Home

User Manual - The University of Sydney

1. Select Calibrations to be Deleted IT Plate Position Calibrations T Tip Ejector Calibration Volume Calibrations Reset Defaults 3 Select the calibration settings to be deleted 4 Click on the Delete button The selected calibrations will now be deleted 5 9 Configure run settings The Run settings menu provides options to configure a range of pipetting functions The default run settings are the recommended settings However in some circumstances it is useful to adjust the run settings 5 36 QlAgility User Manual 01 2009 QIAgility Software The default run settings are as follows Level Sensor On Error Mode Interrupt run on all errors Pipetting speeds 150 ul second for all liquid groups except 70 ul second for viscous reagents Standard extra 50 ul volume Master mix extra 30 ul minimum extra volume plus 1 ul volume extra volume per reaction Air volumes 7 ul Tip re use Use each tip for one operation only 5 9 1 Configure tip air intake To configure the tip air intake 1 Select Options Run Settings Configure tip air intake 2 The Air dialog box will appear x Air Volume OK These values control the amount of air that is taken up by the pipetting head before Cancel taking liquid from the plate specified Samples Fr E pl Reagent Fr E pl Standards Fr E pl Diluent and master mix p E pl Intermediate reactions Fr E pl Resto
2. Please select the location of your master mix Ai Tip el Tecan tip AZ Tip 6p Tecan tip Mi Mis plate 5 tube ra Ce o Ma Bt Tip 50u Tecan tip 2 Bescher 2000p deet well CR PA Reagent block ut Ct Sample 700i PCR tube Generic CE Reaction 200s PCR tube Generic 13 Left click on a well in the Master Mix Block to select the location of the master mix The Master Mix Component Selection dialog box will appear ber a i omponent Selection x Make ire up bo thes voor ei ching er TC voin es g Delat sample vikaan for thes tne H Ch Him much teagend ta manualy sed per inaction F En E Pane rotin Ira Kipi peer te dee epee Er E Adora Oh dated Bld ee Pire leste Comporend volumes Select Agen and ther vaimea in une 6 fe r i Jager duree a uam free Use A Ute Hee Peo Jesse Name June et ve rection Yea a 14 Configure the components of the master mix as outlined in Section 5 12 4 15 Click on the OK button to continue 5 128 QlAgility User Manual 01 2009 QIAgility Software 16 The Standards Editor screen will appear PCR ertup wizard Standards editor UR Skardas Elo Corie ach the rs To ce a and check ho bs Ih a sa ha sped gen ces yuan nam td and esgeri bleck andud ace GN pen Les Lo sue Show Fr escent bleck andad DORA n tra Ea Los Sue
3. or QIAgility Operator in the Domain Groups panel 5 32 QlAgility User Manual 01 2009 QlAgility Software Droge mar Droge D Wee s ung Admin Pagal Ure go VW _ Dos 5 Click on the button to move the selected group into the QlAgility User s Groups panel C SUPPORT aiia mar Droge D s Urez Dune Sudrnirish nines Digli Cherig Hi n Lgi E Al 6 To assign the user to more than 1 group repeat steps 4 and 5 7 Click on the Close button to return to the main software window 5 7 3 Change current user To change users the current user must shut down the software and log out of Windows The new user must then log in to Windows and restart the software Alternatively select Options User management Change Current user The Change User dialog box will appear The new user must input their username and password and then click on the OK button QlAgility User Manual 01 2009 5 33 QlAgility Software Change User ou can use this window to log on as a different user for example to log on temporarily as an administrative user to repair fun Username Administrator Password OK Cancel 5 8 Manage calibration data The Calibration Management menu provides options to transfer calibration settings and other software settings f
4. 2 Click on the Import button The Import Names dialog box will appear 5 114 QlAgility User Manual 01 2009 QIAgility Software 17 Specly concent aton rare Min Max Min Concertestion Max Concertaion T Ze Use selected refs INSIDE tange Use selected rels OUS TIDE sange Cancel Import 3 Click on the LI button Select the file type to import i e csv txt or select the file and then click on the Open button 4 Select the Column Separator Comma is the default when selecting a CSV File Other separators e g tab can be used If needed the ASCII code for any character can be specified making the import function universal Tab The Tab character will be used as a separator Comma The Comma character will be used as a separator ASCII Char The specified ASCII value e g 9 Tab 44 Comma 32 Space 58 Colon will be used as a column separator 5 Some text based spreadsheets contain strings of or symbols If these are not required as part of the sample names select Remove from fields separate with Enter the symbol to be removed Multiple QlAgility User Manual 01 2009 5 115 QlAgility Software character sequences can be removed by separating them with 77 6 In the Import Options panel select the starting import row and well in the Start importing FROM row and Start importing TO well fields
5. 6 u oo ooo OGG GG ee Ch oc O00000 DOO PbO tee eS GOD SCR EEEE EEEE CEE or Alp fiando Lial Levet Tip Sensor Tip seune Stee ET EH Menu bar D Toolbar Mode indicator Software workspace 5 6 1 Menu bar The menu bar contains 5 menus File Control Wizards Options and Help All software functions can be controlled from these menus This section outlines the options that are available from these menus In addition when the right hand pane is open the following con is available from the menu bar See Section 5 6 4 for QlAgility User Manual 01 2009 5 13 QlAgility Software more details about the options that are available from this Icon File menu Right hand pane icon The File menu provides access to file related functions New Open Save As 5 14 File Control Wizards Options Help New Ctrl N Open Ctrl 0 Save As Ctrl s Lab notebook Protocol description Unlock protocol 1 HotStarTaq1_signed3 Q45 2 HotStarTaq1_signed3__2008 11 20_10 11 55 Q45 3 HotStarTaq1_signed3 Q45 4 HotStarTaq1_signed3__2008 11 19_13 01 26 Q45 5 HotStarTaqi_signed3__2008 11 19_09 03 08 045 6 HotStarTaq1 QA5S 7 QuantiFast MP PCR 2 GD Q45 8 RT PCR 4 085 Exit Ctrl Q Opens a splash screen which displays options to create a new run file open a recently used run fil
6. Accessories 5 56 Adapters 3 7 C Calibration 7 1 plate height 7 7 plate position 7 4 tip ejector 7 1 tip offset 7 11 volume 7 13 Cautions 1 1 Cleaning 8 2 COM port 5 143 Computer 3 10 Conductive Filtered Tips 3 9 E Errors 6 11 9 5 error codes 9 8 Exporting data 5 113 F Feet 3 3 H HEPA filter 6 4 replacement 8 3 QlAgility User Manual 01 2009 Hood 3 2 Importing data 5 113 Installation 4 1 COM port 4 7 computer setup 4 6 connecting the computer to the QlAgility 4 6 HEPA filter 4 7 power cord 4 7 releasing transport locks 4 4 requirements 4 1 software 4 6 UV lamp 4 7 Intended use 2 3 L Liquid level tracking liquid level estimate 3 10 liquid level sensing 3 9 Log files 6 16 Maintenance 8 1 Master mix block 3 6 O Operating conditions 1 Operation 6 1 pausing aborting a run 6 11 preparing the worktable 6 8 software 6 1 starting a run 6 10 Index 1 Index P Packing 4 10 Pipetting head 3 6 Plate functions diluent 5 55 mix 5 55 5 72 reaction 5 55 5 85 reagent 5 54 5 70 sample 5 54 5 82 standard 5 55 5 65 tip 5 55 5 64 Post run report 6 15 Pre run report 6 13 Q Q Protocols 6 5 QProtocols folder 5 9 QIAgility external features 3 2 hardware features 2 internal features 3 4 mechanical data 2 R Reagent Block 3 7 Right hand pane mix 5 72 progress report 5 124 reaction 5 85 reagent 5 7
