic compatibility EMC standards 181 Chemical Sate ty nsec cio rsin e ang wine Bod ce nie land wwe E eee age Hae eee 182 Biological hazard safety nuunuu nunnan ete enn 183 WARNING GENERAL SAFETY Using this product in a manner not specified in the user documentation may result in personal injury or damage to the instrument or device Ensure
179. libration data 0 0 0 iertarea a Ne a NA EE EAE 44 Preparing the calibration plate or array card nannan nannan nrnna 44 Prepare the background calibration plate 00 00 eee eee eee eee eee 45 Perform the background calibration 000 cece eee eee eee eens 46 Uniformity calibration seee re ee e eee eee eee ea Ea S A ees 48 When to perform the calibration 00 000 c eee eee eee eee eeee 48 Preparing the calibration plate or array card 0000 cece eee eee eee eee aes 48 Prepare the ROI calibration plate 2 2 2 2 002s 48 Perform the uniformity calibration 0000 cee eee eee eee eee teens 49 Dye calibration circs he i Pee Fahd Ha eee Gain taaa Pence iat Rede eee ees 52 When to perform the calibration 0000 cee eee nennen 52 About the dye calibration data n a naasna cece eee eee e eee ees 52 Preparing the calibration plate or array card 00 000 eee eee eee eee eee eens 53 Prepare the dye calibration plates 0 0c cece eee eee e eens 53 Perform the dye calibration 0 0c eee eee eee eee eeees 54 Normalization calibration 2 c200 tiraa aa a a She a e a eee en a ERa ee 37 When to perform the calibration 0000 cece cece eee eee e eee eee 57 About the calibration data eour ienee a eee c cece cee eee nent n tenes 57 Preparing the calibration plate or array card n s sannau nann ce eee e nnna 57 Prepare the
180. lity of interest Note lt drive gt is the location where the software is installed 2 Ifthe website does not contain the information of interest contact Life Technologies Change the sample block When to change the sample block Materials required How to handle the sample block 106 WARNING PHYSICAL INJURY HAZARD During instrument operation the sample block and heated cover can reach 100 C Allow the sample block to cool to room temperature before removing You can change the sample block To change the consumable format of the QuantStudio 6 or 7 Flex System e In the event of a hardware failure e Safety glasses e Powder free gloves e Sample block To prevent damaging or contaminating the sample block handle the assembly as shown below After the assembly has been removed from the QuantStudio 6 or 7 Flex System place the sample block on a clean dry surface or in its shipping container QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Change the sample block 1 Appendix B Maintenance Change the sample block Power off and unplug the QuantStudio 6 or 7 Flex System then allow it to cool for 15 minutes Open the access door Firmly press down on the handle of the sample block then remove it from the QuantStudio 6 or 7 Flex System Place the sample block on a clean dry surface Install the new sample block into the QuantStudio
181. ll Fencunmables Goneumable Berens Storage Shelf life at storage C temperature Fast 96 Well Spectral Calibration Plate with FAM Dye Fast 96 Well Spectral Calibration Plate with VIC Dye Fast 96 Well Spectral Calibration Plate with ROX Dye Fast 96 Well Spectral Calibration Plate with TAMRA Dye Fast 96 Well Region of Interest ROI and Background Plates Use the consumable e Fast 96 Well Region of Interest ROI 4432638 lt 20 by the expiration date Calibration Plate on the packaging e Fast 96 Well Background Plate Fast 96 Well Normalization Plates with FAM ROX and VIC ROX Dyes e Fast 96 Well Normalization Plate with FAM ROX Dye e Fast 96 Well Normalization Plate with VIC ROX Dye RNase P Fast 96 Well Instrument Verification Plate Fast 96 Well Background Plate 4481308 4432600 4432607 4432614 4432632 4443774 4432656 160 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix G Parts and Materials G Kits consumables and accessories 76 well bl Cancurnable Beno Storage Shelf life at storage consumables j C temperature 96 Well Spectral Calibration Plate with FAM Dye 4432538 96 Well Spectral Calibration Plate with VIC Dye 4432545 96 Well Spectral Calibration Plate with ROX Dye 4432551 96 Well Spectral Calibration Plate with TAMRA Dye 4442918 96
182. ment 19 power switch 19 prepare custom dye plate 153 preparing array cards 36 64 background plate 45 dye plate 53 normalization plate 57 RNase P plate 63 ROI plate 41 48 printing action logs 138 141 144 audit reports 139 user report 136 processor requirements 24 pure dye 192 purge audit records 139 Q quantity 192 quencher 192 R racks robot 22 Raw Data Plot about 192 reaction mix 192 reagents 192 real time PCR 192 reference sample 192 region of interest ROD calibration 192 registration software 104 regression coefficient 192 regression line 192 reject well 193 relative standard curve method 193 reminders calibration 31 33 90 121 remote monitoring computer setup 119 guidelines 120 instrument 120 instrument setup 118 removal lamp 99 repetitive motion safety 180 replace halogen lamp 99 instrument fuses 102 replicate group 193 replicates 193 reporter 193 reports action log 138 141 144 audit 139 electronic signature 144 object audit history 138 141 144 system configuration history 138 139 140 141 144 user 136 requirements component clearances and positioning 168 electrical 169 environmental 169 exhaust venting 169 physical clearances 168 SMTP server 31 121 weight 168 restore audit records 139 instrument settings 86 results transfer to USB drive 84 results transfer to USB drive 84 reverse primer 193 reverse transcriptase 193 RNase P 384 Well Instrument Verification
183. ment laser Moving parts Parties mobiles Potential biohazard Danger biologique potentiel Ultraviolet light Rayonnement ultraviolet Potential slipping hazard Danger de glisser potentiel On On marche Off Off arr t On Off On Off marche arr t Standby En attente Earth ground terminal Borne de mise a la terre Protective conductor terminal main ground Borne de conducteur de protection mise a la terre principale GCOO PEE PEE Ei Terminal that can receive or supply alternating current or voltage Borne pouvant recevoir ou envoyer une tension ou un courant de type alternatif 174 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix Safety Symbols on this instrument Symbol English Francais _ Terminal that can receive or supply Borne pouvant recevoir ou envoyer alternating or direct current or une tension ou un courant continu ou voltage alternatif a Do not dispose of this product in Ne pas liminer ce produit avec les gS 1 unsorted municipal waste d chets usuels non soumis au tri SP CAUTION To minimize negative aa environmental impact from disposal CAUTION Pour minimiser les MEE of electronic waste do not dispose of cons quences n gatives sur electronic waste in unsorted l environnement la suite de municipal waste Follow local l limination de d chets municipal waste
184. minor differences in the optical path Values calculated from the regression line in standard curves including the R2 value slope and y intercept You can use the regression coefficients to evaluate the quality of results from the standards See also standard curve In standard curve and relative standard curve experiments the best fit line from the standard curve Regression line formula Cy m log Qty b where m is the slope b is the y intercept and Qty is the standard quantity See also regression coefficients QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide reject well relative standard curve method replicate group replicates reporter reverse primer reverse transcriptase Rh ROX dye run method sample sample definition file QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Glossary An action that the software performs during analysis to remove one or more wells from further analysis if a specific flag is applied to the well A method to determine relative quantities This method compensates for target and endogenous control efficiency differences within each run In all experiments unknown samples and dilution series of template such as cDNA are amplified Following a run the instrument software interpolates relative quantities for each unknown sample from the appropriate dilution curve then normalizes the d
185. mitted outliers click Reanalyze to analyze the run If the status of the RNase P Run is Failed after performing step 8 12 repeat the RNase P test using a different RNase P plate or array card If the problem persists contact Life Technologies QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 14 15 16 17 Troubleshooting Chapter 2 Calibrate the Instrument Troubleshooting Review the standard curve a Select the Standard Curve tab b Click the upper left corner of the Plate Layout to select all wells c Confirm that the R value is gt 0 990 If the R value is lt 0 990 repeat the RNase P test using a different RNase P plate or array card If the problem persists contact Life Technologies In the Analysis screen click Next remove the plate or array card when the instrument ejects the tray arm then discard the consumable WARNING PHYSICAL INJURY HAZARD During instrument operation the plate or array card can reach 100 C Before removing the consumable be sure to wait until it reaches room temperature Note If the instrument does not eject the plate or array card remove it as explained in RNase P test troubleshooting on page 75 Click Finish then click Yes when prompted to save the test Optional Click Print Report in the upper right corner of the screen to print a summary of the RNase P test results for your records The tables in this section
186. n select the template a Touch amp then touch USB b Touch the desired template then touch Save In the Save Experiment As screen set the name for the file a Touch the New Template Name field then enter a name for the copied file b Touch the Save to Folder field then select the folder to receive the file c Touch Save Touch B to return to the Main Menu Unplug the USB drive Transfer experiments from a USB drive 1 2 Plug a USB drive into the USB port below the touchscreen If the instrument is in standby touch the QuantStudio 6 or 7 Flex System touchscreen to activate it then press In the Main Menu touch Browse Experiments In the Browse Experiments screen select the experiment a Touch m then touch USB b Touch the desired experiment then touch Gy Save In the Save Experiment As screen touch the experiment that you want to transfer to the USB drive then touch Save Touch B to return to the Main Menu Unplug the USB drive QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 83 84 Appendix A Manual Instrument Operation Operate the instrument from the touchscreen Copy experiment results to a USB drive 1 2 7 8 Plug a USB drive into the USB port below the touchscreen If the instrument is in standby touch the QuantStudio 6 or 7 Flex System touchscreen to activate it then press f0 From the Main Menu of the instrume
187. n guide Improper lifting can cause painful and permanent back injury Things to consider before lifting or moving the instrument or accessories Depending on the weight moving or lifting may require two or more persons If you decide to lift or move the instrument after it has been installed do not attempt to do so without the assistance of others the use of appropriate moving equipment and proper lifting techniques Ensure you have a secure comfortable grip on the instrument or accessory Ensure that the path from where the object is to where it is being moved is clear of obstructions Do not lift an object and twist your torso at the same time Keep your spine in a good neutral position while lifting with your legs Participants should coordinate lift and move intentions with each other before lifting and carrying For smaller packages rather than lifting the object from the packing box carefully tilt the box on its side and hold it stationary while someone else slides the contents out of the box 178 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix Safety Instrument safety A CAUTION Moving Parts Moving parts can crush pinch and cut Keep hands clear of moving parts while operating the instrument Disconnect power before servicing Electrical AN WARNING Fuse Installation Before installing the instrument verify that the fuses are properly installed and
188. n the libraries by selecting entries then clicking View Audit History From the Audit Reports dialog box you can perform the actions in the following table To Action Display audit histories 1 Select a tab to display e System Configuration History Security audit and electronic signature configuration records including audit history for each user account e Action Record System specified audit events 2 Optional Select Filter by then filter the table e Sort the table e Specify filters date range user name action object or record type object or record name reason then click Refresh Note The Reason field in System Configuration History is not used e Select one or more records then click View Report Review the action log The Action Record log lists system specified audit events All items in the action log are audited silently except for the items noted as configurable Configurable items may include comments in the action log e Audit Settings Update e Auditing Event Archive Restore Purge e Configuration Import Export e Data Audit Archive Restore Purge e Login Success Failure e Logout Success e Run Start Stop Completed Failed Aborted Error e User Account Create Update 138 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix E Security Audit and Electronic Signature Audit report generation
