Applied Biosystems QuantStudio 6 Flex User Manual Download Page 55

Page: 55 / 194

Block

Plate

96-well 0.1-mL block

QuantStudio

™

3/5 Spectral Calibration Plate 1, (FAM

™

, VIC

™

, ROX

™

, and SYBR

™

dyes), 96-well,

0.1 mL

QuantStudio

™

3/5 Spectral Calibration Plate 2 (ABY

™

, JUN

™

, MUSTANG PURPLE

™

dyes),

‑

well Fast (0.1

‑

mL) Plate

QuantStudio

™

3/5 Spectral Calibration Plate 3 (TAMRA

™

, NED

™

and Cy

5 dyes)

‑

well Fast (0.1

‑

mL) Plate

384-well block

QuantStudio

™

5 Spectral Calibration Plate 1, (FAM

™

, VIC

™

, ROX

™

TAMRA

™

, and SYBR

™

dyes),

384-well

QuantStudio

™

5 Spectral Calibration Plate 2 (ABY

™

, JUN

™

, MUSTANG PURPLE

™

, NED

™

, and

5 dyes), 384-well

• Centrifuge with plate adapter
• Powder-free gloves
• 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.

Remove the dye calibration plate from the freezer, then thaw it at room

temperature for 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

℃

). Do not remove the plates from their packaging until you

are ready to run them.

Before using each dye plate, vortex the plate for 5 seconds, centrifuge it for

2 minutes at < 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.

Chapter 2

Calibrate the instrument

Dye calibration

QuantStudio

™

6 and 7 Flex Real-Time PCR Systems v1.6 Maintenance and Administration Guide

Summary of Contents for QuantStudio 6 Flex

Page 1: ... Not for use in diagnostic procedures QuantStudio 6 and 7 Flex Real Time PCR Systems USER GUIDE Maintenance and Administration for use with QuantStudio Real Time PCR Software v1 6 Publication Number MAN0018828 Revision A 0 ...

Page 2: ...tware v1 6 Important Licensing Information These products may be covered by one or more Limited Use Label Licenses By use of these products you accept the terms and conditions of all applicable Limited Use Label Licenses TRADEMARKS All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified Internet Explorer Excel Microsoft and Windows are registered...

Page 3: ... Front 16 Rear 17 Barcode scanner 18 Twister Robot components 19 Electrical protective devices 22 Instrument software 22 Computer requirements 22 Software installation 23 Third party software 23 Instrument consumables 24 Interchangeable sample blocks heated covers and plate retainers 25 CHAPTER 2 Calibrate the instrument 26 Calibration overview 27 Calibration and maintenance schedule 27 Calibratio...

Page 4: ...te or array card 46 Prepare the background calibration plate 46 Perform the background calibration 47 Uniformity calibration 49 When to perform the calibration 49 Preparing the calibration plate or array card 50 Prepare the ROI calibration plate 50 Perform the uniformity calibration 51 Dye calibration 53 When to perform the calibration 53 About the dye calibration data 53 Preparing the calibration...

Page 5: ...0 Define the date and time 91 Define the instrument settings 91 Define the maintenance reminders 93 Define the network settings 93 Define the system shortcuts 94 Review the instrument statistics 94 Review the instrument version information 95 Enable or disable instrument security 95 View the instrument log 96 APPENDIX B Maintenance 97 Decontaminate the sample block 97 Materials required 98 How to ...

Page 6: ...etworked QuantStudio 6 and 7 Flex Systems 113 About the ethernet port 114 Example network layouts 114 Networking guidelines and best practices 115 Network setup workflow 116 Collect the required network information 116 Connect the QuantStudio 6 or 7 Flex System to the network 117 Materials required 117 Define the instrument internet protocol settings 117 Connect the computer to the network 118 Mat...

Page 7: ...or disable security 131 Set account setup and security policies 132 Set up messaging notifications 132 User account management 134 Create or edit user accounts 134 Determine the name of the logged in user 135 Create or edit a user role 135 View or print a user report 137 Audit trail management 138 Access the audit screen and enable or disable auditing 138 Modify the auditing settings 139 Audit rep...

Page 8: ...the software 155 APPENDIX G Parts and materials 158 How to order 158 How to order from the system software 158 Kits consumables and accessories 159 Standard 96 well consumables 160 Fast 96 well consumables 160 384 well consumables 161 Array card consumables 161 QuantStudio 6 and 7 Flex Systems accessories 162 QuantStudio 6 and 7 Flex Systems empty plates and array cards 162 General use materials a...

Page 9: ...Cleaning and decontamination 176 Instrument component and accessory disposal 176 Laser safety barcode scanner 176 Workstation safety 177 Safety and electromagnetic compatibility EMC standards 177 Safety standards 178 EMC standards 178 Environmental design standards 178 Chemical safety 179 Biological hazard safety 181 APPENDIX J Documentation and support 182 Related documentation 182 Customer and t...

Page 10: ...are Getting Started Guide Pub No 4489822 High Resolution Melt Module for QuantStudio 6 and 7 Flex Real Time PCR System Software Getting Started Guide Pub No 4489823 QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Quick Reference Pub No MAN0018829 Audience This user guide is written for laboratory staff who operate and maintain the QuantStudio 6 and 7 Flex Real Time PCR Systems Assumptions This...

Page 11: ... Caution risk of danger Consult the manual for further safety information Attention risque de danger Consulter le manuel pour d autres renseignements de sécurité Contents of this manual This guide is divided into the following chapters and appendixes Chapter appendix Content Chapter 1 Getting started Introduces the QuantStudio 6 and 7 Flex Systems including descriptions of all related hardware and...

Page 12: ...CR 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 Instrument specification and layout Describes the QuantStudio 6 and 7 Flex System specifications requirements layout and connections About...

Page 13: ...Twister Robot Supports the Twister Robot Does not support the TaqMan Array Card block Supports the TaqMan Array Card block Features a coupled five 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 Real Time PCR Systems use fluorescent based polymerase chain reaction PCR reagents to provide Quantit...