7. Change plate function Help menu Help Contents Save support package Choose support package 5 22 Launches the Plate Configuration dialog box which enables the user to change the plate type in a selected position on the software worktable See Section 5 10 1 Launches the Select Accessory window which enables the user to add or remove an accessory from a selected position on the software worktable See Section 5 10 1 Enables selection of plate function A tick will appear next to the plate function that has been selected See Section 5 10 1 Contents Save support package Choose support package Self diagnostic tools bz Enable serial communications logging View axis usage counters Explore save directory FQ Display log File Fil About Sl gility Opens a pdf file of the QIAgility User Manual version 1 0 Creates a zipped support package Select a file location and then click on the OK button This package contains information about run settings calibration data and log information See Section 6 7 3 Enables the user to view recent support packages Support packages can be sorted based on name of run file time of completion and type of error which occurred during the run See Section 6 7 3 QlAgility User Manual 01 2009 QIAgility Software Self diagnostic tools Enable serial communication s logging View axis usage counter
8. Retry operation Ignore error and Skip step See Section 9 3 for more information about specific warnings and errors QlAgility User Manual 01 2009 6 11 Operating Procedures Abort run Click this button to abort the run Retry operation The instrument will discard the current tip The Y arm will move to its resting position This provides access to the worktable allowing the error to be resolved Click on the OK button to continue with the run Ignore error The instrument will continue with the run as normal Skip step The instrument will skip the step and continue with the run Exhausting tip supply during a run If the tip supply is exhausted during a run the instrument will pause to allow the user to replenish the tips The Replace Tips dialog box will appear Plates 50 Tecan tip 96 well plate vertical 42 50yl Tecan tip 96 well plate vertical B2 To replace the tips 1 Add the correct tips to one of the available tip locations on the worktable 2 Select the Tip plate where the tips have been replaced by checking the box next to the correct plate 3 Click on the OK button to continue the run Note If the Cancel button is selected the run will be aborted 6 12 QlAgility User Manual 01 2009 Operating Procedures 6 7 6 7 1 Reports log files Pre run repori The pre run report is automatically generated before
9. Start importing Defines the first row in the file from which FROM row the data will be imported Start importing Defines the first well in the Sample or TO well Reaction plate to which the data will be imported 7 Select the remaining options in the Import Options panel as desired and select the column from which this information will be imported Note The software will automatically limit the number of rows imported to prevent overrunning the end of the import tile and to prevent exceeding the available wells on the plate Limit sample Defines the maximum number of rows of count to data that can be imported trom the file Sample name Instructs the software to import the sample from column name from a specific column in the file Load ID from Instructs the software to import an ID from column a specific column in the file Load Conc Instructs the software to import a from column concentration value from a specific column in the file 8 To add the imported data directly to a sample bank select Add to sample bank named Then select New Bank or Existing Bank See Sections 5 11 1 and 5 12 5 for more intormation about how to manage sample banks 9 The Row Filter function allows the user to filter the imported data based on a concentration range If 5 116 QlAgility User Manual 01 2009 QlAgility Software desired select this function and then define the options as req
10. User paused Displays all support packages in which the job user paused the run file User aborted Displays all support packages in which the job 3 user aborted the run file The support packages can be sorted by selecting Choose by Date and Choose by Exception tab In addition support packages can be viewed based on the type of exception To do this select All Exceptions User paused job or User aborted job from the drop down menu Importing and exporting reaction sample data Sample and reaction data can be imported and exported See Section 5 12 7 Extraction data from earlier purifications can be imported and used as sample data In addition data can be exported for use in downstream applications for example with the Rotor Gene Q Shutting down the software and the instrument l Click Sim the top right corner of the screen or select File Exit to shut down the software If the current run file has already been saved proceed to Step 5 If the current run file has not been saved the following message will appear P Bo vou want to save the changes you made to C Program tf Files STAgiliby GProtocals HotStarTagi_signed3 QA57 Yes No Cancel Select the Yes or No button QlAgility User Manual 01 2009 Operating Procedures 4 It Yes is selected the Save File dialog box will appear Select a file location and then click on the
11. Das Ger t muss zum Betrieb immer geerdet sein Es ist verboten die Schutzleiter im Ger t oder in der Netzzuleitung zu trennen oder zu entfernen Gef hrliche Spannung im Ger t Auch in ausgeschaltetem Zustand kann an einigen Stellen im Ger t Netzspannung anliegen wenn das Ger t am Stromnetz angeschlossen ist Das ffnen oder Entfernen von Geh useteilen kann diese stromf hrenden Teile freilegen Risque d lectrocution Toute interruption du conducteur de protection l int rieur ou l ext rieur de l instrument ou d connexion du raccord du conducteur de protection terre peut rendre l instrument dangereux Il est interdit d interrompre volontairement ce conducteur Pr sence de tensions mortelles dans l instrument Lorsque l instrument est reli au secteur les raccords peuvent tre sous tension et des parties sous tension peuvent tre d couvertes en ouvrant des capots ou en retirant des pi ces l exception de celles auxquelles il est possible d acc der manuellement 1 6 QlAgility User Manual 01 2009 Safety Information WARNING Hazardous chemicals W3 Some chemicals used with this instrument may be A hazardous or may become hazardous after completion of the protocol run Always wear safety glasses gloves and a lab coat The responsible body e g laboratory manager must take the necessary precautions to ensure that the surrounding workplace is safe and that the instrument operators are n
12. Enable Lamp Switches the UV lamp on Disable Lamp Switches the UV lamp off Close Closes the UV Lamp Control dialog box The UV lamp can be enabled using timed control or manual control Under manual control the instrument arm does not move and shadowing will result Under timed control the instrument arm moves between 2 locations in 5 s intervals If using timed control define the exposure time and click on the Start button If using manual control click on the Enable Lamp button A message box will appear Read it carefully Click on the Yes button to start operation of the UV lamp Note To switch the UV lamp off click on the Stop button Operating the HEPA filter When the HEPA filter is switched off the HEPA filter icon in the toolbar appears red To operate the HEPA filter 1 2 Click on the icon in the toolbar The HEPA filter will switch on and the HEPA filter icon in the toolbar will appear green To switch the HEPA filter off click on the icon in the toolbar QlAgility User Manual 01 2009 Operating Procedures 6 4 Executing a run 6 4 1 Q Protocols Q Protocols are run files which have been developed to directly facilitate specific PCR applications Q Protocols are installed within the QProtocols subfolder To access this folder select Installation directory of QlAgility Software QlAgility QProtocols e g C Program Files QIAgility QProto