189. nable Notifications setting From the Enter e mail addresses for notifications field enter the email address that you want to receive the test emails Click Test Configuration to test the mail server settings 32 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Enable or change the calibration reminders Confirm that the email account you specified in step 5d received the test messages from the QuantStudio 6 and 7 Flex Real Time PCR System Software If not consult your network administrator to confirm that the mail server settings are defined correctly Run Status Not Started 50 3 O Enable Notifications CQ Run Notification Settings Amplification Plot Enable Notifications Yes No Temperature Plot Run Method C settings View Run Data Test the current parameters When you press the Test Configuration sample Run Started Instrument Error GIAE Cea Run Stopped and Run Completed messages will be sent TF Modify the 1 Open the Calibration Reminders screen for the QuantStudio 6 or 7 Flex System notification a From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home settings for a tab click Instrument Console monitored b From the Instrument Console select the icon for your instrument then instrument click Manage Instrument Note If the Manage I
190. name of the logged in user Create or edit a user role 134 To Action Edit a user 1 From the Users screen select a user account then click Edit account Note If you select multiple users only Status and Role will be changed 2 Edit settings as needed You cannot edit the user name of an existing user 3 Click Save Activate a 1 From the Users screen select the user suspended 2 Click Edit user account 3 Change the Status from SUSPENDED to ACTIVE then click Save Disable IMPORTANT You cannot delete a user because user records are required inactivate a for auditing To disable a user account inactivate it as follows user account From the Users screen select the user Click Edit Change the Status from ACTIVE to INACTIVE then click Save 1 2 3 Reset a 1 From the Users screen select the affected user account then forgotten click Edit password 2 Enter a replacement password for the user then re enter the password for confirmation 3 If you assigned the user a temporary password then select Password Expires at First Login to require the user to specify a new password at log in 4 Click Save The title bar of the QuantStudio 6 and 7 Flex Real Time PCR System Software window displays the name of the user User roles determine the permissions associated with a user account The QuantStudio 6 and 7 Flex Real Time PCR System Software includes three default user ro
191. nd gloves e Prepare and run calibration plates and array cards within the recommended time limits listed below Consumable Time to thaw After thawed run within All 96 384 well calibration 30 minutes 120 minutes consumablest All array card calibration 30 minutes 120 minutes consumables RNase P plate 96 384 well 5 minutes 30 minutes RNase P array card8 15 minutes 60 minutes t All 96 well plates and 384 well plates used in the calibration of the instrument ROI background uniformity dye and normalization t All array cards used in the calibration of the QuantStudio 7 Flex System only ROI background uniformity dye and normalization or use with QuantStudio ex System only F ith Q Studio 7 Flex S l e Plates only Do not discard the packaging for the calibration plates Each plate can be used to calibrate the QuantStudio 6 and 7 Flex Systems 3 times for up to 6 months if it is stored in its packing sleeve e Store calibration plates or array cards in a dark place until you are ready to use them The fluorescent dyes in the wells of calibration consumables are photosensitive Prolonged exposure to light can diminish the fluorescence of the dyes e Do not allow the bottoms of the plates or array cards to become dirty Fluids and other contaminants that adhere to the bottoms of the consumables can contaminate the sample block and cause an abnormally high background signal e Confirm that yo
192. ndicates that one or more wells produced spectra that deviate significantly from the other wells on the plate or array card Note If the calibration failed the QC tab can provide information regarding the cause of the failure 10 Unload the calibration plate or array card a After the calibration touch z on the touchscreen to eject the plate or array card Note If the instrument does not eject the plate or array card remove it as explained in Background calibration troubleshooting on page 71 b Remove the plate or array card from the instrument tray and discard it A WARNING PHYSICAL INJURY HAZARD During instrument operation the plate or array card temperature can reach 100 C Allow the consumable to cool to room temperature before removing c Touch z on the instrument touchscreen to close the instrument tray 11 From the Background Calibration screen click Finish to complete the calibration then click Yes when prompted to save the results 12 Optional Click Print Report in the upper right corner of the screen to print a summary of the calibration results for your records QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 47 Chapter 2 Calibrate the Instrument Uniformity calibration Uniformity calibration When to perform the calibration Preparing the calibration plate or array card Prepare the ROI calibration plate 48 The uniformity calibration g
193. ne or more steps Examples PCR stage cycling stage also called amplification stage and hold stage A sample that you dilute and amplify along with unknown samples This dilution series can contain known starting quantities of the target of interest absolute standard curve or it can be of known dilution factor relative standard curve Following the run the software interpolates the Cy values of the unknowns to this curve yielding either specific quantities of the target for absolute curves or relative quantities for relative dilution curves See also standard curve In standard curve and relative standard curve experiments e The best fit line in a plot of the Cy values from the standard reactions plotted against standard quantities See also regression line e A set of standards containing a range of known quantities Results from the standard curve reactions are used to generate the standard curve The standard curve is defined by the number of points in the dilution series the number of standard replicates the starting quantity and the serial factor Method for determining absolute target quantity in samples With the standard curve method the software measures amplification of the target in samples and ina standard dilution series Data from the standard dilution series are used to generate the standard curve Using the standard curve the software interpolates the absolute quantity of target in the samples QuantStudio
194. nes e The QuantStudio 6 and 7 Flex Real Time PCR System Software can monitor up to 10 instruments e We do not recommend that a QuantStudio 6 or 7 Flex System be monitored by more than 10 computers simultaneously e Unless you are sure that your QuantStudio 6 or 7 Flex System and computer exist on the same subnet we recommend that you use the IP address of the QuantStudio 6 or 7 Flex System to add it for remote monitoring 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab click Instrument Console QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Download experiment files Enable or change the calibration reminders Appendix C Networking C Monitor the QuantStudio 6 or 7 Flex System 2 From the Instrument Console select the icon for your instrument then click Manage Instrument TM Note If the Manage Instrument button is inactive add your QuantStudio 6 or 7 Flex System to the My Instruments group 3 From the Instrument Manager click Monitor then click Information 4 From the Monitor Instrument screen click Monitor Running Instrument The QuantStudio 6 and 7 Flex Real Time PCR System Software displays the status attributes calibration status and plot data for the selected QuantStudio 6 or 7 Flex System If a communications warning appears contact your network administrator to troubleshoot the problem You can lose
195. nstrument button is inactive add your QuantStudio 6 or 7 Flex System to the My Instruments group c From the Instrument Manager click XK Maintenance then click Calibration Reminders 2 From the Calibration Reminders Setting table configure the notification settings for the calibrations in interest For each calibration that you want to monitor a From the Send a Reminder column select the check box to configure the QuantStudio 6 and 7 Flex Real Time PCR System Software to email a reminder to perform the calibration b From the Reminder Interval column enter the number of days before the calibration expires that the software should send a reminder email 3 From the Enter e mail addresses for notifications field enter the email address es that you want to receive notifications Separate multiple email addresses with commas QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 33 34 Enable or change the calibration Chapter 2 Calibrate the Instrument reminders 4 Click Apply to change the notification settings Calibration Reminders Settings Calibration Background Date Last Calibrated 13 07 2012 11 12 58 PD 13 07 2012 11 27 13 PD Expiry Interval Date Calibration Ex 09 01 2013 11 12 58 PST 12 08 2012 11 27 13 PDT Send an Email Re Reminder Interval Reminder Date 02 01 2013 11 12 58 PST 05 08 2012 11 27 13 P 13 07 2012 11
196. nstrument monitor The instrument monitor screen displays the a The Instrument type QuantStudio 6 Flex System or QuantStudio 7 Flex System b Status of all calibrations including the date and time of each calibration c Maintenance status of the instrument d Properties of the instrument q g _ 278860001 384 Well Block 1 QuantStudio 6 Flex System READY ES Monitor Running Es ent Calibra tion Status mam Amma I Monitor 5 ROI l06 20 2013 09 49 16 SGT GUEST emperature g Background 06 20 2013 09 57 23 SGT GUEST Uniformity 06 20 2013 10 04 14 SGT GUEST E Dye FAM 06 20 2013 10 11 09 SGT GUEST Current VIC 06 20 2013 10 18 06 SGT cuest Current ROX 06 20 2013 10 27 22 SGT GUEST Current 3 b SYBR 06 20 2013 10 37 27 SGT GUEST Current NED 06 20 2013 10 53 57 SGT GUEST Current TAMRA 06 20 2013 10 44 41 SGT GUEST Current MELTDOCTOR 06 21 2013 14 40 54 SGT GUEST Current E Normalization FAM ROX 06 20 2013 11 01 35 SGT GUEST Current VIC ROX 06 20 2013 11 08 56 SGT T Current E HRM RNase P 06 21 2013 09 26 48 SGT UEST Current Maintenance La e RAHA nN a A Lamp Life 46 hours Total Cycles for Block 3 856 Total Degrees for Block 121 250 Instrument Properties aaas TT CD Instrument Label ruo Serial Number 278860001 Instrument Firmware Version 1 0 3 IP Addres
197. nt touchscreen touch Collect Results From the list of experiments touch the experiment s of interest or touch e7 Select All Touch Z Save to USB From the Copy Results To USB screen check that the name of the USB drive is correct to ensure that it is mounted then touch Z Save to USB Touch a to return to the Main Menu Unplug the USB drive Note After the results from a completed run have been collected the corresponding experiment displays Collected and it can be deleted Delete results Once you have collected results from the QuantStudio 6 or 7 Flex System you can use the touchscreen to delete the files from the instrument hard drive 1 2 From the Main Menu of the instrument touchscreen touch Collect Results From the list of experiments touch the experiment s of interest then touch fl Delete When asked to confirm the deletion touch OK Touch A to return to the Main Menu QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Maintain the instrument from the touchscreen Appendix A Manual Instrument Operation Maintain the instrument from the touchscreen Back up and restore the instrument settings The QuantStudio 6 and 7 Flex Systems touchscreen provides access to a few maintenance functions that cannot be accessed remotely from the QuantStudio 6 and 7 Flex Real Time PCR System Software Unlike the maintenance performed using the QuantStudio
198. ntercept 196 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Index 205 Index 206 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Headquarters 5791 Van Allen Way Carlsbad CA 92008 USA Phone 1 760 603 7200 Toll Free in USA 800 955 6288 For support visit www lifetechnologies com support technologies www lifetechnologies com 05 November 2013
199. ntially hazardous situation that if not avoided may AN result in minor or moderate injury It may also be used to alert against unsafe practices WARNING Indicates a potentially hazardous situation that if not avoided AN could result in death or serious injury DANGER Indicates an imminently hazardous situation that if not avoided TAX will result in death or serious injury Except for IMPORTANTs the safety alert words in user documentation appear with an open triangle figure that contains a hazard symbol These hazard symbols are identical to the hazard symbols that are affixed to the instrument See the Safety appendix for descriptions of the symbols Symbols on this instrument 12 Symbols may be found on the instrument to warn against potential hazards or convey important safety information In this document the symbol is used along with the user attention words to highlight important safety information The following table gives the meaning of these symbols Symbol English Francais Caution risk of danger Attention risque de danger Consult the manual for further safety Consulter le manuel pour d autres information renseignements de s curit QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Contents of this manual About This Guide Contents of this manual This guide is divided into the following chapters and appendixes Chapter appendix C