Page 14: ...Before the PCR For presence absence experiments data collection before the PCR is optional but recommended 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 Presence absence The instrument collects raw fluorescence data following each extension step of the PCR A d...

Page 15: ...e information about the spectral dye calibration kits available for the QuantStudio 6 and 7 Flex Systems contact Thermo Fisher Scientific Filter set Color Filter wavelength nm 1 Supported dye Excitation Emission x1 m1 Blue 470 15 520 15 FAM dye SYBR Green x2 m2 Green 520 10 558 12 JOE dye HEX dye TET dye and VIC dye 2 x3 m3 Yellow 549 5 10 586 5 10 Cy 3 dye NED dye and TAMRA dye x4 m4 Orange 580 1...

Page 16: ...ntific 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 Appendix F Calibration consumable preparation Instrument hardware The QuantStudio 6 and 7 Flex Systems consist of the components shown in the following figure and described in the subsequent table 1 3 2 7 8 5 9 6 4 Front Chapt...

Page 17: ...eated cover and the sample block 4 Lamp Illuminates the plate or array card during a run 5 Heated cover Covers the plate or array card during a run to prevent condensation and leakage through the cover 6 Sample block Heats the plate or array card during a run 7 Side door Opens to allow extension of the tray arm 8 Plate adapter Secures the plate or array card to the tray arm 9 Tray arm Conveys the ...

Page 18: ... 5 20 mm 7 Power port The 100 240 VAC port that provides power to the instrument 1 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 Cat No 4453271 that you can purchase to assist you with data entry The barcode scanner uses a 670...

Page 19: ...eturn character the equivalent of pressing the Enter key 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 accessory that consist...

Page 20: ...bles as they are loaded into the QuantStudio 7 Flex System G Base cover Removable cover that contains four access bolts which secure the Twister Robot to the Sciclone ALH 3000 base H Racks Provide storage for PCR consumables before and after they are run by the QuantStudio 7 Flex System one of three shown I Power LED When lit indicates the Twister Robot is powered on Rear view Component Descriptio...

Page 21: ...pecific 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 Chapter 1 Getting started Instrument hardware 1 QuantStudio 6 and 7 Flex Real T...

Page 22: ...ically 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 soft...

Page 23: ...ware to the computer running the QuantStudio Real Time PCR Software confirm that the software will not restrict Ethernet communication or interfere with the software operation Third party software 1 Install the third party software to the computer that contains the QuantStudio Real Time PCR Software 2 Perform several test experiments using plates that do not contain reagents Note The goal of the t...

Page 24: ...oAmp 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 µL MicroAmp Optical Adhesive Film MicroAmp Optical 96 Well Reaction Plate with Bar Code 100 µL 96 well plate 0 1 mL MicroAmp Optical Adhesive Film MicroAmp Optical 96 Well Fast Reaction Plate with Bar Code 50 µL 384 well plate MicroAmp Optical Adhesive Film Micr...

Page 25: ...ware 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 Chapter 1 Getting started Interchangeable sample blocks heated covers and plate retainers 1 QuantStudio 6 and 7 Flex Re...

Page 26: ...tion calibration TaqMan Array Card only 59 Verify the instrument performance 62 Troubleshooting 72 How to identify contamination 81 Remove a plate stuck within the instrument 81 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 c...

Page 27: ... the instrument then power on the computer after 30 seconds Clean the surface of the instrument with a lint free cloth Monthly Perform a background calibration 1 Run disk cleanup and disk defragmentation Perform an instrument self test Semi annually every 6 months Perform an ROI calibration Perform a background calibration 1 Perform a uniformity calibration Perform a dye calibration TaqMan Array C...

Page 28: ...re The instrument requires regular planned maintenance by Thermo Fisher Scientific 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 incr...

Page 29: ... instrument verification Finish You can use the Instrument Console of the QuantStudio Real Time PCR Software to view the calibration status of an instrument 1 In the QuantStudio Real Time PCR Software Home tab click Instrument Console 2 From the Instrument Console open the Instrument Manager a Select your instrument icon from the My Instruments group b Click Manage Instrument Note If the Manage In...

Page 30: ... 7 Flex System b The status of all calibrations including the date and time of each calibration c The maintenance status of the instrument d The properties of the instrument 3a 3b 3c 3d Figure 1 Information screen for the instrument with a 96 well plate block or a 384 well plate block Chapter 2 Calibrate the instrument Calibration overview 2 30 QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 M...

Page 31: ... 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 Chapt...

Page 32: ...ct your systems administrator or information technology department for the following information Network address of an SMTP server A user name and password for the server if required for access The Secure Sockets Layer SSL setting of the server on or off 1 In the QuantStudio Real Time PCR Software select Tools4Preferences 2 From the Preferences dialog box select the SMTP Settings tab 3 Define the ...

Page 33: ...cument click Run in the Experiment Menu then click Notification Setting to view the notification settings for the experiment c In the Notification Settings of the experiment document select Yes to enable the Enable Notifications setting d From the Enter e mail addresses for notifications field enter the email address that you want to receive the test emails Chapter 2 Calibrate the instrument Enabl...

Page 34: ...ibration Reminders 2 In 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 Send a Reminder column select the check box to configure the QuantStudio Real Time PCR Software to email a reminder to perform the calibration b In the Reminder Interval column enter the number of days before the...

Page 35: ...reen for the instrument with a 96 well plate block or a 384 well plate block Chapter 2 Calibrate the instrument Enable or change the calibration reminders 2 QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Maintenance and Administration Guide 35 ...

Page 36: ...plate 96 384 well 5 minutes 30 minutes RNase P array card 3 15 minutes 60 minutes 1 All 96 well plates and 384 well plates used in the calibration of the instrument ROI background uniformity and dye 2 All array cards used in the calibration of the QuantStudio 7 Flex System only ROI background uniformity dye and normalization 3 For use with the QuantStudio 7 Flex System only Plates only Do not disc...

Page 37: ...libration 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 TaqMan Array Card Sealer Centrifuge with array card buckets and array card carrier clips Permanent marker or pen Pipettor 200 µL with pipette tips Powder free gloves Safety glasses IMPORTANT Wear powder free glov...