13. Master Mix Component Selection dialog box which enables the master mix to be configured Opens the Master Mix Reagent Insertion Order dialog box which enables the order in which reagents and diluent are added to the master mix to be adjusted Enables a user to select a saved master mix setup Select the correct file and then click on the Open button to continue Select to save the master mix setup Enter a file name and a location then click on the Save button This option is useful when the master mix is used regularly but the sample and reaction contiguration changes Master Mix Component Selection dialog box Summan Make mix up to this volume not including samele NTC volame bas Ch Delad sample ag lor thes rex fp gr How meh reagent to manually misel per reaction fo g RF y loriy ts ryg eeri aiir 1 CA 0365 belote r Detak reaction volume fa r Component volumes Select magerts and their volumes to use in this m r water volume is automatically cakuised 1 Sel tapered hinged 1 5m tapered hinged 1 end tapered hanged 1 Sen tapered hinged 1 Bel tapered hinged 1 Bel tapered hinged 1 Send Lage ent hanged 1 Sel tapered hinged Reagent biock felancda Reagent hack standa Pine Je ec Name Ue Vol per Reaction x Ure i Urenone 25 Less J ox Make mix up to Defines the volume that the mix will be this volume made up to QlAgility User Man
14. QlAgility User Manual 01 2009 2 3 Introduction 2 3 1 Requirements for QlAgility users This table covers the general level of competence and training necessary for transportation installation use maintenance and servicing of the QIAgility Task Personnel Training and experience Delivery No special requirements No special requirements Installation QIAGEN Instrument Appropriately trained and Service Laboratory experienced personnel familiar technicians or equivalent with use of computers and automation in general Routine use Laboratory technicians Appropriately trained and running or equivalent experienced personnel familiar methods with use of computers and automation in general Servicing QIAGEN Field Service Specialists only 2 4 QlAgility User Manual 01 2009 General Description 3 1 General Description The QlAgility System performs fully automated PCR setup The QlAgility System comprises the QlAgility a computer and QlAgility Software These components have been optimized to work together across a wide variety of applications and provide unmatched accuracy precision and speed for PCR setup There are 2 possible configurations with HEPA filter UV lamp and without HEPA filter UV lamp QIAgility principle The QlAgility uses a single channel pipet to automate PCR setup up to 96 PCR reactions can be set up in approximately 30 minutes Level sensing facilitated by conductive tips e
15. Reaction List will be updated with the sample bank pooling step Add sample bank duplication step If a sample bank of 8 samples was copied 5 times using standard reaction steps 40 tips would be required When the Add sample bank duplication step option is used only 8 tios are required for this operation To copy a sample bank l 2 3 4 Left click on a Reaction plate The Reaction right hand pane will appear Click on the Special button Select Add sample bank duplication step QlAgility User Manual 01 2009 5 101 QlAgility Software 5 The Bank Duplication dialog box will appear m Select a Tip Setting option Ce Multi eject Using 1 tip per sample to aspirate total volume and multi eject all duplications Multi Eject Settings Re use tips Using 1 tip per sample to aspirate and eject each duplication volume separately C Use new tips Using a new tip for each sample and for each duplication volume Select the sample bank to be duplicated Sample bank Sample Bank 1 16 well s DI m Select the reaction plates to duplicate into ES well plate vertical C2 a First well at Volume 5 H Add Reaction plates I A Bank Duplication f x This feature duplicates a bank of samples into multiple reaction plates I reaction wells used must be clean before the start of this step Cancel Total volume Du incl 2 pl e
16. error insufficient liquid Ignore all All level sensing errors will be ignored errors Note These options are disabled if a Q Protocol is loaded and locked 3 Atick will appear next to the option that has been selected Note All errors are reported in the post run report regardless of which liquid level tracking error is selected This cannot be disabled 5 9 9 Set tip usage options Tip reuse can provide a significant reduction in the number of tips which are used during a run To configure tip usage 1 Select Options Run Settings Set tip usage options 5 46 QlAgility User Manual 01 2009 QIAgility Software 2 The Tip Usage dialog box will appear x Settings OK ch tip for one operation only Will use one tip for each take eject cycle Gives highest precision but will use large numbers of tips for all operations increasing run cost and run completion time Maximum number of times to re use tips fe JV Allow multiple ejections from a single liquid pickup Allow multi dispensing to non empty wells by tips contaminated P with existing target well contents without contaminating source wells Cancel Multi Eject Settings Use each tip for one operation only Re use tips where possible Maximum number of times to re use tips Allow multiple injections from a single liquid pick up One tip will be used for each aspirate eject cycle This option giv
17. 1 Left click on a Reaction plate The Reaction right hand pane will appear Click on the Special button Select Add sample bank pooling step ae ae The Sample Pooling dialog box will open 5 98 QlAgility User Manual 01 2009 QIAgility Software sample INTCH res iso paol samples to common opaa weils bp ovelyang barks or malen mutt pat of a bank to be ege kreeg and each posted bank mult hie the are a Esh banki sat hawe itt caw volume Maman batal ohare is 200 l Caner p To Election Mode de Mubepeckup Ling bp pet temple to mulled picete all pooling que and eect ai C Amun ms Lang bp per sample In aap and ec nach Geck ipad separari Usenee hpi Wong a new tp dot each pooled bp per sample m the treie bark Tage peection plate E ve plate enea E a LN First wt D Repicarer a omg T agia bark An ga Modu EN Add lerne Sangin Post Ma Seiten Mes eranl 3 H Hee vehar j Ek EI ba user ondrenale value RTE Total pool sch mg O ul by Se gap Toit beosecd resp Laigest avedsble bo pos 200 pl i Multi pickup Instructs the instrument to use a single tip to multi aspirate and to eject all pooling liquids This allows a total volume up to the volume of the largest tip size on the worktable to be pooled Sample contamination may occur Re use tips Instructs the instrument to use a single tip to aspirate an
