ThermoFisher Scientific QuantStudio 12K Flex OpenArray AccuFill System User Manual Download

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Figure 2 Instrument deck

Tip box holders (2); tip box installed in left holder

OpenArray

™

Plate holders (4)

Sample plate holder with sample plate installed

Waste bin

Figure 3 Left side panel

Power switch

Power cord outlet

USB port

Chapter 1

Product information

About the instrument

QuantStudio

™

12K Flex OpenArray

™

AccuFill

™

System User Guide

Summary of Contents for QuantStudio 12K Flex OpenArray AccuFill System

Page 1: ...agnostic procedures QuantStudio 12K Flex OpenArray AccuFill System USER GUIDE Use and maintenance for use with OpenArray AccuFill Instrument OpenArray AccuFill Software v2 0 Catalog Number 4471021 Pub...

Page 2: ...are v1 2 see Related documentation on page 99 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...

Page 3: ...perations 14 Important guidelines for handling an OpenArray Plate 15 Set the preferences 15 Set the general settings 15 Set the folder defaults 15 Set the plate mapping defaults full run workflow 16 C...

Page 4: ...hout sample plate information 44 Verify the run setup and start the run quick run workflow 45 CHAPTER 7 Set up and start a run with the full run workflow 47 Overview of the full run workflow 47 Overvi...

Page 5: ...tive devices 72 Network requirements 73 Printer requirements 73 Safety requirements 74 Safety practices 74 Required safety equipment 74 Third party software 74 Computer requirements 75 Antivirus softw...

Page 6: ...ntific 89 Instrument safety 89 General instrument safety 89 Physical injury 91 Electrical safety 93 Cleaning and decontamination 94 Instrument component and accessory disposal 94 Safety and electromag...

Page 7: ...es of the OpenArray AccuFill Software v2 0 Flexible workflow options including a full run workflow and quick run workflows Download or generation of TPF or SPF files from within the software Creation...

Page 8: ...nto the through holes because the through holes draw the liquid in by capillary action No bubbles are trapped during the dispensing process because there are no closed wells For more information about...

Page 9: ...er 2 OpenArray Plate holders 4 3 Sample plate holder with sample plate installed 4 Waste bin 1 2 3 Figure 3 Left side panel 1 Power switch 2 Power cord outlet 3 USB port Chapter 1 Product information...

Page 10: ...to develop and enforce secure use of passwords Overview of the software The v2 0 software performs the following functions Sets up the OpenArray AccuFill Instrument to load OpenArray Plates with samp...

Page 11: ...late that is divided into eight sections Note The file must contain column headers that match the items listed above The sample ID is populated in the OpenArray AccuFill Software The other values are...

Page 12: ...al SPF file plus the sample information Generated by the instrument during a run based on the original SPF file Contains the prefix Loaded Imported into the compatible real time PCR system to perform...

Page 13: ...page 13 2 Set up and start the run quick run workflow Configure the run Configure the run with sample plate information page 43 Configure the run without sample plate information page 44 Verify the ru...

Page 14: ...place and the notched edge to the left into the sample plate holder Press on the plate until you hear it snap into place See Figure 2 on page 9 Note Do not remove the foil from the sample plate until...

Page 15: ...after run completes checkbox If this option is selected the loading history log is displayed after the run is complete see View loading history log on page 83 If this option is deselected the Deck pa...

Page 16: ...sample plate file or OA csv file is saved when mapping plates The folder where the instrument log or the loading history is saved when it is exported Default location C OpenArray Export Data The sele...

Page 17: ...5 Select the Pipettor Fixed Adjustable 6 Click Save Chapter 2 Basic operations and one time procedures Set the preferences 2 QuantStudio 12K Flex OpenArray AccuFill System User Guide 17...

Page 18: ...ly after starting the software A self test is initiated the first time that one of the following items is clicked after starting the software Full Run Quick Run Service4Diagnostics The other features...