Page 38: ...nd the fill reservoir toward the vent port Pipet the entire 100 µL 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 5 Repeat step 4 to fill the remaining array card with the appropriate calibration reagents 6 Centrifuge the ar...

Page 39: ...IMPORTANT Do not try to save time by doing one spin for 2 minutes The two sets of ramps are important 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 parti...

Page 40: ...led array card from the fixture and 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 fr...

Page 41: ...reases in fluorescence during a run with the wells on the plate or array card The 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 Perform the ROI calibration once every 6 months IMPORTANT For the 96 well plate block and the 384 well...

Page 42: ...on of interest for the well position is sufficiently bright Red circles around some of the wells indicate that the wells did not calibrate The absence of a circle indicates that the region of interest for the well position is not sufficiently bright IMPORTANT Wear powder free gloves and safety glasses when you prepare plates or array cards Prepare the calibration consumable appropriate for your Qu...

Page 43: ... ROI calibration plate for 5 seconds b Centrifuge the plate for 2 minutes at 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 1 In the QuantStudio Real Time PCR Software Home tab click Instr...

Page 44: ...ORTANT 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 tap to close the instrument tray 7 After loading the plate or array card start the calibration a At the bottom of the Setup tab select Check the box when the ROI calibration plate has been loaded then click Next ...

Page 45: ...t in the dark at room temperature until you are ready to perform the uniformity calibration 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 Tap on the instrument touchscreen to close the instrument tray 11 In the ROI Calibration screen click Finish to complete the calib...

Page 46: ...tes or array cards Prepare the calibration consumable appropriate for your QuantStudio 6 or 7 Flex System Prepare the background calibration plate on page 46 Preparing array cards for instrument calibration on page 37 Materials required Background Plate Centrifuge with plate adapter Powder free gloves Safety goggles Prepare the plate IMPORTANT Wear powder free gloves and safety glasses when you pr...

Page 47: ...nts that adhere to the plate bottom can contaminate the sample block and cause an abnormally high background signal 1 In the QuantStudio Real Time PCR Software Home tab click Instrument Console 2 In the Instrument Console select the icon for your instrument then click Manage Instrument Note If the Manage Instrument button is inactive add your instrument to the My Instruments group 3 In the Instrum...

Page 48: ... of the moving parts hazard and have been adequately trained c From the instrument touchscreen tap to close the instrument tray 7 After loading the plate or array card start the calibration a In the Setup tab select Check the box when the background 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 ru...

Page 49: ...information regarding the cause of the failure 10 Unload the calibration plate or array card a After the calibration tap 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 Troubleshooting b Remove the plate or array card from the instrument tray and discard it WARNING PHYSICAL INJURY HAZARD During instrument o...

Page 50: ...re 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...

Page 51: ...3 From the Instrument Manager start the calibration a Click Maintenance then click Uniformity b From the Uniformity Calibration screen click Start Calibration 4 Click Next then prepare for the calibration as instructed 5 At the bottom of the Setup tab enter the reagent information for the ROI plate or array card that you are using 6 Load the calibration plate or array card into the instrument a Fr...

Page 52: ...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 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 cal...

Page 53: ...d 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 ...

Page 54: ...stem Prepare the dye calibration plates on page 54 Preparing array cards for instrument calibration on page 37 Required materials to prepare calibration plates Note We recommend calibrating with all Spectral Dye Calibrations Plates available for your block configuration even if you are not using all the dyes in the plates This is recommended for optimal system performance Table 2 Spectral calibrat...

Page 55: ... 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 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...

Page 56: ...aintenance then click Dye b In the Dye Calibration screen select System Dye Calibration then click Start Calibration 4 In the Dye Calibration screen select the dye to calibrate from the Dye Name drop down list then perform the calibration as instructed 5 At the bottom of the Setup tab enter the reagent information for the dye plate or array card that you are using 6 Load the dye plate or array car...

Page 57: ...d have been adequately trained c From the instrument touchscreen tap to close the instrument tray 7 After loading the plate or array card start the calibration a In the Dye Calibration screen select Check the box when the dye calibration plate has been loaded then click Next b In the Run screen click Start Run IMPORTANT Do not attempt to open the access door during the run The door is locked while...

Page 58: ...ents field click Finish then click Yes when prompted to save the results Failed Troubleshoot the failed calibration see Troubleshooting 10 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 dye spectra ...

Page 59: ...er free gloves and safety glasses when you prepare the array cards For detailed instructions to prepare the calibration array card see Preparing array cards for instrument calibration on page 37 Normalization calibration is only required for the TaqMan Array Card block 1 In the QuantStudio Real Time PCR Software Home tab click Instrument Console 2 In the Instrument Console select the icon for your...

Page 60: ...ned in each array card appear next to the barcode on the front of it IMPORTANT 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 array card start the calibration a In the Normalization Calibration screen tab select Check the ...

Page 61: ... 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 10 Unload the array card a After the calibration tap on the touchscreen to eject the array card Note If the instrument does not eject the array card remove it as explained in Troubleshooting on page 72 b Remove the array card...

Page 62: ...e 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 Figure 5 illustrates the arrangement of the standard and unknown populations on a 96 well and Fast 96 well RNase P plate The RNase P plate contains five replicate groups of standards 1250 2500 500...

Page 63: ...oftware 1 Generates a standard curve from the averaged threshold cycle Ct values of the replicate groups of standards 2 Calculates the concentration of the two unknown populations using the standard curve 3 Calculates the following to assess the QuantStudio 6 or 7 Flex System performance CopyUnk2 3 σCopyUnk2 CopyUnk1 3 σCopyUnk1 where CopyUnk1 Average copy number of unknown population A σCopyUnk1 ...

Page 64: ...rification Plate Centrifuge with plate adapter Powder free gloves Safety goggles Prepare the plate IMPORTANT When performing the RNase P instrument verification test 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 safet...

Page 65: ...fuge array card carrier clips and buckets Powder free gloves Safety goggles Pipettor 200 µL with pipette tips RNase P Array Card Instrument Verification Reagents Kit TaqMan 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...