18. BH Configure Plate Heights Plates To Calibrate 96 well plate vertical 200ul PCR tube C1 Mix plate 5 tube positions 5ml tapered tube M1 Mix plate 5 tube positions 1 5ml tapered tube M1 Reagent block standard 200 flat tapered 200ul PCR tube A1 Reagent block standard 200 flat tapered 2ml self standing screw cap tube R1 Reagent block standard 200 Tat tapered 1 5ml tapered hinged tube A1 KI IR IR KI lt KI Select All Clear All Settings IV Require confirmation from user Take average of how many wells H Control Autodetect checked items Abort Manual Setup highlighted item Autodetect applies to plates with ticked checkboxes Manual setup applies to the currently highlighted plate Plates to Lists the plates that are currently located on Calibrate the worktable Select All Selects all of the plates in the Plates to Calibrate list Clear All Deselects all of the plates in the Plates to Calibrate list QlAgility User Manual 01 2009 7 7 Instrument Setup and Calibration Require Instructs the software to present a message confirmation to the user after automatic plate height from user calibration is performed This enables the user to confirm the value to be recorded as the auto detected height Take average Defines the number of wells from which to of how many take an average wells Autodetect Initiates the aut
19. QIAgility M RS 232 computer RS 232 QlAgility M USB computer converter RS 232 QlAgility E PCMCIA computer converter RS 232 QlAgility Note The laptop that is supplied with the QlAgility does not support the RS 232 connection and therefore must be connected to the QlAgility via the USB port QlAgility User Manual 01 2009 3 11 General Description This page left intentionally blank 3 12 QlAgility User Manual 01 2009 Installation Procedures 4 1 WARNING A Installation Procedures This section provides instructions on unpacking and installing the QlAgility Requirements Site The QlAgility must be located out of direct sunlight away from heat sources and away from sources of vibration and electrical interference Refer to Appendix A for the operating conditions temperature and humidity The site of installation should be free of excessive dratts excessive moisture excessive dust and should not be subject to large temperature fluctuations Use a level workbench that is dry clean vibration proof and large enough to accommodate the QIAgility computer and tip receptacle box Refer to Appendix A for the weight and dimensions of the QlAgility The QlAgility must be placed within approximately 1 5 m of a properly grounded earthed AC power outlet The power line to the instrument should be voltage regulated and surge protected Note We recommend that the QIAgility
20. QlAgility User Manual 01 2009 5 73 QlAgility Software Total reactions Sets the minimum volume of master mix to to prepare if create if the master mix is not used in any unused reactions in the run This allows the user to create a master mix without assigning it to reactions It can be used as a premade master mix for multiple subsequent runs Defines the volume in terms of the total number of reactions Extra if Indicates that when master mix is made unused without aliquoting to reactions the total volume should include the additional amount which is defined in the determined Master mix extra volume option in the Run settings menu Wait for Select to wait for confirmation after adding confirmation the final component of the master mix after adding final ingredient Wait for Select to wait for confirmation after confirmation performing the final mix after performing final mix No of times to Defines the number of times that the mix each master mix will be mixed after addition of reagent each reagent Mixing maximizes recovery of reagent from the tip interior and equalizes the concentration of liquid remaining on the tip interior with the liquid in the mixture No of times to Defines the number of times to mix after mix at end addition of the last reagent 5 74 QlAgility User Manual 01 2009 QlAgility Software Configure Mix Adjust Insertion Order Load Save Opens the
21. Save button 5 Ifthe current run file has already been saved the following message will appear Cs 8 6 k Do you wish to quit QIAgility 6 Click on the Yes button 7 The tollowing dialog box will appear Quitting QIAgility D Stop Immediately 8 Select Move to Safety Position recommended or Stop Immediately See below for details about these options If Stop Immediately was selected proceed to step 11 9 The software will now shut down If Move to Safety Position recommended was selected the pipetting head will now move to a safe location The following message will appear 1 The robot can now be safely turned off 10 Click on the OK button 11 Set the power switch of the QIAgility to the off position Moving to a safety position This is the recommended method of shutting down the instrument The instrument will complete its homing routine and then the pipetting head will be lowered to a known safe location The user is prompted when it is safe to switch the QlAgility User Manual 01 2009 6 19 Operating Procedures instrument off All the instrument axes are disengaged and can be moved freely As the instrument is switched off a small click is heard as the pipetting head drops 1 2 mm further Shutting down immediately This is a faster way of shutting down The instrument axes remain engaged and the pipetting head remains in an upward
22. aspirate False triggering occurs when the level sensor spuriously reports that it has found the liquid surface when it hasn t actually reached the liquid during its downward probe The software considers all liquid surface levels found between the tube base and the top of tube to be valid and reports false triggering errors when the level found by the sensor is above the top of the tube Such conditions can occur when static electricity is present on the plasticware as this may cause an QlAgility User Manual 01 2009 Appendix C apparent change in capacitance similar to that caused when the tip makes contact with liquid False triggering which occurs Within the tube is undetectable False triggering of the level sensor which occurs during aspirate operations usually causes insufficient volume to be aspirated and hence a deficiency in volume transferred to the target well This function presents options to reduce the impact of false triggering caused by static electricity Recommended settings cause the pipettor to probe the surface at least twice looking for successive level detections which are within a small tolerance before proceeding with the aspirate Level sensor false trigger handling options eject False triggering of the level sensor which occurs during eject operations may cause insufficient volume to be delivered to the target well This function presents options to reduce the impact of false triggering caused b
23. but the desired final concentration is not achieved Normalize to Defines the concentration to which samples conc will be normalized This excludes the contribution that other reagents and master mix make to the reaction Setting up a reaction list Note If the total number of reactions configured on one plate exceeds the number of reaction wells a warning will appear This warning must be resolved before the run can be started 1 Left click on a plate with Reaction function 2 The Reaction right hand pane will appear 3 Click on the Add button 4 Select a sample bank from the drop down menu in the Samples panel Note Only one sample bank can be selected per reaction QlAgility User Manual 01 2009 5 93 QlAgility Software J 10 If desired select Pre mix before taking sample and enter the number of times to mix Select the components of the reaction Available master mixes are listed in the Mixes and reagents in mix wells panel and available unmixed reagents are listed in the Unmixed reagents panel Left click in the boxes next to the required components to select them A tick will appear next to the components which have been selected Click on the button to select the target reaction plate The Plate well Selector window which displays a schematic of the worktable setup will appear EN ie x Please select a plate At Tip p Ceeskucttee