200. o 6 and 7 Flex Real Time PCR System Software that you can install without the aid of Life Technologies service personnel You can obtain updates directly from the service section of the Life Technologies website For the latest services and support information for the QuantStudio 6 or 7 Flex System 1 Go to www lifetechnologies com us en home technical resources software downloads 2 From the Software Downloads page select Applied Biosystems QuantStudio 6 and 7 Flex Systems from the menu 3 From the Applied Biosystems QuantStudio 6 and 7 Flex Systems Software Downloads page click Updates Patches The website opens the page describing the latest software updates for the QuantStudio 6 or 7 Flex System Prepare for the upgrade To prepare for the software update back up all data files and experiments by creating a copy of the directory that you are using to store files The default directories are e Installation directory lt drive gt Program Files Applied Biosystems QuantStudio 6 and 7 Flex Software e Data directory lt drive gt Applied Biosystems AppData QuantStudio 6 and 7 Flex Software e User files directory lt drive gt Applied Biosystems QuantStudio 6 and 7 Flex Software User Files experiments Note lt drive gt is the location where the software is installed Install the software Install the software update according to the instructions that download with the software
201. o having the instrument serviced at your facility or before sending the instrument for repair maintenance trade in disposal or termination of a loan Decontamination forms may be requested from customer service Instrument To minimize negative environmental impact from disposal of electronic waste do no component and dispose of electronic waste in unsorted municipal waste Follow local municipal waste ordinances for proper disposal provision and contact customer service for information disposal accessory CSP about responsible disposal options QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 179 Appendix Safety Barcode scanner laser safety Barcode scanner laser safety Laser classification Laser safety requirements The optional barcode scanners included with the QuantStudio 6 and 7 Flex Systems are categorized as Class 2 II lasers Class 2 II lasers are low power visible light lasers that can damage the eyes Never look directly into the laser beam The scanner is designed to prevent human access to harmful levels of laser light during normal operation user maintenance or during prescribed service operations WARNING LASER HAZARD Class 2 II lasers can cause damage to eyes Avoid looking into a Class 2 II laser beam or pointing a Class 2 II laser beam into another person s eyes Workstation safety 180 Correct ergonomic configuration of your workstation c
202. o order a replacement RNase P plate or array card If the replacement consumable fails contact Life Technologies for assistance Instrument does not eject the RNase P plate or array card the consumable is stuck within the instrument Adhesive cover may have adhered the plate or array card to the heated cover within the instrument Remove the plate or array card from the instrument as explained in Remove a plate stuck within the instrument on page 78 Negative control well displays the AMPNC flag indicating that the well amplified Contamination in one or more PCR reaction components contained in the negative control well Contact Life Technologies to order a replacement RNase P plate or array card kit If the replacement RNase P consumable fails contact Life Technologies for assistance Well displays the BADROX flag indicating that the passive reference signal is unacceptable for the normalization of the reporter dye signal e Droplets on the sides of the wells e Improper sealing or seal leaks e Condensation on the plate or array card If a well is flagged confirm the results 1 Select the flagged wells in the plate layout or well table 2 View the amplification plot R vs Cycle and review the data in the C region for abnormalities 3 Examine the plate or array card to check for condensation and or inconsistent reaction volumes 4 Contact Life Technologies to order a replacem
203. oftware Home tab click Instrument Console From the Instrument Console select your QuantStudio 6 or 7 Flex System from the list of instruments then review the Heated Cover Firmware Version field in the Instrument Properties pane The installation is successful if the QuantStudio 6 or 7 Flex System powers on and if the Heated Cover Firmware Version field displays a version number Check the calibration status of the QuantStudio 6 or 7 Flex System see View the calibration status of an instrument on page 29 If the calibrations for the new sample block heated cover have expired perform the following calibrations in the specified order a ROI calibration b Background calibration c Uniformity calibration d Dye calibration e Normalization calibration IMPORTANT If the calibrations for the new sample block heated cover are valid you do not need to recalibrate the QuantStudio 6 or 7 Flex System QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix B Maintenance Change the plate adapter Change the plate adapter When to change the plate adapter Materials required Change the plate adapter Change the plate adapter in the event of a hardware failure or if you want to change the consumable format of the QuantStudio 6 or 7 Flex System WARNING PHYSICAL INJURY HAZARD During instrument operation the plate adapter can reach 100 C Allow the p
204. ogies does not recommend installing the QuantStudio 6 and 7 Flex Real Time PCR System Software to computers running the Windows Vista operating system If used with the operating system the QuantStudio 6 and 7 Flex Real Time PCR System Software generates errors when saving experiment eds files The default installation of the instrument partitions the computer hard drive to create the logical drives as explained below Drive Software Description C Microsoft Windows OSt Operating system files QuantStudio 6 and 7 Flex Used to calibrate and perform experiments on the Real Time PCR System QuantStudio 6 and 7 Flex System Software Stores the installation files application data files and user files experiments exports and imports C or D QuantStudio 6 and 7 Flex Used to automate the creation of new experiments drive System Command Line Utility and the export of existing experiments Twister Robot Softwaret Controls the Twister Robot stores all of the taught positions for the robot and includes the VBA code required to operate the Twister Robot with the automation control software t We recommend that you do not install programs to the C drive QuantStudio 7 Flex System only TM Before you install third party software to the computer running the QuantStudio 6 and 7 Flex Real Time PCR System Software confirm that the software will not e Restrict Ethernet communicati
205. on e Interfere with QuantStudio 6 and 7 Flex Real Time PCR System Software operation see below To confirm that third party software does not interfere with the QuantStudio 6 and 7 Flex Real Time PCR System Software 1 Install the software to the computer that contains the QuantStudio 6 and 7 Flex Real Time PCR System Software QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 1 Getting Started 1 Instrument consumables 2 Perform several test experiments using dummy plates plates that do not contain reagents Note The goal of the test experiments is to run plates under conditions that match normal instrument operation Therefore the characteristics of the test experiments plate layout and run method must closely resemble your actual experiments Confirm that the QuantStudio 6 and 7 Flex Systems perform each test experiment without producing errors If the QuantStudio 6 and 7 Flex Systems perform the tests successfully perform experiments normally If the QuantStudio 6 and 7 Flex Systems encounter errors during the test runs the software may not be compatible with the QuantStudio 6 and 7 Flex Real Time PCR System Software Instrument consumables The QuantStudio 6 and 7 Flex Systems support a series of specialized consumables through interchangeable sample blocks Use the consumables appropriate for the sample block of your QuantStudio 6 or
206. onitoring 119 120 requirements 24 specifications 168 conforming symbols 176 connections 171 consumables accessories 160 general use 165 kits 160 contamination identifying 78 sample block 96 control 188 control instrument over a network 114 create custom background plate or array card 150 custom dye plate 153 experiments from the instrument 81 creation array cards for calibration 36 Ct algorithm 188 CTFAIL quality flag 66 custom dyes add to software 154 calibration 152 create plate 153 cycle threshold 188 cycling stage 188 D data transfer to from the instrument 83 84 121 data collection 189 date time instrument 88 decontamination safety 179 decontamination sample block 78 96 deleting instrument data 84 delta Rn 189 derivative melt curve plot 189 derivative reporter 189 DHCP support 114 dimensions instrument 168 disable security instrument 92 security software 131 disabling calibration reminders 31 90 121 DNS support 114 dye calibration 189 about 52 about the data 52 performing 54 plate preparation 53 troubleshooting 69 dyes supported 17 E electrical requirements 169 safety 179 electromagnetic compatibility EMC standards 181 198 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide electronic signature administrators actions that allow e sig 143 enable or disable 142 functions that require e sig 143 is signed field 147 when security is disabled 142 el
207. ontent Chapter 1 Getting Started Introduces the QuantStudio 6 and 7 Flex Systems including descriptions of all related hardware and software Chapter 2 Calibrate the Instrument Describes how to maintain a QuantStudio 6 or 7 Flex System including calibration and performance verification Appendix A Manual Instrument Operation Describes how to operate the QuantStudio 6 and 7 Flex Systems manually using the touchscreen interface Appendix B Maintenance Describes how to replace the user serviceable parts of the QuantStudio 6 and 7 Flex Systems and how to resolve infrequent problems that can occur during normal use Appendix C Networking Describes how to install the QuantStudio 6 and 7 Flex Systems to a local area network for remote monitoring and control Appendix D Power On or Off Store and Move Describes how to store move and reinstall the components of the QuantStudio 6 and 7 Flex Systems Appendix E Security Audit and Electronic Signature Describes how to configure the security audit and electronic signature functions of the QuantStudio 6 and 7 Flex Real Time PCR System Software Appendix F Calibration Consumable Preparation Describes how to prepare consumables for custom dye calibration Appendix G Parts and Materials Describes how to order parts accessories and consumables for the QuantStudio 6 and 7 Flex Systems Appendix H
208. or each meaning of each selected action enter the number of e signatures from each user role that are required before the software can execute the associated action For example in the following figure at least two users from the Administrator user role must sign an experiment using the Reviewed and Approved Plate Set Up meaning before a user can start the associated run Actions requiring signatures Signature Required Action eet Report Meaning Administrator Technician Scientist LM Staton scale Reviewed and Approved Plate Set Up 2 o D Reviewed and Approved Results ia 0 0 Reviewed and Approved Template 0 0 0 3 Click Apply Settings If the system is configured to check for a signature before starting a run or printing a report and the data are not signed the QuantStudio 6 and 7 Flex Real Time PCR System Software displays a message when the user clicks Start Run or Print Report Example The e signature system is configured to require signatures from two users from the user account named Administrator before a user can start a run The experiment has not been signed A user attempts to begin the run The following message is displayed QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 143 Appendix E Security Audit and Electronic Signature Generate e signature reports Missing Required Signatures i The requested operation cannot be performed
209. or the QuantStudio 6 or 7 Flex System a From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab click Instrument Console b From the Instrument Console select your QuantStudio 6 or 7 Flex System from the list of instruments on the network then click Add to My Instruments TM Note You must add a QuantStudio 6 or 7 Flex System to your list before you can manage it c After the QuantStudio 6 or 7 Flex System is added to your list select it then click Manage Instrument d From the Instrument Manager click K Maintenance then click Calibration Reminders 2 From the Calibration Reminders Setting table configure the notification settings for the calibrations in interest For each calibration that you want to monitor a In the Expiry Interval column enter the number of days that elapse before the type of calibration expires on the QuantStudio 6 or 7 Flex System b In the Send a Reminder column select the check box to configure the QuantStudio 6 and 7 Flex Real Time PCR System Software to email a reminder to perform the calibration c In the Reminder Interval column enter the number of days that elapse before the software emails recipients a reminder to perform the calibration 3 From the Enter e mail addresses for notifications field enter the email address es that you want to receive email notifications Separate multiple email addresses with commas 4 Click Apply to ch