Page 66: ...n b Load 100 µL 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 GR2158 Microfluidic Card Card Ports detail 2 1 1 Fill port 2 Vent port Chapter 2 Calibrate the instrument Verify the instrument performance 2 66 QuantStudio 6 and 7 Flex Real Time PCR Sys...

Page 67: ...are photosensitive Prolonged exposure to light can diminish the fluorescence of the dye 1 In the QuantStudio Real Time PCR Software Home tab click Instrument Console 2 In the Instrument Console select the icon for your instrument then click Manage Instrument Note If the Manage Instrument button is inactive add your system to the My Instruments group 3 In the Instrument Manager start the RNase P ru...

Page 68: ...ch to close the instrument tray 7 After loading the plate or array card start the instrument verification test a In the Overview screen select Check the box when the RNase P plate has been loaded then click Next b In 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 st...

Page 69: ...he wells of the plate or array card Beginning with well A1 the wells are numbered from left to right and top to bottom 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 anot...

Page 70: ... 8 12 repeat the RNase P test using a different RNase P plate or array card If the problem persists contact Technical Support 14 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 R2 value is 0 990 If the R2 value is 0 990 repeat the RNase P test using a different RNase P plate or array card If the prob...

Page 71: ... Print Report in the upper right corner of the screen to print a summary of the RNase P test results for your records Chapter 2 Calibrate the instrument Verify the instrument performance 2 QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Maintenance and Administration Guide 71 ...

Page 72: ...bration 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 ...

Page 73: ...e heated cover Remove the plate or array card from the instrument as explained in Remove a plate stuck within the instrument on page 81 Instrument malfunction Multiple possible causes Contact your local Thermo Fisher Scientific Field Service Office Chapter 2 Calibrate the instrument Troubleshooting 2 QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Maintenance and Administration Guide 73 ...

Page 74: ...of the wells centrifuge the plate or array card for a longer time then repeat the calibration 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 If the calibration fails again determine the source of the contamination as explaine...

Page 75: ...n 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 If the calibration fails again contact Technical Support One or more wells produced spectra that deviate significantly from the rest of the plate or array card 1 While viewing the calibratio...

Page 76: ...he plate or array card for a longer time then repeat the calibration 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 another 3 If the problem persists contact Technical Support Spectra contain peaks in more than one filters One or m...

Page 77: ...ate the well s with abnormal signal in the Plate Layout tab 2 Rotate the 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 Identical The sample block is contaminated Decontaminate the sample block Reversed The normalization array card is contaminated Discard the consumable the...

Page 78: ...d 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 81 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 Thermo Fisher Scientific to or...

Page 79: ...ealing or seal leaks Condensation on the plate or array card Inconsistent volumes across the plate or array card If a well is flagged confirm the results 1 Select the flagged well s and the associated replication group s in the plate layout or well table 2 View the amplification plot Rn vs Cycle and review the data for abnormalities 3 Hold the plate or array card up to a light source and check for...

Page 80: ... pipettors 2 Contact Thermo Fisher Scientific to order a replacement RNase P plate or array card 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 Technical Support for assistance Well displays the SPIKE flag indicating that the amplification curve contains one or more data points inconsistent with the other po...

Page 81: ...ate or array card is contaminated Discard it then perform the background calibration using a new background consumable 4 If the calibration fails after you replace the background plate or array card and decontaminate the sample block contact Technical Support Remove a plate stuck within the instrument If the QuantStudio 6 or 7 Flex System does not eject a plate after you touch on the touchscreen t...

Page 82: ...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 Real Time PCR Software The following table summarizes the functions that are available from the touchscreen Category Function Available in secure mode 1 Operation...

Page 83: ...ge 83 Run an experiment see page 84 Transfer experiments templates and results data see page 85 Note If the instrument is operating in secure mode users can only open and close the side door see Enable or disable instrument security on page 95 1 If necessary download the experiment template to the QuantStudio 6 or 7 Flex Real Time PCR System see Transfer experiments from a USB drive on page 86 2 I...

Page 84: ...me PCR System touchscreen to activate it then tap 2 In the main menu tap 3 When the side door opens load the appropriate plate or array card Ensure that the consumable is properly aligned in the holder A Load 96 384 well plates with the A1 position at the top left corner of the plate adapter B Load both plates and array cards with the barcode facing the front of the instrument 4 In the main menu t...

Page 85: ...art the experiment Note When the run is complete tap to unload the plate You can download the experiment results to a computer if the QuantStudio 6 or 7 Flex Real Time PCR System is connected to a network or you can copy the data to a USB drive see Transfer experiments templates and results data on page 85 You can transfer experiments templates and results data to from the QuantStudio 6 and 7 Flex...

Page 86: ...uch USB b Touch the desired experiment then touch Save 5 In the Save Experiment As screen touch the experiment that you want to transfer to the USB drive then touch Save 6 Touch to return to the Main Menu 7 Unplug the USB drive Copy experiment results to a USB drive 1 Plug a USB drive into the USB port below the touchscreen 2 If the instrument is in standby touch the QuantStudio 6 or 7 Flex System...

Page 87: ...your laboratory policies Back up and restore the instrument settings see page 87 Perform an instrument self test see page 89 Update the instrument firmware see page 89 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 Real Time PCR Software You can use the QuantStudio 6...

Page 88: ...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 se...

Page 89: ...PORTANT 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 Thermo Fisher Scientific personnel to service the instrument b Touch 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 remo...

Page 90: ... the software version number to confirm that the firmware has been upgraded Administrate the instrument from the touchscreen 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 in...

Page 91: ... the format for your region d Touch each Time field enter the appropriate time units then touch 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 to return to the Main Menu 1 In the main menu of the instrument touchscreen tap Settings then tap Configure the Instrument 2 Tap the Instrument Name field enter up ...

Page 92: ...ndby Time out field c Enter the number of minutes 1 300 that the instrument should remain idle until it enters standby mode then tap Done Note When in standby mode the instrument 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 Tap the Cover Idle Temperature field c Enter the temper...