24. shom Dach Het Edit Opens the Edit Standard dialog box which enables a standard to be configured Load Enables a predefined standard dilution series configuration to be loaded trom a file Save Enables the current standard dilution series configuration to be saved in a file Show Illustrates the location of the standard dilution series on the worktable 17 Select a standard trom the list The following dialog box will appear xi r Details f R Number of dilution concentrations fi including first undiluted standard Concentration of undiluted standard f Dilution ratio ile f 0 QlAgility User Manual 01 2009 5 129 QlAgility Software Number of dilution concentrations Concentration of undiluted standard Dilution ratio Defines the total number of wells in the dilution series including the initial undiluted stock well of the standard Defines the concentration of the starting undiluted stock well of the standard dilution series Defines the dilution ratio for successive wells in the standard dilution series Concentrations of successive wells in the series are determined by multiplying the concentration of the preceding well in the series by the dilution ratio 18 Define the Number of dilution concentrations the Concentration of undiluted standard and the Dilution ratio 19 Click on the OK button to continue 20 Repeat steps 17 19 for any
25. software window Set liquid level mode for segment 1 Right click on a plate or segment with Sample or Reaction function 2 Select Set liquid level mode for segment A submenu will appear 5 56 QlAgility User Manual 01 2009 QlAgility Software Do not use The instrument performs pipetting liquid level operations at the height calibration position for the plate segment Detect liquid The instrument performs pipetting level using operations for the plate segment using the sensor liquid level sensor See Section 3 4 Use liquid level The instrument performs pipetting estimate operations for the plate segment using the liquid level estimate function See Section 3 4 Use default The instrument performs pipetting liquid level operations for the plate segment using the mode Tip method that has been defined in the Sensor Options menu See Section 5 9 7 for more details about how to configure liquid level tracking options trom the Options menu 3 Select 1 of the 4 options for detecting the liquid level from the submenu A tick will appear next to the method which has been selected Note All other plates segments unless otherwise defined using this function will use the method that is defined in the Options menu See Section 5 9 7 for more details about how to contigure liquid level tracking options from the Options menu 5 10 2 Setting tip availability Tip availabili
26. 1 9 Safety Information WARNING DE WARNING A CAUTION Risque de dommages corporels et mat riels Le QlAgility est trop lourd pour tre soulev par une personne Pour viter des dommages corporels ou mat riels ne pas soulever l instrument tout seul Risk of personal injury and material damage W7 Do not attempt to move the QlAgility during operation Verletzungsgefahr und Besch digung des Gerdtes Den QlAgility w hrend eines Laufes nicht bewegen Risque de dommages corporels et materiels Ne pas essayer de bouger le QlAgility pendant son fonctionnement Risk of electric shock Do not open any panels on the QlAgility Risk of personal injury and material damage Only perform maintenance that is specifically described in this user manual Gef hrdung durch Elektrizit t Unter keinen Umst nden darf das Geh use des QlAgility ge ffnet werden Verletzungsgefahr und Besch digung des Ger tes Keine Pflege und Wartungsarbeiten durchf hren die nicht in diesem Handbuch beschrieben sind Risque d electrocution Ne pas ouvrir les panneaux du QlAgility Risque de dommages personnels et materiels R aliser uniquement la maintenance d crite sp cifiquement dans ce manuel The term CAUTION is used to inform you about situations that could result in damage to the instrument or other equipment Details about these circumstances are given in a box like this one QlAgility User Manual 01 2009 Safety
27. Alternatively if no changes have been made click on the Cancel button The pre run Checklist dialog box will appear Checklist lol x Please acknowledge the following messages and hit OK to continue Blue messages are warnings and must be checked to continue Red messages are errors and prevent the run from starting DJ Please confirm that tips tubes plates and liquids have been setup correctly as per the Pre Run Report U Tips During this run the robot will run out of 50 pl tips Check all boxes and hit OK to continue Please make sure the tip discard chute is open and the tip disposal box is empty Cancel Pre Run Report Gk 5 Click on the Pre Run Report button The pre run report will be displayed 6 14 QlAgility User Manual 01 2009 Operating Procedures 6 7 2 Post run report Upon completion of a run a Post run report will appear This report contains the same information as the Pre run report but also contains the following information Duration HN Date M Start time E Completion time M Run duration Exceptions M Date and time of exception M Instrument activity at time of exception M Details of the exception E User response Note Any exceptions are highlighted in the post run report Reaction plate details Well number Well location Programmed final well contents Actual tinal well contents Volume pipetted total to well Fin
28. Change plate type Change accessory Change plate Function Da Wf a 7 5 no options When the selected plate or segment has available Tip Reaction Mix or Sample function further options will be available in this panel See Sections 5 10 2 5 11 1 and 5 12 4 for further details about these options Set liquid level Enables the method of tracking liquid level mode for to be selected for a specitic plate segment segment All other plates segments unless otherwise detined using this function will use the method that is defined in the Options menu See Section 5 9 7 for details about how to configure the liquid level tracking options from the Options menu 5 50 QlAgility User Manual 01 2009 QlAgility User Manual Toggle Image Toggle Zoom Delete Cal bration data Change plate type Change accessory Change plate function 01 2009 QIAgility Software Click to toggle between an image and a schematic of the current plate type This option has the same function as the Switch plate button Click to toggle between an enlarged view and a normal view of the current plate type This option has the same function as the Zoom plate button Deletes all calibration settings associated with the plate Opens the Plate configuration dialog box which enables the plate type and the tubes associated with a plate to be changed See Changing the plate t
29. Gerdtes bleichen und Plastikteile sch digen Der QlAgility darf nicht ins direkte Sonnenlicht gestellt werden QlAgility User Manual 01 2009 1 11 Safety Information D t rioration de l instrument La lumi re directe du soleil peut d colorer des parties de l instrument et endommager des parties en plastique Placer le QlAgility en dehors de la lumi re directe du soleil CAUTION Damage to the instrument C3 A Do not use bleach solvents or reagents containing acids alkalis or abrasives to clean the QlAgility Besch digung des Ger tes Es d rfen keine Bleiche noch s ure oder laugehaltige Reinigungs oder Scheuermittel benutzt werden Deterioration de l appareil Ne pas utiliser d eau de Javel de solvants ou de r actifs contenant des acides des substances alcalines ou abrasives pour nettoyer le QlAgility 1 7 Symbols on the QlAgility Type plate on EN CE mark C the back of the instrument Plakette auf DE CE Zeichen der R ckseite des Ger tes Marquage CE N Plaque l arri re de l appareil On the back E Warning symbol of the instrument 1 12 QlAgility User Manual 01 2009 Safety Information R ckseite des Ger tes A l arri re de l appareil Type plate on the back of the instrument Plakette auf der R ckseite des Ger tes Plaque l arri re de l appareil Type plate on the back of the instrument Plakette auf der R ckseite des Ger tes Plaque l arr