210. ord for the server if required for access e The Secure Sockets Layer SSL setting of the server on or off Define the mail server settings 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Preferences 2 From the Preferences dialog box select the SMTP Settings tab QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 121 E Appendix C Networking Monitor the QuantStudio 6 or 7 Flex System 3 From the SMTP Settings tab define the settings for the SMTP server e Outgoing Mail Server SMTP field Enter the network address of a Simple Mail Transfer Protocol SMTP server Optionally you can specify the transmission control protocol TCP port for the server by appending the port number to the server name separating the two using a colon For example smtp mycompany com 2023 Note If a TCP port is not specified the QuantStudio 6 and 7 Flex Real Time PCR System Software uses the default port number 25 e Encryption Required Select if the mail server has SSL enabled e Authentication Required Select if the mail server requires a user name and password e User Name and Password fields If the mail server requires authentication enter the user name provided by your systems administrator 4 Click OK Modify the notification settings for a monitored QuantStudio 6 or 7 Flex System 1 Open the Calibration Reminders screen f
211. ordinances for lectroniques ne pas liminer ce proper disposal provision and contact d chet lectronique avec les d chets customer service for information usuels non soumis au tri s lectif Se about responsible disposal options conformer aux ordonnances locales sur les d chets municipaux pour les dispositions d limination et communiquer avec le service a la client le pour des renseignements sur les options d limination responsable conformity Description mark CE Indicates conformity with European Union Directives see Safety and electromagnetic compatibility EMC standards on page 181 c UL Jus Indicates conformity with safety requirements for Canada and U S A Indicates conformity with Australian standards for electromagnetic compatibility QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 175 Appendix Safety Symbols on this instrument Conforming The following table describes symbols that may be displayed on the Life Technologies symbols QuantStudio 6 and 7 Flex Systems consumables or reagents Symbol Description BATCH CODE This symbol is accompanied by the manufacturer s batch code It indicates the lot number CATALOGUE NUMBER The manufacturer s catalogue number will appear after or below this symbol CONSULT INSTRUCTIONS FOR USE This symbol indicates that you should consult the product insert for further
212. ortant for a good fill into the array card 7 When the second run is finished open the centrifuge and check that the fluid levels in the reservoirs of each array card have decreased by the same amount Also check all wells for bubbles and note the locations as possible problems Correct fill Incorrect partial fill peu Re Ws OUUU If necessary centrifuge the array cards for an additional minute to fill any unfilled wells Do not exceed three 1 minute runs or centrifuge the array card for longer than 1 minute at a time 8 Seal the array card s a With the carriage roller assembly of the Array Card Staker Sealer in the Start position place a filled array card into the fixture with the foil side up so that the fill reservoirs are the farthest away from the carriage b Press down on all four corners of the array card to ensure that it is fully seated within the fixture 38 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Preparing array cards for instrument calibration c Use the two alignment pins in the fixture to position the array card correctly d Seal the array card by running the carriage slowly over it Run the carriage over the array card in one direction only Do not apply downward force on the carriage as you move it forward over the card e Remove the sealed array card from the fixture and
213. outliers that caused the initial analysis to fail Error may cause some wells to be amplified insufficiently or not at all These wells typically produce Cy values that differ significantly from the average for the associated replicate wells If included in the calculations these outlying data outliers can result in erroneous measurements 9 From the Amplification Plot select Ct vs Well from the Plot Type menu 10 Confirm the uniformity of each replicate population controls standards and unknowns on the plate or array card by comparing the groupings of Cry values a From the Plate Layout select the wells containing Unknown Population A b From the plot confirm that the Cys of the replicate population are equivalent Note The numbers on the X axis of the plot correspond to the wells of the plate or array card Beginning with well A1 the wells are numbered from left to right and top to bottom QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 67 68 Chapter 2 Calibrate the Instrument Verify the instrument performance c If an outlier is present in the selected population select the corresponding well of the plate layout then click Omit to remove the well from the analysis If the total number of outliers for the replicate population exceeds the limit in the table below repeat the test using another RNase P plate or array card Maximum number of outlier wells t
214. pens load the appropriate plate or array card Ensure that the consumable is properly aligned in the holder e A Load 96 384 well plates with the A1 position at the top left corner of the plate adapter e B Load both plates and array cards with the barcode facing the front of the instrument In the Main Menu touch Browse Experiments In the Experiments screen touch the desired experiment then touch either Start Run to start the run immediately then go to step 10 or e View Edit to view or edit the experiment before starting the run Modify the experiment parameters as needed To e Adda stage or step to the thermal profile touch the stage or step to the left of where you want to add the stage or step then touch Add e Adda melt curve to the end of the thermal profile touch EA Add Melt Curve e Change the time or temperature of a stage or step touch the time temperature field of the stage or step modify the settings as desired then touch Close e Change the cycle parameter of a stage touch the cycle field modify the setting as desired then touch Close e Delete a stage or step from the thermal profile touch the stage or step you want to remove then touch i Delete When finished modifying the parameters touch g Save In the Save Experiment screen touch each field to set the experiment name reaction volume barcode and any additional information to save to the experiment When finished
215. plate that is added to PCR reactions The IPC can be used to distinguish between true negative results the target is absent in the samples and negative results caused by PCR inhibitors incorrect assay setup or reagent or instrument failure See internal positive control IPC See negative control IPC wells A plot of data collected during the melt curve stage Peaks in the melt curve can indicate the melting temperature Tn of the target or they can identify nonspecific PCR amplification In the software you can view the melt curve as normalized reporter Rp vs temperature or as derivative reporter R vs temperature The melt curve shape and the difference in melting temperature Tm values In the thermal profile a stage with a temperature increment to generate a melt curve The temperature at which 50 of the DNA is double stranded and 50 of the DNA is dissociated into single stranded DNA In a melt curve experiment the melt curve plot displays the melting temperature In Melt Curve experiments the region before and after the melting temperature Tm The task for targets or SNP assays in wells that contain water or buffer instead of sample No amplification of the target should occur in negative control wells Previously called no template control NTC In presence absence experiments wells that contain IPC blocking agent instead of sample in the PCR reaction No amplification should occur in negative control bloc
216. protective equipment which includes but is not limited to protective eyewear face shield clothing lab coat and gloves All work should be conducted in properly equipped facilities using the appropriate safety equipment for example physical containment devices Individuals should be trained according to applicable regulatory and company institution requirements before working with potentially infectious materials Read and follow the applicable guidelines and or regulatory requirements in the following In the U S U S Department of Health and Human Services guidelines published in Biosafety in Microbiological and Biomedical Laboratories found at www cdc gov biosafety Occupational Safety and Health Standards Bloodborne Pathogens 29 CFR 1910 1030 found at www access gpo gov nara cfr waisidx_01 29cfr1910a_01 html Your company s institution s Biosafety Program protocols for working with handling potentially infectious materials Additional information about biohazard guidelines is available at www cdc gov In the EU Check local guidelines and legislation on biohazard and biosafety precaution and refer to the best practices published in the World Health Organization WHO Laboratory Biosafety Manual third edition found at www who int csr resources publications biosafety WHO_CDS_CSR_LYO_2004_11 en QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 183 Appendix Safety
217. r 3 If the problem persists contact Life Technologies e Spectra contain peaks in more than one filters e One or more raw spectra exceed the maximum limit for the instrument Fluorescent contaminants are present on the sample block or dye plate or array card Confirm that contaminants are not present by performing a background calibration If the background calibration does not show sample block contamination the dye plate or array card may be contaminated Instrument does not eject the dye plate or array card the consumable is stuck within the instrument The adhesive cover may have adhered the plate or array card to the heated cover within the instrument Remove the plate or array card from the instrument as explained in Remove a plate stuck within the instrument on page 78 Instrument malfunction Multiple possible causes Contact your local Life Technologies Field Service Office B 6unooysayqnos juauunsjsu ay ayeuqneg za4ajydeyg aping UONENSIUIUPY pUe aaueuajuleW SWAaISAS Yd WIL JE Y X 4 pue 9 olpnisiueng 7L Table 5 Normalization calibration troubleshooting Problem symptom Possible cause Action Normalization calibration failed Abnormally low spectra across all wells of the plate or array card CAUTION PHYSICAL INJURY HAZARD During operation the sample block can reach 100 C Before removing the plate or array card wait until the block r
218. r Excel Microsoft Windows Vista and Windows are Healthcare Safari Apple and Macintosh are registered trademarks o registered trademarks of Microsoft Corporation Cy is a registered trademark of GE f Apple Inc Mozilla and Firefox are registered trademarks of Mozilla Foundation Adobe and Acrobat are registered trademarks of Adobe Systems Inc Twister is a registered trademark of Calliper Life Sciences Inc TaqMan is a registered trademark of Roche Molecular Systems Inc used under permission and license 2013 Life Technologies Corporation All rights reserved Contents About This Guide annnnnnnnnn neuen caw av nen orcas pana aene 11 AU FOX lt a Om ame ne NR AEN E E CE SR we 11 AUCIEN CO science hati tocn oe Petes he Soir Aaa ene blot eee Set wae an peal eit 11 ASSUMPTIONS srs ose eie Reis a ee tee ee Se ee ee ne eee eee oe ees 11 UWS r attentlonWwords s 2 2 06 oi hoch eid do oie ibe lites oA ad hod Roath aac 12 Symbols on this instreument sre seri arn danse sien a GPS a al 12 Contents of thissmanual esios ee a A E EE E wens td Man tae eae ee a i 13 CHAPTER 1 Getting Started cc csnctci daca decem el aeind haem 15 Differences between the QuantStudio 6 and 7 Flex Real Time PCR Systems 16 About the QuantStudio 6 and 7 Flex Real Time PCR Systems 0 000 cece c eee eeee 16 Data collection sis dse oases noted ate etd Coe eects ee eee ei T 16 Instrument filters and supported dyes
219. r report 136 user role 134 security auditing and electronic signature module See audit See security security users account suspension 146 login 147 overview 146 password change 147 permissions 146 session timeout 146 self test performing 86 semi annual maintenance 28 serial factor 194 serial port 22 serial port RS232 19 server settings mail 31 service pack updates 106 session timeout 131 146 set up instrument security 92 software security 131 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 203 Index settings date time 88 instrument name 88 instrument security 92 network instrument 90 system shortcuts 91 signing electronic signature 147 slope 194 Smart Monitoring 90 SMTP requirement 31 121 software licenses maintenance 104 third party 24 update 105 specification halogen lamp 99 installation 63 instrument 168 SPIKE quality flag 66 stage 194 staker sealer 36 standard 194 standard curve 194 standard curve method 194 standard quantity 195 standby mode 124 standby time out 88 starting quantity 195 static IP support 114 statistics instrument 91 status lamp 99 step 195 storage instrument 126 surge protector 23 symbols CE 188 conforming 176 oninstrument 174 system configuration history contents 139 140 display 138 141 144 system dye 195 system shortcuts instrument 91 T target 195 204 target color 195 task 195 technical replicate 195 technolog