Page 93: ...e Set Network Information screen displays the Media Access Control MAC address of the QuantStudio 6 or 7 Flex Real Time PCR System below the Autodiscovery and Smart Monitoring check boxes The MAC address can be used to uniquely identify the system on the network 2 Tap Autodiscovery to make the system discoverable by computers that are running the QuantStudio Real Time PCR Software 3 Tap Smart Moni...

Page 94: ...te 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 Set Shortcut b Touch 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 Remove Shortcut or t...

Page 95: ...cannot connect to the QuantStudio 6 and 7 Flex Systems that do not match security settings Note Secure mode limits the number of features that are available from the system touchscreen It does not provide user authentication functionality through the instrument touchscreen 1 If the instrument is in standby tap the touchscreen to activate it then tap 2 In the main menu tap Settings then tap Set Adm...

Page 96: ...n menu to filter the log Select Earliest First or Latest First to determine the order to sort the records 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 Thermo Fisher Scientific personnel to service t...

Page 97: ...he 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 Real Time PCR System cover There are no components inside the instrument that you can safely service yourself If you suspect a problem contact a Thermo Fisher Scientific Ser...

Page 98: ...During instrument operation the 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 81 2 Power off and unplug the QuantStudio 6 or 7 Flex Real Time PCR System then allow it to co...

Page 99: ...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 system until it is seated correctly 7 Close the access door IMPORTANT Confirm that the access door is completely closed The QuantStudio Real Time PCR Software displays an error message if...

Page 100: ...olution to a waste beaker 13 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 14 If the contamination remains contact Thermo Fisher Scientific Replace the halogen lamp Replace the halogen lamp at or before 2000 hours of life WARNING PHY...

Page 101: ...00 hours replace the lamp see Replace the lamp on page 101 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 IMPORTANT Always wear powder free gloves when you handle the lamp Finger prints shorten the lamp life 1 Record the lamp installation a In the main menu of the touchsc...

Page 102: ...MPORTANT 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 Real Time PCR System a Slide the lamp release lever upward b Firmly grasp the lamp place it into the slotted mount then carefully slide the lamp downward into place Appendix B Maintenance Replace the hal...

Page 103: ...ses for failure see Replace the instrument fuses on page 103 10 After replacing the lamp perform the following calibrations in the specified order a ROI calibration b Background calibration c Uniformity calibration d Dye calibration e Normalization calibration TaqMan Array Card block only f RNase P test Replace the instrument fuses Replace the QuantStudio 6 or 7 Flex System fuses when the fuses fa...

Page 104: ...e 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 Install the QuantStudio Real Time PCR Software See Computer requirements on page 22 for a list of hardware and operating system requirements for the QuantStudio 6 and 7 Flex Real Ti...

Page 105: ...tivate the license as instructed After you successfully activate the license you will receive an email containing the activated license file LIC to install on your computer Activate a license and receive a license file LIC see Activate a license on page 105 The following steps describe how to install the license file to in order to unlock the High Resolution Melting HRM Software or the SAE module ...

Page 106: ...r 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 Installation directory drive Program Files x86 Applied Biosystems QuantStudio Real Time PCR Software Data directory drive Applied Biosystems AppData QuantStudio Real Time PCR Software User files directory drive Applied Biosystems QuantStudio...

Page 107: ...L INJURY HAZARD During instrument operation the sample block and heated cover can reach 100 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 In the event of a hardware failure Safety glasses Powder free gloves Sample block To prevent damaging or contaminating the sample block han...

Page 108: ...6 Close the access door IMPORTANT Confirm that the access door is completely closed The QuantStudio Real Time PCR Software displays an error message if the door is not completely closed and latched or if the sample block is not seated correctly 7 Plug in and power on the QuantStudio 6 or 7 Flex Real Time PCR System 8 In the QuantStudio Real Time PCR Software Home tab click Instrument Console 9 In ...

Page 109: ... During instrument operation the sample block and heated cover can reach 100 Allow the heated cover to cool to room temperature before removing You can change the heated cover 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 Heated cover To prevent damaging or contaminating the heated cover handle the assembl...

Page 110: ...and place it on a clean dry surface 4 Install the new heated cover into the QuantStudio 6 or 7 Flex Real Time PCR System IMPORTANT Align the arrows on the front handle as shown below If the arrows are not aligned push the heated cover into the system until the handle locks into place Correct Incorrect 5 If you are installing a heated cover of a different consumable format replace the sample block ...

Page 111: ...ted 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 TaqMan Array Card block only 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 Real Time PCR System Change the plate a...

Page 112: ... the latch to allow the adapter to lower into place If necessary apply pressure as indicated until the adapter snaps into place 5 From the Main Menu touch 6 If you are installing a tray adapter of a different consumable format replace the sample block and heated cover if necessary Materials required Change the plate adapter Appendix B Maintenance Change the plate adapter B 112 QuantStudio 6 and 7 ...

Page 113: ... 6 or 7 Flex System for use on a network Set up a computer for remote monitoring Test the network connection by engaging the remote monitoring feature When the QuantStudio 6 or 7 Flex Real Time PCR System is connected to a network computers on the network that are running the QuantStudio Real Time PCR Software can control or monitor it The software can control up to 4 instruments and monitor up to...

Page 114: ... other nodes that are separated by a router hub or another network device 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 Real Time PCR System is set for DHCP APIPA is automatically enabled and the system provides an IP address when no address is supplied by the DHCP server...

Page 115: ...simultaneously monitor the system remotely Although the system supports remote monitoring from multiple computers each connection taxes the instrument microprocessor Too many connections can overburden the system and result in instrument errors Note The effects of an overburdened system are evident in the Temperature Plot during a run Symptoms can include extended hold times or brief unexpected pl...

Page 116: ... local area network Start Collect the required network information Connect the QuantStudio system to the network Connect the computer to the network Monitor the system to test the network connection Finish Collect the required network information Obtain the following information from your network administrator Network policy for obtaining IP addresses DHCP or static IP IMPORTANT When the QuantStud...

Page 117: ... System The Smart Monitoring feature allows Thermo Fisher Scientific service personnel to monitor the status of the 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 ...