30. Note On completion of each run the software automatically saves a support package However for problems that occur outside the context of a run it is important to manually create the support package immediately after a suspected error has occurred Support packages are important when reporting a problem to QIAGEN Technical Services To create a support package 1 Select Help Save support package 2 The Browse for Folder dialog box will open 3 Select a location in which to save the support package 4 Click on the OK button To select the correct support package 1 Select Help Choose support package 2 The Support Package Chooser dialog box will appear Bann Package haddi Yeu an wia Ge baih I beer the rala support packaged and cand Vers are location d recertan fou Can view the availabe tuppi packaged by date er by comelated pe Choose by Date Chone by Exception Te belie baski shows all ces ernennen fos the guner w s bre Se supe pc zez deleeraed lo match the paires e whe these meoepbeond gearen The deta can aloo be Heed i ra ar ten komm e St specific sehen ce by peleching on Delt how AlE pepion e leed Choose by Sorts listed support packages by date Date Choose by Sorts listed support packages by exception Exception QlAgility User Manual 01 2009 6 17 Operating Procedures 6 8 6 9 6 18 All Exceptions Displays all support packages which contain an exception
31. Opens the Bank Duplication dialog box which enables copying of sample banks The user can control tip usage Opens the Sample Dilution dialog box which enables a sample bank to be diluted by addition of varying quantities of diluent and sample Enables the user to perform a serial dilution The user can select which dilutions to add to reactions Enables the user to prepare a stock plate of normalized samples and a working plate using a minimal number of tips If a minimal number of tips is used the sample plate will be contaminated with diluent QlAgility User Manual 01 2009 QlAgility Software Add remove Enables a reaction plate to be specitied as waste pool a waste receptacle All samples in a sample bank bank can be moved to a single well members Adding a pause into the reaction list It can be useful to introduce a pause into the reaction list if an incubation time is required between pipetting operations Note Pauses are processed during sample processing only after master mix and reagents have been aliquoted to reactions To introduce a 30 second pause 1 Left click on a Reaction plate 2 The Reaction right hand pane will appear 3 Click on the Special button 4 Select Add pause 30 sec 5 The reaction list will be updated To introduce a pause of defined length 1 Left click on a Reaction plate The Reaction right hand pane will appear Clic
32. Q Protocol according to your needs The user can adjust the lab notebook set tip availability see Section 5 10 2 modify sample banks see Section 5 11 1 assign plate IDs barcodes see Sections 5 12 5 5 12 6 and 5 12 7 and assign well IDs barcodes to sample reaction wells see Sections 5 12 5 5 12 6 and 5 12 7 6 6 QlAgility User Manual 01 2009 Operating Procedures 6 4 2 Selecting a saved run file To open a saved run file 1 Select File Open or click on the icon ux Look in 5 Data D EICH ES My Recent SupportPackages Documents Desktop My Documents Sr My Computer em e DEENEN File name D Places Files of type OlAcilty Document D QAS DI Cancel v7 2 Select a file and then click on the Open button To open a recently used run file using the toolbar 1 Click on the icon on the toolbar 2 Select the Recent tab QlAgility Pure Precision 35553 New Recent Protocols HotStarT aql_signed3 Open QuantiFast MP PCR 2 GD Cancel Browse 3 Select a run file from the list and then click on the Open button QlAgility User Manual 01 2009 6 7 Operating Procedures To open a recently used file from the File menu 1 Select File from the menu bar Recently used run files are listed in the File menu File Control Wizards Options Help New Ctrl N Open Ctrl 0 Save As Ctrl 5 Lab not
33. Section 9 4 1 for more details of Steps Cycle Pipettor See Section 9 4 1 for more details Head 9 10 QlAgility User Manual 01 2009 Troubleshooting 9 4 1 Check See Section 9 4 2 for more details Commun ications Liquid Sensor See Section 9 4 2 for more details Test Close Closes the dialog box Go Home Homes all axes and resets the positional reference for the instrument for subsequent movements Clear Clears the content of the messages text box Messages Mechanical tests Check Home Opto Alignment This test ensures that the optical homes in X Y and possibly Z axes in QlAgility instruments are 3 4 and 5 steps away from their L297 software home respectively Check for loss of steps This test establishes whether the instrument has reliable movement The default iteration setting of 5 will take approximately 20 25 minutes to complete Reported loss of steps on the P axis can be ignored Reported loss of steps on the Z axis of 8 steps is acceptable If there are errors on the X or Y axis save a support package and contact QIAGEN Technical Services See Section 6 7 3 for details about how to save a support package Cycle Pipettor Head After calibration or if the instrument has been unused for a long period of time it is recommended to cycle the pipetting head This helps to distribute the grease evenly An iteration of 400 is recommended QlAgility User Manual 01 2009 9 11 Troublesho
34. Sequence Each plate type has a specific pipetting order and specific label order Where these are different e g vertical pipetting order and horizontal label order the sequence in which wells are listed in the grid changes according to the well display order selection This function is useful for example when it is convenient to dispense liquids by column vertical pipetting order but to export the data by row horizontal label order QIAgility User Manual 01 2009 QIAgility Software Copy all Select to copy the Reaction Data list The data can be pasted into an Excel file Paste to current Pastes data from the system clipboard e g cell a list of Yes No values from a spreadsheet into the Reaction Data column Row height Select to adjust row height A submenu will appear Select Grow to increase the row height and select Shrink to decrease the row height Export Select to export the Reaction Data list A submenu will appear Select either Export to CSV or Export to Excel Assign ID s Enables groups of reactions to be assigned the same value in the ID column Left click and drag to select a group of cells Right click on the selection and select Assign ID s Set Enables groups of reactions to be assigned Concentrations the same value in the Conc column Left click and drag to select a group of cells Right click on the sele