220. replacement halogen lamp may be defective Replace the lamp again If the second lamp does not illuminate check the QuantStudio 6 or 7 Flex System fuses for failure see page 102 10 After replacing the lamp perform the following calibrations in the specified order a ROI calibration o Background calibration Uniformity calibration 2 p Dye calibration Normalization calibration f RNase P test D QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 101 Appendix B Maintenance Replace the instrument fuses Replace the instrument fuses Replace the QuantStudio 6 or 7 Flex System fuses when the fuses fail CAUTION FIRE HAZARD For continued protection against the risk of fire replace fuses only with listed and certified fuses of the same type and rating as those currently in the QuantStudio 6 or 7 Flex System Materials required e Fuses 12 5A Time Lag T 250VAC 5 x 20 mm 2 e Fuses for AU NZ only 6 3A Time Lag T 250VAC 5 x 20 mm 2 e Safety glasses e Powder free gloves e Screwdriver flathead Replace the fuses 1 Power off then unplug the QuantStudio 6 or 7 Flex System Allow it to cool for 15 minutes 2 Using a flat head screwdriver unscrew and remove the fuse holder 3 Remove each fuse from its fuse holder and inspect it for damage Carbon typically coats the inside of failed fuses Good Failed 4 Replace each failed fuse
221. roubleshooting 69 normalized quantity 191 normalized quantity mean 191 normalized quantity SE 191 normalized reporter Rn 191 NOSIGNAL quality flag 66 notifications security auditing electronic signature 132 notifications maintenance 31 90 NTC 191 Index 0 object audit history display 138 141 144 OFFSCALE quality flag 66 online Help See Help system operating system requirements 24 update 106 order calibration and verification kits 160 from the software 158 from the website 158 how to 158 outlier 191 OUTLIERRG quality flag 66 P passive reference 191 password administrator 130 changing 147 expiration 131 restrictions 131 pdf action log 138 141 144 audit reports 139 performing background calibration 46 dye calibration 54 normalization calibration 58 RNase P test 66 ROI calibration 42 uniformity calibration 49 permissions user account 134 146 physical injury safety 178 planned maintenance 28 plate layout 191 preparation guidelines 25 signing 147 plate adapter 18 installation 111 plates calibration 35 plates calibration 25 pollution requirement 169 port QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 201 Index Ethernet 114 118 power 19 RS232 serial 22 serial RS232 19 USB 19 positions robot racks 22 positive control 191 power LED 21 port 19 22 requirements 169 power instrument on off 124 power line regulator 23 power port instru
222. rray card that you are using Reagent Information Plate Barcode Reagent Name Reagent Part Number Reagent Lot Number Reagent Expiration Date E Check the box when the RO calibration plate has been loaded and when you have ensured you have entered all reagents information correctly eave o gt Z 287880008 x 6 Load the calibration plate or array card into the instrument a From the instrument touchscreen touch B to eject the instrument tray b Load the plate or array card into the plate holder so that e Well A1 of the plate or array card is in the top left corner of the plate adapter e The barcode faces the front of the instrument 00000256 MIIMIMININIMINNINMIN IMPORTANT Plates and array cards should be loaded and unloaded by operators who have been warned of the moving parts hazard and have been adequately trained c From the instrument touchscreen touch B to close the instrument tray 7 After loading the plate or array card start the calibration a From the bottom of the Setup tab select Check the box when the ROI calibration plate has been loaded then click Next 42 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument 2 ROI calibration b From the Run screen click START RUN IMPORTANT Do not attempt to open the access door during the run The door is locked while the instrument is in operation Note Before starting th
223. rsion information View the QuantStudio 6 and 7 Flex Systems log See Enable disable instrument security on page 92 t Tasks for users responsible for day to day use of the instrument Tasks for users who maintain the instrument tt Tasks for systems administrators or for information technology personnel QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix A Manual Instrument Operation Operate the instrument from the touchscreen Operate the instrument from the touchscreen The touchscreen provides limited control of the QuantStudio 6 and 7 Flex Systems to run experiments and transfer data You can perform the following functions from the touchscreen to operate the QuantStudio 6 and 7 Flex Systems without using the QuantStudio 6 and 7 Flex Real Time PCR System Software m Create an experiment from a template 0 6c cece eee eee 81 E Run an experiment icici eee nnen kisansa sanaaa nena daw ee ed ae 82 m Transfer experiments templates and results data 00 e eee ee 83 Note If the QuantStudio 6 or 7 Flex System is operating in secure mode see Enable disable instrument security on page 92 users can only open and close the side door Create an 1 If necessary download the experiment template to the QuantStudio 6 or 7 Flex experiment from a System as described in Transfer experiments from a USB drive on page 83
224. rts below the touchscreen IMPORTANT Do not use the USB ports on the rear panel of the QuantStudio 6 and 7 Flex Systems The rear USB ports are for use by Life Technologies personnel to service the instrument Back up the instrument settings 1 Plug a USB drive into the USB port below the touchscreen 2 From the Main Menu of the instrument touchscreen touch Tools then touch Backup Settings 3 From the Backup Settings screen touch Backup 4 Wait for the backup to complete then touch EJ to return to the Main Menu 5 Unplug the USB drive QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 85 Appendix A Manual Instrument Operation Maintain the instrument from the touchscreen Perform an instrument self test 86 Note For administrative purposes you can reuse the instrument settings saved to the USB drive to configure more than one QuantStudio 6 or 7 Flex System Note that you must configure the network settings for each instrument individually Restore the instrument settings 1 Plug the USB drive that contains the instrument settings into the USB port below the touchscreen 2 From the Main Menu of the instrument touchscreen touch Tools then touch Restore Settings 3 From the Restore Settings screen select the settings to restore a Touch the settings that you want to restore from the list b Touch ine Restore to upload the instrument settings from
225. rty Fluids and other contaminants that adhere to the bottom of the reaction plate can contaminate the sample block and cause an abnormally high background Correct Incorrect Liquid is at e Not centrifuged with enough force or bottom of well e Not centrifuged for enough time Preparing an array IMPORTANT Perform the following procedure only if you are verifying the cardforinstrument Performance of a QuantStudio 7 Flex System with an array card sample block verification Required materials e Array Card Staker Sealer e Centrifuge with centrifuge array card carrier clips and buckets e Powder free gloves e Safety goggles e Pipettor 200 uL with pipette tips e RNase P Array Card Instrument Verification Reagents Kit Array Card RNase P Array Card Instrument Verification Reagents Kit including tubes with reagent mix for each port 8 tubes total Preparing the RNase P Array Card IMPORTANT Wear powder free gloves while preparing the array card 1 Remove the Array Card RNase P Kit from the freezer then allow it to warm to room temperature for approximately 15 minutes IMPORTANT You must fill and run the RNase P array card within 60 minutes of thawing the Array Card RNase P Kit 2 Remove an array card from its box and place it on a clean dry surface 64 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Verify
226. ry to make the QuantStudio 6 or 7 Flex System discoverable by computers that are running the QuantStudio 6 and 7 Flex Real Time PCR System Software Touch Smart Monitoring to enable the feature on the QuantStudio 6 or 7 Flex System The Smart Monitoring feature allows Life Technologies service personnel to monitor the status of the QuantStudio 6 or 7 Flex System remotely through an internet connection Smart Monitoring employs multiple layers of security including a Secure Sockets Layer SSL and Lightweight Directory Access Protocol LDAP authentication to provide real time troubleshooting and problem resolution for the QuantStudio 6 or 7 Flex System For a detailed description of the Smart Monitoring Service see the Smart Monitoring Service Product Bulletin Leveraging the power of the Internet while maintaining system security Part no 121PB07 03 Set the Internet Protocol TCP IP Properties for either DHCP or Static IP communication QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Define the system shortcuts Review the instrument statistics Review the instrument version information Appendix A Manual Instrument Operation Administrate the instrument from the touchscreen Network service Action DHCP Touch Obtain an IP address automatically Static IP 1 Touch Use the following IP address 2 Touch the IP Address field enter the IP address using the keyp
227. s hold temperature and hold time duration are set as part of the tdd file Data collection can also be turned on or off for the ramp or the hold parts of the step in each tdd file For cycling stages a step is also defined by the AutoDelta status Dye supplied by Life Technologies and calibrated on the QuantStudio 6 and 7 Flex Systems Before you use system dyes in your experiments make sure the dye calibration is current in the Instrument Console The nucleic acid sequence to amplify and detect From the software a color assigned to a target to identify the target in the plate layout and analysis plots From the software the type of reaction performed in the well for the target or SNP assay Wells containing identical reaction components including sample important for evaluating precision From the software a display of temperatures for the instrument cover and instrument block during the instrument run The type of nucleic acid to add to the PCR reaction Refers to the entire process of performing a run including setup run and analysis Part of the run method that specifies the temperature time ramp and data collection points for all steps and stages of the instrument run QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 195 Glossary experiment document file eds threshold threshold cycle Cy Tm touchscreen uniformity calibration unknown variant
228. s 172 28 1 105 Block Type 384 Well Block Controller Firmware Version 1 0 2 Optics Firmware Version 24 Thermal Block Firmware Version 20 A Heated Cover Firmware Version 10 L instrument Con 20 RN a 278860001 x 30 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 2 Calibrate the Instrument Enable or change the calibration reminders Note While viewing the Monitor screen you can generate reports of the calibration history and status for the instrument The following options are available from the Instrument Manager Print Calibration Log Prints the calibration history of the instrument Print Maintenance Summary Prints a summary of the current instrument calibrations Note The details for an instrument in the My Preferred list can be exported even if the network connection has been interrupted The exported details from the disconnected instrument would contain the data most recently downloaded from the instrument before the interruption Enable or change the calibration reminders Collect the required information Define the mail server settings The calibration reminder settings allow you to configure the QuantStudio 6 and 7 Flex Real Time PCR System Software to alert you by email when the QuantStudio 6 or 7 Flex System requires calibration The notifications settings feature is optional and it does not affect instrument performance IMPORTANT
229. screen and enable or disable security Set account setup and security policies Use the Security screen to disable and enable security control restrictions and security policies for all user accounts and set up notifications when certain security events occur Note Security is disabled by default To enable or disable security 1 In the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Security gt Settings In the Security Settings dialog box select the System tab Select or deselect Enable Security Note the following e The software requires you to enter your user name and password when you enable security e The enable commands are grayed when a run is in process e When security is disabled the is not active in lower parts of the screen e Disabling Security inactivates Auditing and E Signature IMPORTANT If you disable security you inactivate audit and electronic signature functions however no audit record is generated to indicate that audit and electronic signature functions are disabled IMPORTANT If you enable or disable the QuantStudio 6 and 7 Flex Real Time PCR System Software security auditing and electronic signature feature you must similarly enable or disable the QuantStudio 6 and 7 Flex Systems security see Enable disable instrument security on page 92 The QuantStudio 6 and 7 Flex Real Time PCR System Software cannot connect to QuantStudio