Page 118: ...ur 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 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 3 From the desktop righ...

Page 119: ...ed in the Internet Protocol TCP IP Properties 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 See Install the software on page 106 Note You must install the QuantStudio Real Time PCR Software in order to monitor...

Page 120: ...e If the Manage Instrument button is inactive add your instrument to the My Instruments group 3 In the Instrument Manager click Monitor then click Information 4 In the Monitor Instrument screen click Monitor Running Instrument The QuantStudio Real Time PCR Software displays the status attributes calibration status and plot data for the selected system If a communications warning appears contact yo...

Page 121: ...n the SMTP Settings tab define the settings for the SMTP server 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 spe...

Page 122: ...days that elapse before the type of calibration expires on the system b In the Send a Reminder column select the check box to configure the QuantStudio Real Time PCR 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 In the Enter e mail addresses...

Page 123: ...hscreen Power on the QuantStudio 6 or 7 Flex Real Time PCR System To power on the QuantStudio 6 or 7 Flex System from a powered off state 1 Tap anywhere on the touchscreen to determine if the QuantStudio 6 or 7 Flex Real Time PCR System is in standby mode Does the touchscreen display the Standby screen after you touch it Yes The instrument is ready for use Go to step 4 No Go to step 2 to power on ...

Page 124: ...o start the software IMPORTANT If the 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 softwaree b If the QuantStudio Real Time PCR Software Login appears enter your user name and password then click Log In Note Security is a separately licensed module If your system requires thi...

Page 125: ...B 2 RS 232 2 Power off the computer a From the desktop select Start4Shut Down b From the Shut Down Windows dialog box select Shut Down then click OK 3 Power off the monitor 4 QuantStudio 7 Flex System only If you have a Twister Robot toggle the power button on the rear of the Twister Robot Store the QuantStudio 6 or 7 Flex System The QuantStudio 6 or 7 Flex System can be powered off and stored for...

Page 126: ...ot toggle the power button on the rear of the Twister Robot 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...

Page 127: ...are 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 H...

Page 128: ...fting and carrying 1 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 2 Install the sample block and heated cover assemblies 3 Perfor...

Page 129: ...d Dye e Normalization TaqMan Array Card block only Appendix D Power on or off store and move Move the QuantStudio 6 or 7 Flex System D QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Maintenance and Administration Guide 129 ...

Page 130: ...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...

Page 131: ...eal Time PCR Software select Tools4Security4Settings 2 In the Security Settings dialog box select the System tab 3 Select or deselect Enable Security Note the following The software requires you to enter your user name and password when you enable security The enable commands are grayed when a run is in process When security is disabled the is not active in lower parts of the screen Disabling Secu...

Page 132: ...on Settings to specify when and how the software notifies the administrator of certain security events For information see Set up messaging notifications on page 132 7 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 Lead...

Page 133: ...cation 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 Email Notification If an event triggers notification the QuantStudio Real Time PCR Software sends an email to the addresse...

Page 134: ...ibed in Create or edit a user role on page 135 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 Ed...

Page 135: ...ings as needed 1 In the QuantStudio Real Time PCR Software select Tools4Security4Settings 2 In the Security Settings dialog box select the Roles tab From the Roles tab you can perform the actions in the following table To Action Create a user role 1 Click Create 2 Enter a role name and optional description 3 Select permissions see Permissions and default user roles on page 136 To select all permis...

Page 136: ...the Quickstart function Yes Yes Yes Start a run Yes Yes Yes Stop a run Yes Yes Yes Targets Library Create targets Yes Yes Yes Edit targets Yes Yes Yes Delete targets Yes Yes Yes Analysis Settings Library Create analysis settings includes default settings Yes Yes Yes Edit analysis settings includes default settings Yes Yes Yes Delete analysis settings Yes Yes Yes Run Methods Library Create a run me...

Page 137: ...brary add edit delete delete all import or export Yes Yes Yes Manage the target library add edit delete delete all import or export Yes Yes Yes Manage the analysis settings library add edit delete delete all import or export Yes Yes Yes Note The landscape and portrait functions are not available for the User or Roles reports To print either report in landscape save the report electronically PDF th...

Page 138: ...ivate 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 In the QuantStudio Real Time PCR Software select Tools4Security4Settings 2 In the Security Settings dialog box select the Audit tab 3 Select or deselect Enable Audit 4 Click Apply Settings Access the audit screen and enable ...

Page 139: ...ter a reason 2 As needed click Create or select a reason from the list then click Edit or Delete Audit report generation You can use the QuantStudio Real Time PCR Software to generate reports of audit history from both the Security Settings dialog box and from open experiments templates or studies View audit histories from the Security Settings dialog box see page 139 View audit histories from an ...

Page 140: ...ngs Update Auditing Event Archive Restore Purge Configuration Import Export Data Audit Archive Restore Purge Login Success Failure Logout Success Run Start Stop Completed Failed Aborted Error User Account Create Update 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 IMPO...

Page 141: ...r 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 Review the system configuration history The following table summarizes the actions that can be audited using the QuantStudio Real Time PCR Software The...

Page 142: ... 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 signature File Name Update Update the file name File Version Update Update the ...

Page 143: ...e 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 Summary Report to open the Print Preview dialog box 2 Preview save or print the report 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 Cli...

Page 144: ... 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 In the e Signature tab of the Security Settings dialog box click Add in the e Signature Meanings settings 2 In the Create Meaning dialog box enter a description of the e Signature meaning then click OK 3 Select what data is signed for the selected meanin...

Page 145: ...iment or study Start Run Initiates a run from the QuantStudio Real Time PCR Software 2 For 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 Pla...

Page 146: ...s 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 Real Time PCR Software to generate reports of e signature history from open experiment EDS or template EDT files Task Description Display the e sig records 1 In the QuantStudio Real Time PCR Software open an experiment or template file 2 From the open expe...

Page 147: ...t 5 Click OK in the confirmation message Save or print the table of e signature events 1 In the QuantStudio Real Time PCR Software open an experiment or template file 2 From the open file click Audit then click Print E Signatures 3 Save or print the record Click Save select a location for the export file enter a name for the file then click Save or Click Print 4 Click OK in the confirmation messag...