Page 19: ...tarting a run Do not reuse tips 4 Remove the cover from each tip box Note Ensure that the tip box covers are removed from the instrument deck 5 Close the instrument door The system is ready to start a...

Page 20: ...epare the instrument for the self test see Set up the system on page 19 3 Click Start test The system performs a self test The status of the self test is displayed in the dialog box The Quick Run scre...

Page 21: ...6 5 Figure 4 Deck screen 1 Deck button 2 Tip boxes 1 and 2 3 Sample plate 4 Waste bin 5 Plate holder for OpenArray Plates up to 4 6 Instrument status Figure 5 Toolbar The instrument status is listed...

Page 22: ...reconnect the instrument to the computer with the software 3 In the Reconnect dialog box click Reconnect A dialog box displays whether the reconnection was successful If the reconnection was successf...

Page 23: ...following information Product Information TaqMan OpenArray Custom 1 Enter the Lot number or Batch number 2 Enter one Serial number from the lot Note Only one serial number is required The serial numb...

Page 24: ...2 Click Choose file 3 Navigate to the location of the file to use as a template then select the file 4 Enter the Serial numbers or Barcodes to be associated with the new TPF or SPF files Note A lot nu...

Page 25: ...apping of samples in 96 well plates to a 384 well plate CSV This is used if samples are prepared in 96 well plates The sample plate file can be used as a reference when transferring samples from a 96...

Page 26: ...ut sample files optional section click Choose File navigate to the location of the CSV file then select the file The format of the sample plate file is validated For the requirements of the sample pla...

Page 27: ...ple each section contains one sample 1 OpenArray Plate 1 Sample 1 2 OpenArray Plate 2 Sample 1 3 OpenArray Plate 3 Sample 1 4 OpenArray Plate 4 Sample 1 5 OpenArray Plate 5 Sample 1 6 OpenArray Plate...

Page 28: ...te Sample 1 Load 1 Sample 48 Sample 49 Load 2 Sample 96 Subarray D12 Subarray A1 OpenArray Plate Figure 10 Example sample mapping for two samples per subarray Chapter 5 Map plates Configure the experi...

Page 29: ...4 OpenArray Plate Sample Plate Sample 1 Sample 48 Sample 49 Sample 96 Sample 97 Sample 144 Load 1 Load 2 Subarray A1 Subarray D12 Figure 11 Example sample mapping for three samples per subarray Chapte...

Page 30: ...ple names are copied They are not automatically filled For example if Sample 1 is the first sample name all of the wells that are filled by the click and drag feature are Sample 1 They are not named s...

Page 31: ...h sample 1 S1 in row A 2 96 well plate with sample 2 S2 in row B 3 384 well plate with sample 1 and sample 2 in alternating wells of row A Chapter 5 Map plates Map a 384 well plate from 96 well plates...

Page 32: ...1 in row A 2 96 well plate with sample 2 S2 in row B 3 384 well plate with sample 1 in each well of row A 4 384 well plate with sample 2 in each well of row B Chapter 5 Map plates Map a 384 well plate...

Page 33: ...amples If Sample Run 2 is selected the bottom half of the 96 well plate is defined with the samples This feature allows for two runs with a 96 well plate if only 48 wells of the physical plate are use...

Page 34: ...splayed when half of the 384 well plate is used 1 1 Swap button 4 Optional Click Import to import a sample file CSV format A sample file can be imported from the Map plates pane if it was not imported...

Page 35: ...d from the Map plates pane if it was not imported from the Configure design pane Note If a sample plate file is imported from the Map plates pane the information will overwrite any information from fi...

Page 36: ...yout The toolbar in the Map plates pane allows you to adjust the view 2 1 3 4 5 6 7 8 Figure 18 Toolbar 1 Undo action 2 Redo action 3 Zoom in 4 Zoom out 5 Fit size if the window size was changed 6 Pla...

Page 37: ...ous set of multiple wells Click drag to copy to a continuous set of multiple wells The well table view displays the details of each well in a table format Each plate is displayed in a separate table U...