230. setting the maintenance reminders The following figure shows the workflow for calibrating the QuantStudio 6 and 7 Flex Systems Whether you are performing all calibrations or just a subset perform them in the sequence shown below Start Perform an ROI calibration Perform a background calibration Perform a uniformity calibration Perform dye calibrations Perform a normalization calibration Perform an RNase P instrument verification test v Finish You can use the Instrument Console of the QuantStudio 6 and 7 Flex Real Time PCR System Software to view the calibration status of a QuantStudio 6 or 7 Flex System 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab click Instrument Console 2 From the Instrument Console open the Instrument Manager QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 29 Calibration overview Chapter 2 Calibrate the Instrument a Select your instrument icon from the My Instruments group Fie _ Edi Instrument _ Analysis i E New Experiment 2 Ope A B cose M b Click Manage Instrument Re from sea Manage Instrument My Instruments shea patel Note If the Manage Instrument option is inactive connect your QuantStudio 6 or 7 Flex System to the My Instruments group ys Acie All Groups v Bc a My Instruments 1 3 From the Instrument Manager click Monitor then click Information to open the i
231. six color filter set that supports the dyes shown in the following table For more information about the spectral dye calibration kits available for the QuantStudio 6 and 7 Flex Systems please contact Life Technologies Filter wavelength nm t Filter set Color Supported dye Excitation Emission x1 m1 Blue 470 15 520 15 FAM and SYBR Green dyes x2 m2 Green 520 10 558 12 JOE HEX TET and VIC dyest x3 m3 Yellow 549 5410 586 5410 Cy 3 NED and TAMRA dyes x4 m4 Orange 580 10 623 14 ROX and Texas Red dyes x5 m5 Red 640 10 6824 14 Cy 5 and LIZ dyes x6 m 68 Deep red 662 10 711412 Nonett t The central wavelengths are the optimized wavelengths QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 17 1 Chapter 1 Getting Started Instrument hardware t The HEX TET and LIZ dyes from Life Technologies fall within the emission wavelength range of the system therefore they can be added and adapted for use in experiments on the system To add any of these dyes to the Dye Library perform a custom dye calibration For more information see Calibration Consumable Preparation on page 149 QuantStudio 7 Flex System only ttThis filter set currently does not support any dyes supplied by Life Technologies Filters xtemt x2 ma x3 m3 xa ma x5 m5 x6 m6 Wavelength l l l nm Emission Spectra FAM d
232. slope close to 3 32 indicates optimal 100 PCR amplification efficiency Display of data collected during the cycling stage of PCR amplification The Amplification Plot can be viewed as e Baseline corrected normalized reporter AR vs cycle e Normalized reporter R vs cycle e Threshold cycle Cy vs well Part of the instrument run in which PCR amplifies the target The amplification stage called a cycling stage in the thermal profile consists of denaturing primer annealing and extension steps that are repeated Fluorescence data collected during the extension stage are displayed in an amplification plot and the data are used to calculate results With chemistry the last two steps of a PCR stage are typically combined See also cycling stage In a PCR reaction mix two target specific primers or two primers and a probe used to amplify a target PCR reaction component in assays The assay mix contains primers designed to amplify a target and a probe designed to detect amplification of the target QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 187 Glossary automatic baseline automatic threshold background calibration baseline baseline corrected normalized reporter AR blocked IPC CE mark CE chemistry control Cr C algorithm cycle threshold cycling stage 188 An analysis setting in which the software calculates the baseline start and end cycl
233. st for absence of a circle indicates that the region the well position is sufficiently bright of interest for the well position is not sufficiently bright 40 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Preparing the calibration plate or array card Prepare the ROI calibration plate Chapter 2 Calibrate the Instrument 2 ROI calibration IMPORTANT Wear powder free gloves and safety glasses when you prepare plates or array cards Prepare the calibration consumable appropriate for your QuantStudio 6 or 7 Flex System m Prepare the ROI calibration plate nns nauuri eens 41 E Preparing array cards for instrument calibration 0008 36 Materials required e Region of Interest ROI Plate e Centrifuge with plate adapter e Powder free gloves e Safety goggles Prepare the plate IMPORTANT Wear powder free gloves and safety glasses when you prepare the plate 1 Remove the ROI calibration plate from the freezer then thaw it at room temperature for approximately 30 minutes IMPORTANT Use the calibration plate within 2 hours of defrosting it Until you are ready to run the plate store it in the dark and at ambient temperature 15 30 C Do not remove the calibration plate from its packaging until you are ready to run it The fluorescent dyes in the wells of the plate are photosensitive Prolonged exposure to light can diminish the fluoresc
234. standard deviation for the replicate group exceeds the current flag setting Droplets on the sides of the wells Improper sealing or seal leaks Condensation on the plate or array card Inconsistent volumes across the plate or array card Well displays the NOAMP flag indicating that the sample did not amplify Missing template Excitation source in the instrument stopped functioning Well displays the NOISE flag indicating that the well produced more noise in the amplification plot than other wells on the plate or array card Droplets on the sides of the wells Improper sealing or seal leaks Condensation on the plate or array card If a well is flagged confirm the results 1 Select the flagged wellls and the associated replication groupls in the plate layout or well table View the amplification plot Rp vs Cycle and review the data for abnormalities Hold the plate or array card up to a light source and check for condensation or evaporation If there are differences in fluid volumes check the heat seal of the wells with lower volumes for signs of damage or evaporation Contact Life Technologies to order a replacement RNase P plate or array card Repeat the test and make sure to properly centrifuge the RNase P consumable If the replacement RNase P plate or array card fails contact Life Technologies for assistance juawnujsu ay ayeuqneg Zz 4ajdeyg 6unooysayqnos
235. strument 0 0 c ccc eee cence eee eens 29 Enable or change the calibration reminders 000 00 cc cece cece cece eee eee eeees 31 Collect the required information 000 cece eee ence eens 31 Define the mail server settingS 00 000 e cece cece e ee ee eee nee 31 Modify the notification settings for a monitored instrument 0 0000ee ee eee 33 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 3 Contents Guidelines for preparing calibration plates and array cards 0 e eee 35 Preparing array cards for instrument calibration 00000 ccc cece eee ee eee eee eee 36 Required materials 224 225 sis sueee eed oes etd UR Ree eee ye eee ek eee eh tedee ime 36 Filling the calibration array cards 000 cece ee eee eens 36 ROM CaliBFAtiOn Sic e8 ee ok bee ak eed ity ay ALR en Psi ca de A ten E detente CeigeMt 40 When to perform the calibration 0000 cece eee eee eee 40 About the calibration data 0 2 0 ikke ene teen eee e ee ee es 40 Preparing the calibration plate or array card 00000 e eee eee ee eee eae 41 Prepare the ROI calibration plate 2 0 0 0 cece ence eee eee 41 Perform the RO calibration serei sereis eka ae a A e E a e dees 42 Background calibration ei cose rend arae n Gales a h a a A a a a ad 44 When to perform the calibration 0000 0 cece eee eee eee eens 44 About the ca
236. t tray 11 From the ROI Calibration screen click Finish to complete the calibration then click Yes when prompted to save the results Note If the QuantStudio 6 and 7 Flex Real Time PCR System Software displays the warning Saving ROI calibration will invalidate other existing calibrations except HRM Calibrations click OK to proceed Note HRM High Resolution Melt is a separately licensed module If your instrument requires this module contact Life Technologies 12 Optional Click Print Report in the upper right corner of the screen to print a summary of the calibration results for your records QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 43 Chapter 2 Calibrate the Instrument Background calibration Background calibration When to perform the calibration About the calibration data Preparing the calibration plate or array card 44 The software uses the background calibration data during subsequent experiments to remove background fluorescence from the experiment data Perform the background calibration monthly During the background calibration the software captures a series of images of the background plate or array card using each instrument filter The software compares the fluorescence from each well to the average for the plate or array card A background calibration passes if the collected images for all filters are free of abnormal fluorescence Backgro
237. tStudio 6 or 7 Flex System Power off the computer a Select Start Shut Down b From the Shut Down Windows dialog box select Shut Down then click OK Power off the monitor QuantStudio 7 Flex System only If you have an Applied Biosystems Twister Robot toggle the power button on the rear of the Twister Robot QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix D Power On or Off Store and Move Move the QuantStudio 6 or 7 Flex System Move the QuantStudio 6 or 7 Flex System Perform this procedure to safely move the QuantStudio 6 or 7 Flex System short distances for example between laboratories of the same building CAUTION PHYSICAL INJURY HAZARD Do not attempt to lift the QuantStudio 6 or 7 Flex System or any other heavy objects unless you have received related training Incorrect lifting can cause painful and sometimes permanent back injury Use proper lifting techniques when lifting or moving the QuantStudio 6 or 7 Flex System At least two people are required to lift it IMPORTANT Moving your QuantStudio 6 or 7 Flex System can create subtle changes in the alignment of the instrument optics Recalibrate the instrument if necessary How to handle the To prevent damaging or contaminating the sample block or the heated cover handle sample block and the assemblies as shown below After you remove each assembly from the QuantStudio 6 or
238. template 2 If the instrument is in standby touch the QuantStudio 6 or 7 Flex System touchscreen to activate it then press J 3 In the Main Menu touch amp View Templates 4 Inthe View Templates screen touch a template then touch New To view the parameters of a template select the desired template then touch View When finished touch to return to the View Templates screen Note You cannot modify the experiment parameters of a template 5 In the Create New Experiment screen touch each field to set the e Touch the New Experiment Name field and use the keypad to enter a name up to 100 characters for the experiment e Touch the Save to Folder field to open the Select Folder Screen e Touch the Reaction Volume field to enter a reaction volume in uL e Optional Touch the Barcode Number field to enter a barcode and touch the Notes field to enter notes up to 200 characters about the experiment 6 When finished either e Touch gm Save amp Exit or e Touch 5 Save amp Start Run to proceed to the Start Run screen QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 81 Appendix A Manual Instrument Operation Operate the instrument from the touchscreen Run an experiment 1 82 If the instrument is in standby touch the QuantStudio 6 or 7 Flex System touchscreen to activate it then press 8 In the Main Menu screen then touch gB When the side door o
239. the USB drive IMPORTANT Do not remove the USB drive from the QuantStudio 6 or 7 Flex System until instructed Note Alternatively touch Restore Default Settings to restore the QuantStudio 6 or 7 Flex System to the factory settings 4 After the QuantStudio 6 or 7 Flex System restarts unplug the USB drive You can use the QuantStudio 6 or 7 Flex System touchscreen to perform a comprehensive self test of the QuantStudio 6 or 7 Flex System subsystems After the self test is complete the QuantStudio 6 or 7 Flex System generates two files that provide a detailed summary of the instrument condition and function In the event of a problem you can save the results files to a USB drive and email them to Life Technologies technical support for a diagnosis Note We recommend running the self test as part of regular maintenance to ensure optimal performance of the QuantStudio 6 or 7 Flex System 1 From the Main Menu of the instrument touchscreen touch Tools then touch Run Self Test 2 From the Self Test screen touch M Start Self Test then wait for the test to complete 3 Optional When the QuantStudio 6 or 7 Flex System completes the self test save the results to a USB drive a Plug a USB drive into the USB port below the touchscreen IMPORTANT Do not use the USB ports on the rear panel of the QuantStudio 6 and 7 Flex Systems The rear USB ports are for use by Life Technologies personnel to