35. The pipetting head is brought into the tip collar 2 The pipetting head is gently pressed against the tip collar 3 The pipetting head is forced against the tip collar Detect tip absence When activated a tick is visible This function automatically detects when the instrument has failed to pick up a tip This is caused when a tip is absent from the pick up position A message is presented with options to ignore and proceed as if the pickup succeeded retry attempt to pickup at the same location abort terminate the run or skip to the next available tip position and retry QlAgility User Manual 01 2009 CG Appendix C C 2 Automatically skip to next if detect tip absence This function is disabled until Detect tip absence is enabled to be activated When activated a tick is visible This function automatically skips to the next available tip position and retries the tip pickup if a tip pickup tails due to tip absence Compensate for liquid loss This function sets a depth in millimeters by which the tip should be further lowered into the wells below the determined or calculated liquid surface position for pipetting operations The default value is O This function is intended for applications which use liquids that evaporate rapidly In addition this function can be used to address a variety of situations where the tip would otherwise be placed too high in the well for pipetting operations Note Us
36. User intervention will be required to continue with the run However if sample availability is limited it may be desirable for a tube to contain less liquid than the detection limit If the default setting is enabled i e Do not ignore errors an error message will appear every time an aliquot is taken from the tube To avoid the need for user intervention every QlAgility User Manual 01 2009 5 45 QlAgility Software time an aliquot is taken a different error level can be selected To set the liquid level tracking error level 1 Select Options Run Settings Ignore errors during run Configure tip air intake Tip Into Configure pipette speed gt bk modify tip availability Use liquid level when pipetting Ee right click menu to alter Ignore errors during run 3 vw Interrupt run on all errors Set master mix extra volume Interrupt run op serious errors Set standard extra volume Ignore all errors Set tip usage options Get default File ration Tip Type 2 Select 1 of the 3 options Interrupt run on all errors Interrupt run on serious error or Ignore all errors Interrupt run This is the default error level All liquid level on all errors tracking errors are reported during a run and user intervention is required every time an error occurs Interrupt run User intervention will be required tor system on serious errors but not for errors caused by
37. Zyl Mae C Bel Same FT GC a 2325 pl Mi C 5 pl Sample G1 C1 25 25 ul Ms Bel Semele HI C1 LAS Ziy MoC hel Sane AZ CI Opens the Reaction Configuration dialog box Enables setup of a new PCR reaction Opens the Reaction Configuration dialog box Enables a reaction to be edited Alternatively double click on a reaction to open the Reaction Configuration dialog box 5 86 QlAgility User Manual 01 2009 QIAgility Software Copy Delete Retarget Up Dn Special Select All e Copies selected reaction Left click on a reaction in the Reaction List and then click on the Copy button If there is more than one reaction in the list a submenu will appear Select Copy in place Copy to end of list or Cancel Deletes selected reactions To delete more than one reaction hold down the Shift or Ctrl key left click on reactions in the Reaction List to select them and then click on the Delete button Enables a reaction to be retargeted to a different reaction plate Left click on the new reaction plate to select it then left click on a reaction in the Reaction List and then click on the Retarget button A message box will appear click on the Yes button to continue Displays a summary of the selected reaction Modities the reaction order Left click on the reaction to be changed in the Reaction List Hold down
38. against the tip ejector Please clear the pipettor hub remove all items from the worktable and ensure the tip ejector is secured Keep the lid open Warning beware personal safety Y axis Position e x axis Position E FI i Tip Ejector Height fo Tip ejector location calibration incomplete Carefully adjust the X Y position of the pipettor manually to a location above the slot then Locate Z Axis or adjust the height manually Locate Ejector Cancel Abort Test Finished 11 Manually adjust the X and Y axis positions using the arrows and then click on the Locate Z Axis button 12 The following message box will appear 13 Click on the Yes button The instrument will now locate the Z axis position 14 Click on the Test button the following message box will appear QlAgility User Manual 01 2009 7 3 Instrument Setup and Calibration CI 4 Are you ready to test the tip ejection The arm will move bo the right wait for confirmation then move into the ejector 15 Click on the OK button x 2 j Please manually place a tip on the head of the robot and hit OK to continue cancel 16 Place a tip onto the pipetting head and then click on the OK button to continue 17 The instrument will now locate the tip ejector and will eject the tip 18 Click on the Finished button 19 The following message box will appear xi YD Sa
39. air on the final ejection This limits accumulation of liquid on the tip interior This is a default setting when tip reuse is selected but is an optional setting when single tip usage has been selected Select to apply default initial ejection volumes i e 1 ul for 50 ul tips and 4 ul for 200 ul tips Select to specify initial ejection volumes The initial ejection volume is the volume that is aspirated and ejected into the source well before ejecting into target wells starts Use this option to specify the extra volume to aspirate 5 If tip reuse is disabled i e each tip will be used only once deselect Use air on multi eject 6 Select either Apply Default Initial Ejection Volumes or select Specify Initial Ejection Volume If Specify Initial QlAgility User Manual 01 2009 5 49 QlAgility Software 5 10 5 10 1 Ejection Volume is selected define the initial ejection volume 7 Define the Additional Extra Volume Note Setting this value to zero may reduce precision H is recommended to set this volume to half the volume of the aliquot Define worktable setup Plate operations The plate operations menu provides options to change plate type change plate function manage tip availability and manage sample banks m we we we SE FY F F F no options available Set liquid level mode for segment kb Toggle Image Toggle Zoom Delete Calibration Data
40. be defined sample bank and added to a new or existing sample bank Remove Opens the Update Sample Bank dialog selected wells box and enables selected wells to be from sample removed from an existing sample bank bank Toggle sample Opens the Sample Banks panel of the bank list Sample right hand pane This option is only available when a Reaction plate is selected See Section 5 12 5 for more information on managing sample banks using the Sample Banks panel Set preload Enables the user to enter the volume of volume liquids which have been preloaded into reaction tubes This option is only available when a Reaction plate is selected Click on the OK button to continue 5 60 QlAgility User Manual 01 2009 QIAgility Software Update Sample Bank dialog box e BH Update Sample Bank x Sample Bank Name Sample Selection Filter Selection Ze New Bank Specify concentration range oOo O Select All Clear All Min Max Existing Bank C Range of Wells Min Concentration First Well Lo zj Max Concentration 0 Number of Wells 0 r S Use selected wells INSIDE range List of wells Banks defined elsewhere Use selected wells DUSTIDE range C Bank wells Apply filter to selected wells C1 Sample 200pl PCR tube Generic o 1 2 3 O O O O New Bank Select to create a new sample bank Inser