Page 38: ...r the instrument to load OpenArray Plates from a 384 well plate in the full run workflow or the quick run workflow with sample information OpenArray Plate To import into a compatible real time PCR sys...

Page 39: ...Chapter 5 Map plates Export plate files 5 QuantStudio 12K Flex OpenArray AccuFill System User Guide 39...

Page 40: ...Configure the run quick run workflow 43 Verify the run setup and start the run quick run workflow 45 Overview of the quick run workflow There are two options for a quick run workflow With sample plat...

Page 41: ...utton 2 Sample plate file name 3 Sample plate color coded to correspond to the OpenArray Plate 4 Tip box status 5 Sample plate to confirm foil is removed 6 OpenArray Plate name and position Chapter 6...

Page 42: ...a 384 well plate from 96 well plates on page 30 Ensure that you have the files required for your workflow for example a sample file in CSV format or a TPF or SPF file Prepare samples DNA and PCR reac...

Page 43: ...n screen Load with sample plate information or Load without sample plate information is set in the preferences see Set the general settings on page 15 A sample plate file 384 well CSV file is required...

Page 44: ...Fill Software v2 0 The QuantStudio 12K Flex Software requires a sample plate file if a real time PCR run is started with a TPF file an SPF file or an EDT file See Figure 23 on page 48 Navigate to the...

Page 45: ...onds to the section of the sample plate If there is more than one sample in a subarray the position box displays all the colors associated with the corresponding sample 2 1 1 Sample plate section 2 Co...

Page 46: ...le information and for two samples per subarray the foil is removed from two sections at a time Note Do not remove the foil from all the sections of the sample plate at once 4 Close the instrument doo...

Page 47: ...un full run workflow 52 Overview of the full run workflow The full run workflow allows you to define all the parameters of the run including the following items Experiment type for example gene expres...

Page 48: ...Only displayed for gene expression and genotyping experiments 3 Pipettor section 4 Add your OpenArray plate serial numbers section 5 Add your input sample files section Chapter 7 Set up and start a ru...

Page 49: ...384 well plates The sample plates are color coded based on the section of the sample plate Chapter 7 Set up and start a run with the full run workflow Overview of the Full Run screens 7 QuantStudio 1...

Page 50: ...your assay Distribute the samples according to the layout determined in the Map Plates workflow Place the sample plate in the sample plate holder on the instrument deck with the notch to the left Do...

Page 51: ...the Experiment type section select an experiment type Gene expression Genotyping 3 sample fixed panel 4 sample fixed panel 2 In the Plate format section select a format The values in the Plate format...

Page 52: ...layout defined in the sample plate file can be edited A sample plate file is in CSV format If the sample plate file was not imported the samples must be added manually 1 Add or edit the sample name 2...

Page 53: ...s highlighted by the software because four OpenArray Plates are being filled The position box displays the color that corresponds to the section of the sample plate 2 1 1 Sample plate section section...

Page 54: ...defined in the experiment setup The instrument door is open The Deck screen is displayed See Chapter 8 Monitor run progress IMPORTANT Each OpenArray Plate must be prepared for PCR immediately after it...

Page 55: ...ument disconnection during run 57 Deck screen during a run 1 2 3 Figure 26 Deck screen during a run 1 Blue box displays location of tip handler on the instrument deck 2 Instrument status shows Busy 3...

Page 56: ...the instrument prompts you to remove the loaded OpenArray Plate seal the case and fill it with immersion fluid see Chapter 9 Prepare the OpenArray Plate for PCR These steps are done for each plate in...

Page 57: ...ct the instrument to the computer see Reconnect the instrument on page 22 A self test must be initiated after the instrument is reconnected The run must be set up again and restarted for any plates th...

Page 58: ...age 58 Remove each OpenArray Plate immediately after it has been filled even if the run was set up to fill multiple plates After the last OpenArray Plate in the run is filled the Remove plate dialog b...