240. the consumable by the expiration date on the packaging 4432620 4432500 162 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix G Parts and Materials G Kits consumables and accessories Array card consumables Consumable Storage Shelf life at storage garuna C temperature Array Card Spectral Calibration Dye Kit Array Calibration with FAM Dye Array Calibration with VIC Dye Array Calibration with ROX Dye Array Calibration with ROI Dye Array Background Buffer Array Calibration with FAM ROX Dye Array Calibration with VIC ROX Dye 4432644 Kit RNase P Array Card Instrument Verification Reagents Port 1 NTC Port 2 Unknown A Port 3 Unknown B Port 4 Standard 200 Copies Port 5 Standard 400 Copies Port 6 Standard 800 Copies Port 7 Standard 1600 Copies Port 8 Standard 3200 Copies Use the consumable lt 20 by the expiration date on the packaging 4432650 Array Card Background Buffer Kit Background Buffer 6 tubes Array Card Kit empty 6 pack 4481307 Note The Array Card block consumables are applicable only to the QuantStudio 7 Flex System QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 163 G Appendix G Parts and Materials Kits consumables and accessories QuantStudio 6
241. the instrument performance 3 Using a permanent marker mark the side of the empty array card with RNase P 4 Transfer 100 uL of each solution into the appropriate port of the array card ff 4234 5 16 7 8 9 10 14 12 13 14 15 16 17 18 19 20 21 22 23 24 PORT A Cc 1 D 2 D 3 S a 4 j a 5 K a 6 a 7 P andard 3 8 For each transfer a Place the array card on a lab bench with the foil side down b Load 100 uL of fluid into a pipette c Hold the pipette in an angled position 45 degrees and place the tip into the fill port The fill port is the larger of the two holes on the left side of the fill reservoir Fill Vent port port 4 6 uu d Dispense the fluid so that it sweeps in and around the fill reservoir toward the vent port Pipet the entire 100 uL into the reservoir but do not go past the first stop of pipettor plunger or you may blow the solution out of the port IMPORTANT Do not allow the tip to contact and possibly damage the coated foil beneath the fill port 5 Centrifuge and seal the array card as explained in steps a through 8 on page 37 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 65 Chapter 2 Calibrate the Instrument Verify the instrument performance 6 Run the prepared array card as soon as poss
242. then click OK QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 125 Appendix D Power On or Off Store and Move Store the QuantStudio 6 or 7 Flex System 3 Power off the monitor 4 QuantStudio 7 Flex System only If you have an Applied Biosystems Twister Robot toggle the power button on the rear of the Twister Robot Store the QuantStudio 6 or 7 Flex System Materials required Prepare the QuantStudio 6 or 7 Flex System 126 The QuantStudio 6 or 7 Flex System can be powered off and stored for extended periods of time The length of the period of inactivity determines the method you use to power off the QuantStudio 6 or 7 Flex System Reaction plate or array card unused 1 If you plan to store the QuantStudio 6 or 7 Flex System for more than a week or you plan to move it load an unused plate or array card into the QuantStudio 6 or 7 Flex System Note The empty plate or array card protects the internal components of the QuantStudio 6 or 7 Flex System during transport or during periods of inactivity lasting more than a week a Touch O in the QuantStudio 6 or 7 Flex System touchscreen b Touch BD to eject the tray arm place a plate or array card onto the plate adapter then press P again to load the plate c Touch 0 to place the QuantStudio 6 or 7 Flex System into stand by mode Toggle the power button on the rear of the Quan
243. this configuration the computers on the network can exchange experiments with the QuantStudio 6 or 7 Flex System computer however the QuantStudio 6 or 7 Flex System can be neither monitored nor controlled remotely because it is physically isolated from the network DHOP server Networked Networked Instrument computer computer QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 115 G Appendix C Networking Networking overview Networking guidelines and best practices 116 Consult a network administrator We recommend that you consult a network administrator before connecting the QuantStudio 6 or 7 Flex System to your laboratory network TM To enable the full functionality of the QuantStudio 6 and 7 Flex Real Time PCR System Software the computer requires a network connection Limit remote monitoring to 10 computers Avoid using more than 10 computers to simultaneously monitor the QuantStudio 6 or 7 Flex System remotely Although the QuantStudio 6 or 7 Flex System supports remote monitoring from multiple computers each connection taxes the instrument microprocessor Too many connections can overburden the QuantStudio 6 or 7 Flex System and result in instrument errors Note The effects of an overburdened QuantStudio 6 or 7 Flex System are evident in the Temperature Plot during a run Symptoms can include extended hold times or brief
244. tion Perform a normalization calibration As needed Perform an RNase P instrument verification run Replace the instrument lamp t You can perform a background calibration to check for contamination t After replacing the instrument lamp perform all calibrations and an RNAse P instrument verification run The instrument requires regular planned maintenance by Life Technologies service personnel to ensure that the instrument is operating within the installation specification The planned maintenance service can help you maximize your productivity by minimizing downtime lowering the cost of ownership by addressing potential problems before they manifest lost data samples or reagents and increasing the quality of your results by maintaining your instrument at optimal performance For more information contact your Life Technologies sales representative QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide About maintenance reminders Calibration workflow View the calibration status of an instrument Chapter 2 Calibrate the Instrument Calibration overview The QuantStudio 6 and 7 Flex Real Time PCR System Software features an automated notification system that alerts you of required calibrations The feature will also prevent you from operating an instrument that is out of calibration See Enable or change the calibration reminders on page 31 for more information on
245. tive control blocked IPC wells The CE Mark an acronym for the French Conformite Europeene of conformity certifies that a product has met the essential requirements of the applicable European Directive See reagents Sample of known genotype or melt curve shape See threshold cycle CT The QuantStudio 6 and 7 Flex Real Time PCR System Software uses the Baseline Threshold algorithm See threshold cycle CT In the thermal profile a stage that is repeated A cycling stage is also called an amplification stage See also amplification stage QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide data collection delta R AR derivative melt curve plot derivative reporter Rr dissociation curve dye calibration EFF error filter flag forward primer heterozygote holding stage Glossary During the instrument run a process in which an instrument detects fluorescence data from each well of the plate or array card The instrument transforms the signal to electronic data and saves the data in the experiment file See baseline corrected normalized reporter DRn The default view of the melting curve It plots the negative derivative data R vs temperature Note An alternative view is the raw data view which plots the normalized fluorescence from reporter dye vs temperature The rate of change in fluorescence as a function of temperature R
246. to control the auditing state disabled or enabled the events that screen and enable are audited and the reasons available to users when audit mode is set to Prompt or or disable auditing Required Note Auditing is disabled by default IMPORTANT If you disable security you inactivate audit and electronic signature functions however no audit record is generated to indicate that audit and electronic signature functions are disabled To enable auditing 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Security gt Settings 2 From the Security Settings dialog box select the Audit tab 3 Select or deselect Enable Audit 4 Click Apply Settings Modify the auditing eran settings Select objects to 1 In the Audit Settings group of the Audit tab select the objects to audit audit and the mode for each enabled item Experiments Experiment Templates or Study 2 Set the Audit Mode for each item you enable for auditing e Optional The event is audited a reason prompt is displayed but the user can cancel and continue without entering a reason e Required The event is audited a reason prompt is displayed and the user must specify a reason e Silent The event is audited no reason prompt is displayed 3 Click Apply Settings Create audit You can create modify and delete the reasons that are available for reason settings selection in the Audit Reason dialog
247. to create a new account Store Log In OR Register To log into the Applied Biosystems Store enter your user name Ifyou do not i and password then click Log In and Submit have an Applied Biosystems User Name account click the link below to create a new Password l raat account Log In and Submit Register Now J Remember my user name and password for future orders Note If you do not have an account with the Life Technologies Store click Register Now to create an account When you are connected to the Life Technologies Store follow the prompts to complete your order QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 159 G Appendix G Parts and Materials Kits consumables and accessories Kits consumables and accessories The following kits consumables and reagents are to be used with the QuantStudio 6 and 7 Flex Systems m Fast 96 well consumables 0 00 cee ccc cece tenet nee n eens 160 M 96 well consumables 0 0 ccc cc cee eee e eee n ee ereere 161 M 384 well consumables 0 00 c ce cece teen tence nee n eens 162 m Array card consumables 0 eee 163 E QuantStudio 6 and 7 Flex Systems accessories 6 6 cece eee eee 164 Note For reagent or consumable shelf life expiration date see the package label Note The QuantStudio 6 Flex System does not support the Array Card block Fast 96 we
248. to the nearest network port internet 2 Power on the QuantStudio 6 or 7 Flex System protocol settings From the Main Menu of the touchscreen touch Settings then touch Set Network Information Note The Set Network Information screen displays the Media Access Control MAC address of the QuantStudio 6 or 7 Flex System below the Autodiscovery and Smart Monitoring check boxes The MAC address can be used to uniquely identify the QuantStudio 6 or 7 Flex System on the network 4 Touch Autodiscovery to make the QuantStudio 6 or 7 Flex System discoverable by computers that are running the QuantStudio 6 and 7 Flex Real Time PCR System Software 5 Touch Smart Monitoring to enable the feature on the QuantStudio 6 or 7 Flex System The Smart Monitoring feature allows Life Technologies service personnel to monitor the status of the QuantStudio 6 or 7 Flex System remotely through an internet connection Smart Monitoring employs multiple layers of security including a Secure Sockets Layer SSL and Lightweight Directory Access Protocol LDAP authentication to provide real time troubleshooting and problem resolution for the instrument For a detailed description of the Smart Monitoring Service see the Smart Monitoring Service Product Bulletin Leveraging the power of the Internet while maintaining system security Part no 121PBO07 03 6 Set the Internet Protocol TCP IP Properties for either DHCP or Static IP
249. transport the QuantStudio 6 or 7 Flex System is clear of obstructions At least two people are needed to lift and carry the QuantStudio 6 or 7 Flex System Keep your spine in a good neutral position Bend at the knees and lift with your legs Do not lift an object and twist your torso at the same time Coordinate your intentions with your assistant before lifting and carrying Reconnect the components of the QuantStudio 6 or 7 Flex System Use the Ethernet cable supplied with the instrument to connect the QuantStudio 6 or 7 Flex System to the network interface card in the computer IMPORTANT Do not use a standard Ethernet cable to connect the QuantStudio 6 or 7 Flex System to the computer Install the sample block and heated cover assemblies Perform a RNase P instrument verification run If the run Passes Do not recalibrate the QuantStudio 6 or 7 Flex System No further action is necessary Fails Perform the following calibrations in the specified order a ROI b Background c Uniformity d Dye e Normalization QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Administrator Overview 0 eee eee ee Configure the security system cece eee eee User account management 00 cece cece eee ees Audit trail management 0 66 60 c cece eee ee Audit report generation 0 2 6 cece eens M
250. ts Permissions Default user roles 5 H 38 AEE g d Category Function aae E a Setup Create and edit experiments or experiment Yes No Yes templates includes running experiments Create edit and import sample attributes Yes No Yes Run Perform a run using the Quickstart function Yes No Yes Start a run Yes No Yes Stop a run Yes No Yes Targets Library Create targets Yes No Yes Edit targets Yes No Yes Delete targets Yes No Yes Analysis Create analysis settings includes default settings Yes No Yes Settings Edit analysis settings includes default settings Yes No Yes Library Delete analysis settings Yes No Yes Run Methods Create a run method Yes No Yes Library Delete a run method Yes No Yes Dye Library Create a custom dye Yes No Yes Delete a dye Yes No Yes 135 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix E Security Audit and Electronic Signature User account management Permissions Default user roles 5 H 8 amp 8 flee ae Category Function 2 aio I a Study Create or edit a study for example edit a plate or Yes No Yes analysis settings Add transfer experiments to a study Yes No Yes Remove experiments from study Yes No Yes Preferences Edit the system preferences Yes No Yes Export the system preferences Yes No