Page 148: ...gs 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 User overview The Security Audit and Electronic Signature SAE module is a component of the Quan...

Page 149: ...ed with your user account Functions for which you do not have permissions are shaded Note If the QuantStudio Real Time PCR Software is configured for password expiration you are periodically prompted to change your password Note If the QuantStudio Real Time PCR Software is configured to monitor failed log in attempts you will be locked out of the software if you repeatedly enter an incorrect user ...

Page 150: ...t 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 The Tools4Security4Sign Data menu option is enabled You are prompted to sign Appendix E Security audit and electronic signature User overview E 150 QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Mainte...

Page 151: ... array card from a spectral calibration kit is not available you can create one as described below 96 384 Well plate sample block MicroAmp Optical 96 384 Well Reaction Plate Safety glasses Optical Adhesive Cover or Optical Flat Caps Pipettor 200 µL with pipette tips Powder free gloves Deionized water TaqMan Array Card block QuantStudio 7 Flex System only TaqMan Array Cards TaqMan Array Card Sealer...

Page 152: ... on the side of the empty card 3 Pipet 100 µL 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 µL 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 the larger of the two holes GR2158 Microf...

Page 153: ...x System you must Determine optimum dye concentration Create a custom dye plate Add the custom dye to the software Perform a dye calibration Centrifuge with plate adapter Custom dye s Safety glasses Powder free gloves MicroAmp Optical 96 384 Well Reaction Plate Optical Adhesive Cover Pipettors and pipette tips 200 µL and 1000 µL Tubes 2 mL and 10 mL Deionized water Note Wear powder free gloves whi...

Page 154: ...elect 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 ...

Page 155: ...iod of time 1 Start the dye calibration a In the Home screen of the QuantStudio Real Time PCR Software click Instrument Console b In the Instrument Console select your system from the list of instruments on the network then click Add to My Instruments c Select the system then click Manage Instrument d In the Instrument Manager click Maintenance then click Dye e In the Background Calibration screen...

Page 156: ...N to start the calibration 5 When the run is complete and the system ejects the plate remove and discard the plate or the 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 Real Time PCR Software click Next 7 Verify the grouping of the dye spectra a In t...

Page 157: ...m dye plate using the next dye concentration greater than the concentration determined in Determine optimum dye concentration on page 153 then perform the calibration again Appendix F Calibration consumable preparation Create a custom dye plate for calibration F QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Maintenance and Administration Guide 157 ...

Page 158: ...t Reader versions to use thermofisher com Operating system Microsoft Internet Explorer Apple Safari Mozilla Firefox Adobe Acrobat Reader Microsoft Windows v6 x or Later None 1 v2 x or Later v4 0 or Later Macintosh None 1 v2 0 4 or Later 1 Browser not available for this platform Note Confirm that cookies and JavaScript are turned on for the website to function correctly 1 To find your assay complet...

Page 159: ...accessories The following kits consumables and reagents are to be used with the QuantStudio 6 and 7 Flex Systems Standard 96 well consumables see page 160 Fast 96 well consumables see page 160 384 well consumables see 384 well consumables on page 161 TaqMan Array Card consumables see page 161 QuantStudio 6 and 7 Flex System accessories see QuantStudio 6 and 7 Flex Systems accessories on page 162 N...

Page 160: ...2 mL 4432382 Fast 96 well consumables Consumable Cat No Storage Shelf life at storage temperature QuantStudio 3 5 10 Dye Spectral Calibration Kit 96 well 0 1 mL Contains all 3 spectral calibration plates listed below A26342 25 C to 15 C Use the consumable by the expiration date on the packaging QuantStudio 3 5 Spectral Calibration Plate 1 FAM VIC ROX and SYBR dyes 96 well 0 1 mL A26336 QuantStudio...

Page 161: ... storage 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 20 C Use the consumable by the expiration date on the packaging Kit RNase P Array Card Instrument Verification Re...

Page 162: ...rray Card Sealer 4331770 Consumable Cat No 96 Well Fast Plate empty 10 pack 4346907 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 pack 1 4445702 Array Card Kit empty 4 pack 1 4445701 Optical Adhesive Covers 25 pack 4481193 1 QuantStudio 7 ...

Page 163: ...0 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 µL and 200 µL with pipette tips MLS Powder free gloves MLS Safety glasses MLS Screwdriver flathead MLS Tissue lint free MLS Deionized water MLS Appendix G Parts and materials General use materials and consumables G Qua...

Page 164: ...e Pub No 4489824 Component Height Depth Width Weight Instrument 1 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 22 4 in 21 6 cm 8 5 in 10 kg 22 0 lbs Monitor 38 0 cm 15 0 in 13 7 cm 5 4 in 37 4 cm 14 7 in 3 0 kg 6 7 lbs Keyboard 2 75 cm 1 1 in 44 5 cm 17 8 in 13 75 cm 5 5 in 0 75 kg 1 65 lbs 1 Weight varies depending on the sample block installed ...

Page 165: ...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 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 su...

Page 166: ...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 60 dB at idle Temperature 15 30 60 85 F Thermal output During operation the net thermal output based on the actual current draw of the QuantStudio 6 and...

Page 167: ...omputer to your LAN 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 Flex Real Time PCR System Performs fluorescence detection and data collection of experiment and calibration plates or array cards Computer Run the QuantStudio Real Time PCR Software that is used t...

Page 168: ...Connects the monitor to the computer DVI port D Barcode scanner cable Connects the optional barcode scanner to the computer USB port E Keyboard cable Connects the keyboard to the computer USB port F Mouse cable Connects the mouse to the computer USB port 1 Supplies 115 230 V depending on the geographic location of the installation 2 Supplied with the QuantStudio 6 and 7 Flex Systems Appendix H Ins...

Page 169: ...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 and so on To obtain SDSs see the Documentation and Support section in this document Symbols on this instrument Symbols may be found on the instrument to warn against potential hazards or convey important safety infor...