Page 59: ...ed 2 Seal the case and fill the OpenArray Plate with immersion fluid See Seal the OpenArray Plate on page 61 3 For Remove plate and foil dialog box only Remove the foil seal from the next section of t...

Page 60: ...loaded the Deck screen displays Run completed successfully Empty the waste bin before performing another run If the run was started with a TPF or SPF file a loaded TPF or SPF file is generated for eac...

Page 61: ...e strip remove before sealing 3 Protective film on the outside of the lid remove before running 4 Notched end align with serial number on plate 3 Seat the lid on the OpenArray Plate with the lid adhes...

Page 62: ...uid hold the case vertically and rotate the plug slowly If the plug handle breaks off prematurely use a Phillips 0 screwdriver to complete this step 8 If needed clean the case with a laboratory wipe t...

Page 63: ...e cleaning use DNA ExitusPlus reagent or 80 95 ethanol Note For chemical hazard alerts see Appendix E Safety 1 Remove the waste bin from the instrument deck CAUTION Wear appropriate personal protectio...

Page 64: ...of the instrument Unplug the power cord from the electrical outlet See Figure 3 on page 9 Contact Applied Biosystems service personnel For the latest service and support information go to www thermof...

Page 65: ...strument OpenArray AccuFill Software Computer 4471021 QuantStudio 12K Flex OpenArray Plate Press 2 0 A24945 Centrifuge capable of spinning sample plates at 1 000 rpm MLS Adjustable micropipettors MLS...

Page 66: ...trogen gas filtered or residue free compressed air canister 2 MLS 1 Each kit contains the items needed to assemble up to 10 plates 12 lids and plugs 12 immersion fluid syringes and 2 carriers Each cus...

Page 67: ...and weights for the packages you will receive and it describes the dimensions of the components after installation and configuration Components packaged Ensure that the building clearances allow for...

Page 68: ...e moving equipment and proper lifting techniques Improper lifting can cause painful and permanent back injury Depending on the weight moving or lifting an instrument may require two or more people Con...

Page 69: ...t all times The computer workspace allows for proper ergonomics during use The workspace should comfortably fit the instrument and the computer The location accommodates the dimensions and weights spe...

Page 70: ...es of strong electromagnetic radiation for example unshielded intentional RF sources Strong electromagnetic radiation may interfere with the proper operation of the device This equipment has been desi...

Page 71: ...er adjacent to heaters cooling ducts or in direct sunlight Electrical requirements CAUTION Do not unpack or plug in any components until they are configured for the proper operating voltage by the ser...

Page 72: ...in environments with large voltage and power fluctuations Recommended devices Power line regulator 1 5 kVA power line regulator Use in areas where the supplied power fluctuates in excess of 10 of the...

Page 73: ...internet connection is recommended An internet connection allows TPF and SPF files to be downloaded from thermofisher com OA platefiles All of the other features of the software are available without...

Page 74: ...propriate fire extinguisher You are responsible for providing an appropriate fire extinguisher for use on or near the equipment The types and sizes of fire extinguishers shall be suitable for use on e...

Page 75: ...to running the OpenArray AccuFill Instrument Thermo Fisher Scientific has tested the following antivirus software on the computer that will run the OpenArray AccuFill Software McAfee Endpoint Security...

Page 76: ...nual start 84 View the instrument statistics The statistics that are reported are based on the lifetime of the instrument Click Service4Diagnostics The Statistics tab is displayed 1 1 Statistics tab T...

Page 77: ...w the status of the sensors 1 Click Service4Diagnostics 2 Select the Sensor Management tab The sensors and the status of each sensor are displayed at the top of the screen 3 View the status of each se...

Page 78: ...test does not test for the presence of this item View the status of the sensors View the status of the sensors on page 77 1 In the Configure presence sensors section of the screen select or deselect...