251. und fluorescence Fluorescence data collected by the instrument includes a fluorescence signal inherent to the instrument referred to as background fluorescence Background fluorescence is a composite signal found in all spectral data that consists of fluorescence from several sources including e Background electronic signal e Contaminants in the sample block e The plastic consumable plate or array card IMPORTANT Wear powder free gloves and safety glasses when you prepare plates or array cards Prepare the calibration consumable appropriate for your QuantStudio 6 or 7 Flex System m Prepare the background calibration plate 0 eee 45 E Preparing array cards for instrument calibration 0 e eee eee ee 36 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Prepare the Materials required background e Background Plate calibration plate E Centrifuge with plate adapter e Powder free gloves e Safety goggles Prepare the plate Chapter 2 Calibrate the Instrument Background calibration IMPORTANT Wear powder free gloves and safety glasses when you prepare the plate 1 Remove the background calibration plate from the freezer then thaw it at room temperature for approximately 30 minutes IMPORTANT Use the calibration plate within 2 hours of defrosting it Until you are ready to run the plate store it in the dark and at ambient temperature 15 30 C
252. unexpected plateaus in the instrument Temperature Plot Observe the restrictions to mDNS and Autodiscovery The QuantStudio 6 or 7 Flex System supports mDNS but only when the QuantStudio 6 or 7 Flex System and computer share a direct network connection and are within the same subnet Consequently network computers that are separated from the QuantStudio 6 or 7 Flex System by a router hub or another network device may not be able to access the QuantStudio 6 or 7 Flex System by its host name Confirm the uniqueness of the instrument name The QuantStudio 6 or 7 Flex System does support name resolution but the instrument name must be unique within the subnet The QuantStudio 6 and 7 Flex Real Time PCR System Software can automatically discover QuantStudio 6 or 7 Flex Systems on the link local network that are configured for Autodiscovery Note The QuantStudio 6 or 7 Flex System does not test the uniqueness of the instrument name when it is set Name QuantStudio 6 and 7 Flex Systems using lowercase letters When you define the QuantStudio 6 and 7 Flex Systems settings enter the instrument name using lowercase letters only QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix C Networking C Network setup workflow Network setup workflow The following figure illustrates the workflow for installing the QuantStudio 6 or 7 Flex System to a local area network
253. ur centrifuge is clean Before centrifugation wipe down the bucket s using a tissue e Vortex and centrifuge all calibration plates to ensure complete mixing and that all reagents are contained at the bottom of the wells The calibration plates must be well mixed and centrifuged before use QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 35 Chapter 2 Calibrate the Instrument Preparing array cards for instrument calibration Preparing array cards for instrument calibration IMPORTANT Perform the following procedure only if you are verifying the performance of a QuantStudio 7 Flex System with an array card sample block The QuantStudio 6 Flex System does not support the array card sample block Required materials e QuantStudio 7 Flex System Array Card Spectral Calibration Dye Kit Array Cards empty Array Card Spectral Calibration Dye Kit including FAM dye mix VIC dye mix ROX dye mix ROI dye mix Background Buffer FAM ROX dye mix and VIC ROX dye mix e Array Card Staker Sealer e Centrifuge with array card buckets and array card carrier clips e Permanent marker or pen e Pipettor 200 uL with pipette tips e Powder free gloves e Safety glasses Filling the IMPORTANT Wear powder free gloves while creating the calibration array cards calibration array a cards This procedure explains how to create all of the array cards required to calibrat
254. user exceeds maximum number of allowed failed authentications login attempts with an incorrect password e User session timed out No activity occurred in a user account for the specified period of inactivity QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix E Security Audit and Electronic Signature User account management 4 Select the notification method e Notify Admin at Login If an event triggers notification the next time any user with an Administrator role logs in the software lists those events indicating the time each event occurred and the user who triggered the event The Administrator has the option of acknowledging the event which removes it from the notification list e Email Notification If an event triggers notification the QuantStudio 6 and 7 Flex Real Time PCR System Software sends an email to the addresses in the adjoining Email Address column of the table The email notification displays the triggered event and displays the time that the event occurred and the user who triggered the event 5 Click OK User account management Create or edit user The software includes a default Administrator user account with permissions defined accounts by the account user role to perform all functions in the software You cannot modify this account 1 From the QuantStudio 6 and 7 Flex Real Time PCR System Software select Tools gt Security gt Sett
255. utes at lt 1500 rpm Note The custom dye calibration plate must be well mixed and centrifuged 5 Verify that the liquid in each well of the plate is at the bottom of the well If not centrifuge the plate again at a higher rpm and for a longer period of time Correct Incorrect Za Liquid is at e Not centrifuged with enough force or bottom of well e Not centrifuged for enough time QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 153 Appendix F Calibration Consumable Preparation Create a custom dye plate for calibration Add the custom dye 1 Start the dye calibration to the software a In the Home screen of the QuantStudio 6 and 7 Flex Real Time PCR System Software click Instrument Console b In the Instrument Console select your QuantStudio 6 or 7 Flex System from the list of instruments on the network then click Add to My Instruments c Select the QuantStudio 6 or 7 Flex System then click Manage Instrument d In the Instrument Manager click Maintenance then click Dye e In the Background Calibration screen click Start Calibration 2 In the Dye window select a custom dye from the list or create the custom dye a Click New Dye b In the Dye Library dialog box click New c Complete the New Dye dialog box then click OK Field option Action Name Enter a name for the custom dye Wavelength Enter the wavelength at which the dye fluoresc
256. website click QuantStudio 6 and 7 Flex Real Time PCR System Software from the list of products then activate the license as instructed After you successfully activate the license the Life Technologies website emails you the activated license file lic to install on your computer After you activate a license and receive an activated license file lic install the file as explained below to unlock the QuantStudio 6 and 7 Flex Real Time PCR System Software or module Note Each license file is generated specifically for the computer that was used to activate the license key 1 TM Save the license lic file to the computer that contains the QuantStudio 6 and 7 Flex Real Time PCR System Software QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix B Maintenance Update the QuantStudio 6 and 7 Flex Real Time PCR System Software 2 From the QuantStudio 6 and 7 Flex Real Time PCR System Software Home tab select Tools gt License Central 3 From the License Central dialog box click Install License 4 From the Open dialog box navigate to and select the license file then click Open 5 Click OK to close the License Central dialog box Note Contact Life Technologies support if the software fails to install the license Update the QuantStudio 6 and 7 Flex Real Time PCR System Software Update the software Life Technologies may release updates to the QuantStudi
257. with a 12 5A Time Lag T 250VAC 5 x 20 mm Fuse Note The voltage and amperage ratings are on the fuse holder Note For AU NZ only replace each failed fuse with a 6 3A Time Lag T 250VAC 5 x 20 mm Fuse 5 Install the fuse holder 6 Plug in then power on the QuantStudio 6 or 7 Flex System The installation is successful if the instrument powers on Note Fuse failure can result from fluctuations in the supplied power to the QuantStudio 6 or 7 Flex System To prevent further failures consider installing an electrical protective device such as a UPS or a surge protector 102 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Appendix B Maintenance Install the QuantStudio 6 and 7 Flex Real Time PCR System Software Install the QuantStudio 6 and 7 Flex Real Time PCR System Software If you have extra software licenses you can install the QuantStudio 6 and 7 Flex Real Time PCR System Software to computers that meet the operating requirements not recommend Computer See Computer requirements on page 24 for a list of hardware and operating system requirements requirements for the QuantStudio 6 and 7 Flex Real Time PCR System Software Install the software 1 Load the QuantStudio 6 and 7 Flex Real Time PCR System Software CD into the computer 2 From the QuantStudio 6 and 7 Flex Real Time PCR System Software Installer click Install QuantStudio 6 and 7 Fle
258. x Real Time PCR System Software 3 Complete the installation as instructed using the default settings e From the Welcome window enter your customer information e From the License Agreement screen accept the terms of the agreement e From the Installation Location screen accept the default location e From the License screen install the license key file that you obtained from Life Technologies The QuantStudio 6 and 7 Flex Real Time PCR System Software installation requires several minutes 4 Eject the CD when the installation is complete QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 103 Appendix B Maintenance Manage QuantStudio 6 and 7 Flex Real Time PCR System Software licenses Manage QuantStudio 6 and 7 Flex Real Time PCR System Software licenses QuantStudio 6 and 7 Flex Real Time PCR System Software license keys and files Activate a license Install a license file 104 You can use the License Central feature to activate or install the licenses that control access to the QuantStudio 6 and 7 Flex Real Time PCR System Software base application and associated modules The QuantStudio 6 and 7 Flex Real Time PCR System Software and associated modules require the installation and maintenance of valid license files for continued operation The license files are generated by the Life Technologies website when a license key is activated Each file pairs a software
259. ye VIC dye TAMRA dye ROX dye Cy 5 dye SYBR Green dye JOE dye Cy 3dye Texas Red dye NED dye Custom dyes The QuantStudio 6 and 7 Flex Systems can run assays designed with custom dyes dyes not supplied by Life Technologies that are excited between 455 to 672 nm and read between 505 to 723 nm To add a custom dye to the Dye Library perform a custom dye calibration For more information see Calibration Consumable Preparation on page 149 Instrument hardware The QuantStudio 6 and 7 Flex Systems consist of the components shown in the following figure and described in the subsequent table Front 18 QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Rear QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide Chapter 1 Getting Started 1 Instrument hardware Component Description A USB ports Provide USB communication with the instrument Can be used to transfer data to and from the instrument Note If multiple USB drives are plugged into the instrument the instrument mounts only the first drive that is installed regardless of the USB port used B Touchscreen Provides access to the instrument functions Can be used to run experiment transfer data and operate the instrument functions without the use of the computer C Access door Provides access to the instrument lamp the heated cover
260. ystems include a suite of software applications that can be used to calibrate run automate and integrate the instrument into a laboratory workflow The installation of the software contains the components described below however additional software may be available for the QuantStudio 6 and 7 Flex Systems Visit the QuantStudio 6 and 7 Flex Systems website for a complete list of compatible software and for updates and patches for the QuantStudio 6 and 7 Flex System software and firmware www lifetechnologies com us en home technical resources software downloads QuantStudio 6 and 7 Flex Real Time PCR Systems Maintenance and Administration Guide 23 1 Chapter 1 Getting Started Instrument software Computer requirements Software installation Third party software 24 The requirements for the computer used to operate the QuantStudio 6 and 7 Flex Systems can vary depending on the version of the QuantStudio 6 and 7 Flex Real Time PCR System Software that you are running To determine the computer requirements for your QuantStudio 6 or 7 Flex System check the QuantStudio 6 and 7 Flex Real Time PCR System Software release notes at the following location lt drive gt Program Files Applied Biosystems QuantStudio 6 and 7 Flex Software QuantStudio 6 and 7 Software README docx Note lt drive gt is the location where the software is installed IMPORTANT Due to a known incompatibility Life Technol

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