Page 170: ...description MISE EN GARDE Risque de danger Consulter le manuel pour d autres renseignements de sécurité MISE EN GARDE Risque de choc électrique MISE EN GARDE Surface chaude MISE EN GARDE Danger biologique potentiel MISE EN GARDE Rayonnement ultraviolet Standard safety symbols Appendix I Safety Symbols on this instrument I 170 QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Maintenance and Admi...

Page 171: ...hazard Symbole et description MISE EN GARDE Laser radiation MISE EN GARDE Parties mobiles MISE EN GARDE Danger de glisser potentiel Additional safety symbols Appendix I Safety Symbols on this instrument I QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Maintenance and Administration Guide 171 ...

Page 172: ... B 1 US B 2 RS23 2 Symbols and descriptions On Power Off Power Location of safety labels Control and connection symbols Appendix I Safety Symbols on this instrument I 172 QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Maintenance and Administration Guide ...

Page 173: ...magnetic compatibility Indicates conformity with the WEEE Directive 2012 19 EU CAUTION To minimize negative environmental impact from disposal of electronic waste do not dispose of electronic waste in unsorted municipal waste Follow local municipal waste ordinances for proper disposal provision and contact customer service for information about responsible disposal options Indicates conformity wit...

Page 174: ...ment 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 Make sure 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 y...

Page 175: ...ce adéquate S assurer que la tension électrique est convenable Ne jamais utiliser l instrument alors que le dispositif de mise à la terre est déconnecté La continuité de la mise à la terre est impérative pour le fonctionnement de l instrument en toute sécurité WARNING Power Supply Line Cords Use properly configured and approved line cords for the power supply in your facility AVERTISSEMENT Cordons...

Page 176: ...ent et de constituer de ce fait un DANGER L instrument doit être correctement décontaminé a si des substances dangereuses sont renversées sur ou à l intérieur de l équipement et ou b avant de le faire réviser sur site ou de l envoyer à des fins de réparation de maintenance de revente d élimination ou à l expiration d une période de prêt des informations sur les formes de décontamination peuvent êt...

Page 177: ... 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...

Page 178: ...tory Use EMC Requirements Part 1 General Requirements FCC Part 18 47 CFR U S Standard Industrial Scientific and Medical Equipment AS NZS CISPR 11 Limits and Methods of Measurement of Electromagnetic Disturbance Characteristics of Industrial Scientific and Medical ISM Radiofrequency Equipment ICES 001 Issue 4 Industrial Scientific and Medical ISM Radio Frequency Generators Environmental design stan...

Page 179: ...ted 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 AVERTISSEMENT PRÉCAUTIONS GÉNÉRALES EN CAS DE MANIPULATION DE PRO...

Page 180: ...r les applications les réactifs et les substrats particuliers utilisés dans le laboratoire Vérifier que les déchets sont convenablement stockés transférés transportés et éliminés en respectant toutes les réglementations locales nationales et ou communautaires en vigueur IMPORTANT Les matériaux représentant un danger biologique ou radioactif exigent parfois une manipulation spéciale et des limitati...

Page 181: ... provincial and or national regulations The following references provide general guidelines when handling biological samples in laboratory environment U S Department of Health and Human Services Biosafety in Microbiological and Biomedical Laboratories BMBL 5th Edition HHS Publication No CDC 21 1112 Revised December 2009 found at https www cdc gov labs pdf CDC BiosafetymicrobiologicalBiomedicalLabo...

Page 182: ...eal Time PCR Systems Maintenance and Administration Guide 4489821 QuantStudio 6 and 7 Flex Real Time PCR Systems Quick Reference 4489826 Customer and technical support Visit thermofisher com support for the latest service and support information Worldwide contact telephone numbers Product support information Product FAQs Software patches and updates Training for many applications and instruments O...

Page 183: ...l Terms and Conditions of Sale at www thermofisher com us en home global terms and conditions html If you have any questions please contact Life Technologies at www thermofisher com support Appendix J Documentation and support Limited product warranty J QuantStudio 6 and 7 Flex Real Time PCR Systems v1 6 Maintenance and Administration Guide 183 ...

Page 184: ...tes optimal 100 PCR amplification efficiency Display of data collected during the cycling stage of PCR amplification The Amplification Plot can be viewed as Baseline corrected normalized reporter ΔRn vs cycle Normalized reporter Rn vs cycle Threshold cycle Ct vs well Part of the instrument run in which PCR amplifies the target The amplification stage called a cycling stage in the thermal profile c...

Page 185: ...ude of normalized fluorescence signal generated by the reporter at each cycle during the PCR amplification From the ΔRn vs Cycle Amplification Plot ΔRn is calculated at each cycle as ΔRn cycle Rn cycle Rn baseline where Rn normalized reporter See also normalized reporter Rn on page 188 In presence absence experiments a reaction that contains IPC blocking agent which blocks amplification of the int...

Page 186: ...ollected by the instrument See amplification efficiency EFF on page 184 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 is calculated from the slope knowing the error allows a CI for the amplification efficiency to be calculated Refers to the entire process of...

Page 187: ...ntrol IPC wells on page 188 A plot of data collected during the melt curve stage Peaks in the melt curve can indicate the melting temperature Tm of the target or they can identify nonspecific PCR amplification In the software you can view the melt curve as normalized reporter Rn vs temperature or as derivative reporter Rn vs temperature The melt curve shape and the difference in melting temperatur...

Page 188: ...ent of the ΔCt mean value found in Comparative Ct experiments computed as the geometric mean The relative standard curve equivalent of the ΔCt SE value found in Comparative Ct 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 Thermo Fisher Scientific instru...

Page 189: ...ndard curve regression line and the individual Ct 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 t...

Page 190: ...icates 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 ...

Page 191: ...oefficient 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 on page 184 and regression line on page 190 In the thermal profile a group of one or more steps Examples PCR stage cycling stage also called amplification stage and hold s...

Page 192: ...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 steps 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 ...

Page 193: ...lex 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 experimen...

Page 194: ...thermofisher com support thermofisher com askaquestion thermofisher com 30 September 2019 ...

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Applied Biosystems QuantStudio 6 Flex, User Manual

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