Page 79: ...ts in the Door Lock Test dialog box If the test fails contact Service Perform a motion test The motion test moves the robotic tip handler across the different axes X axis Left and right Y axis Forward...

Page 80: ...y of the robotic tip handler to pick up tips is tested Ensure that there are tip boxes and a waste bin on the instrument deck The test does not begin unless there are enough tips to perform the test 1...

Page 81: ...orms the plate holder test sequentially 5 Click Start test The status of each task in the plate holder test is displayed If more than one run was specified the number in the Run 1 of field is updated...

Page 82: ...a number in the Run 1 of field The number specified in this field is the total number of times that the instrument performs the load plate test sequentially 6 Select or deselect the Required Resource...

Page 83: ...ter the run is complete the loading history for the completed run is displayed Click Service4Loading History The following items are displayed OpenArray Plate Barcode Sample Plate Barcode Note The sam...

Page 84: ...aved as a CSV file Perform a system self test manual start Clear the instrument deck empty the waste bin and place it on the instrument deck then close the instrument door The self test checks the fol...

Page 85: ...vice 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...

Page 86: ...de danger Consulter le manuel pour d autres renseignements de s curit Location of safety labels on the instrument 1 Figure 32 Front panel caution label 1 Caution label 1 2 Figure 33 Left panel caution...

Page 87: ...mark Description Indicates conformity with safety requirements for Canada and U S A Indicates conformity with China RoHS requirements Indicates conformity with European Union requirements Indicates c...

Page 88: ...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 infor...

Page 89: ...ble solvents Do not use polymeric tubing that has been severely stressed or kinked Do not use polymeric tubing with tetrahydrofuran or nitric and sulfuric acids Be aware that methylene chloride and di...

Page 90: ...the assistance of others the use of appropriate moving equipment and proper lifting techniques Improper lifting can cause painful and permanent back injury Depending on the weight moving or lifting an...

Page 91: ...cking box carefully tilt the box on its side and hold it stationary while someone else slides the contents out of the box CAUTION Moving Parts Moving parts can crush pinch and cut Keep hands clear of...

Page 92: ...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 musculos...

Page 93: ...la terre est imp rative pour le fonctionnement de l instrument en toute s curit WARNING Power Supply Line Cords Use properly configured and approved line cords for the power supply in your facility AV...

Page 94: ...Ne pas utiliser d agents de nettoyage ou de d contamination susceptibles de r agir avec certaines parties de l appareil ou avec les mati res qu il contient et de constituer de ce fait un DANGER L ins...

Page 95: ...rective relating to the electromagnetic compatibility of electronic devices EN 61326 1 IEC 61326 1 Electrical Equipment for Measurement Control and Laboratory Use EMC Requirements Part 1 General Requi...

Page 96: ...Standard Marking for the Restricted Use of Hazardous Substances in Electronic and Electrical Products For instrument specific certificates visit our customer resource page at www thermofisher com us...

Page 97: ...te 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 an...

Page 98: ...the upright position Biological hazard safety WARNING Potential Biohazard Depending on the samples used on this instrument the surface may be considered a biohazard Use appropriate decontamination me...

Page 99: ...2 software 4456986 Customer and technical support Visit thermofisher com support for the latest service and support information Worldwide contact telephone numbers Product support information Product...

Page 100: ...nologies General 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 sup...

Page 101: ...connection instrument 57 disposal of instrument components and accessories 94 documentation related 99 E export plate files 38 F fixed pipette map 30 folder defaults 15 full run configure experiment d...

Page 102: ...74 safety symbols 86 safety required equipment 74 sample mapping 2 samples per subarray 28 3 samples per subarray 29 sample names add or edit full run 52 sample plate place in holder 14 sample plate f...

Page 103: ...y AccuFill System v2 0_UG_MAN0025669 v4 GUID DCCD1A3A EDDF 4207 B597 18073A9A59D8 2021 11 30 19 02 59 en 23 29 37 262Z thermofisher com support thermofisher com askaquestion thermofisher com 30 Novemb...

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