41. calibration is to set this so that the tip is just above the base of the tube well 5 Adjust the height of the tip in the Adjust Height panel 6 Use the up down arrow buttons in the manual height calibration window to raise and lower the pipetting head 7 10 QlAgility User Manual 01 2009 Instrument Setup and Calibration 7 1 4 7 10 To adjust the height correctly the distance between the tio and the tube base must be adjusted as described above In most cases it is not possible to see the distance between the tip and the base the distance must be felt by manually lifting the tube from its support plate If the tip makes forceful contact with the base of the tube well the Level at bottom of well does not reflect the true distance of the base of the tip from the home position Use the Home Z axis button to reset the 0 position and repeat steps 5 7 starting with a lower Level at bottom of well value to avoid driving the tip forcetully into the base of the well Click on the OK button when the correct height calibration has been set Click on the Cancel button when all calibrations are complete Calibrate tip offsets It is recommended that this calibration is performed upon initial installation and when the user starts a new lot number of tips The collar size of 50 ul and 200 ul tips should be equal but small variations sometimes exist Although both tips a
42. copy in the Reaction plates list and then click on the Remove button 5 106 QlAgility User Manual 01 2009 QIAgility Software 14 Click on the OK button to return to the main software window The Reaction List will be updated with the sample dilution step Add serial dilution step 1 Create a sample bank that contains 1 well See Section 5 11 1 for details about how to do this a EE Diluent Sample bank QlAgility User Manual Left click on a Reaction plate This feature performs a custom serial dilution The dilution ratio at each step can be customized The source sample bank needs to have the same number of samples as there are ejector heads on the robot Select the sample bank and the diluent Diluent Diluent v Sample bank Sample Bank 4 1 well s DI Select the Reaction Plate to dilute into ss well plate vertical amp C2 Be First well DE Special settings for Dilutions Min volume 50 k ul Enable mixing during dilution Iv No of times to mix 5 Change tips after each dilution V Select the dilution ratios to use Ratio iP B E Dilutions Ratio 1 2 Ratio 1 3 1 6 from initial Ratio 1 4 1 24 from initial Ratio 1 5 1 120 from initial i Remove NOTES Dilutions 4 Total Diluent volume required 164 17 pl Total Sample volume required 35 83 pl Tips Required 8 x 50 ul Larges
43. function performs dilutions of a bank of samples with a diluent reagent Each dilution in the series is specified by a pair of volumes that describe the amount of sample and amount of diluent to be combined in the reaction By default dilutions of the sample are performed with a single tip to transfer the sample to target reactions A different tip is used for transferring the diluent to target reactions thereby minimizing tip usage l OR WN 5 104 Left click on a Reaction plate The Reaction right hand pane will appear Click on the Special button Select Add sample dilution step The Sample Dilution dialog box will appear ie legue paluma une o moe dhin of a bank of caries Les eme mes carie lue en lhe SH su cher SEUL TOUL Geht Kei Za Zu Select Tip Usage options Gard fe Matce Long 1 bp bo aapinate total volume pet bas and et al dilutions Diani Hide Z tteg Games Mu eiect G tter Reuse mm leute Op for all dito per ample D Use res ipa Using dress Gp hor eath lution Me Gees ES id H i jae F M Bekasi tha age hank el Ve der Oder Hase ang bank imee Bag 1 16 reii Select the Feschen Plate to die inbi B6 vel plate vertical C2 Si Fet ar D Select the Dinon Fai i Liber Sangle vohme EN em Bemwe Total Sampler 2 ul Total Dient 2 ul lip capsi TOTAL sgis voue 1 pl aed TOTAL sert volume 755 pl Tiga Reged none Lages ava
44. highlighted item button 3 A dialog box will appear click on the Yes button to continue QlAgility User Manual 01 2009 7 9 Instrument Setup and Calibration 4 Ifthe plate had a previous calibration a dialog box will appear asking whether to reset the Z axis height Click on the Yes button to reset the height or click on the No button to retain the current setting The Adjust Height dialog box will appear Caution If the current setting is retained and the plate position is too high the tip may jam into the plate and bend the tip BH adjust Height E x f Tip Control Tip Location OK a Cancel Lower tip to current setpoint Home Z axis m Adjust Height Level at bottom 51 0 u of well Do not send tip to exact bottom of well if the tip is touching the exact bottom of the well during ejection this may cause blockages in the tip Raise tip to 0 Lower tip to current setpoint Home Z axis Level at bottom of well Lifts the pipetting head to the current 0 position Places the pipetting head at the height that corresponds to the displayed Level at bottom of well Litts the pipetting head to the top home position and resets the 0 position Indicates the proposed manual plate height calibration value a Z distance measured from the O or home position The goal of manual plate height
45. in the user s country 1 1 Proper Use WARNING Risk of personal injury and material damage w1 Improper use of the QlAgility may cause personal injuries A or damage to the instrument The QlAgility must only be operated by qualified personnel who have been appropriately trained Servicing of the QIAgility must only be performed by QIAGEN Field Service Specialists QlAgility User Manual 01 2009 1 1 Safety Information Perform the maintenance as described in Section 8 QIAGEN charges for repairs that are required due to incorrect maintenance CAUTION Damage to the instrument A Avoid spilling water or chemicals onto the QlAgility Damage caused by water or chemical spillage will void your warranty In case of emergency switch off the QlAgility at the power switch at the rear of the instrument and unplug the power cord from the power outlet 1 2 Electrical safety Disconnect the line power cord from the power outlet before servicing WARNING Electrical hazard W2 Any interruption of the protective conductor earth ground A lead inside or outside the instrument or disconnection of the protective conductor terminal is likely to make the instrument dangerous Intentional interruption is prohibited Lethal voltages inside the instrument When the instrument is connected to line power terminals may be live and opening covers or removing parts is likely to expose live parts To ensure satisfa
46. incorrect checksum was encountered in a received packet The first reply was corrupt The second reply was corrupt The local receive FIFO overflowed An incorrect number of replies was received A specified packet ID could not be found in collection A specified accessory port number does not exist A specified accessory port is unoccupied An unknown accessory was detected A bad temperature reading was taken A bad packet length was received More data was received while processing 01 2009 9 9 Troubleshooting 9 4 Self diagnostic tools These tests are designed to collect information to help with troubleshooting Note These tests should only be performed by experienced users Warning Before conducting self diagnostic tests remove all plates loading blocks and the tip ejector from the worktable Failure to do this may result in permanent damage to the pipetting head 1 Select Help Self diagnostic tools 2 The Robot Self Diagnostic Tools dialog box will appear Robot Self Diagnostic Tools m Messages Go Home zi Clear Messages r Mechanical Tests Electrical Tests Check Home Opto Alignment Check Communications Check for Loss of Steps Liquid Sensor Test Cycle Pipettor Head Check Home Upto Stability Rail Smoothness Rating Check Homo See Section 9 4 1 for more details Opto Alignment Check for Loss See
47. is switched on PER H i Zack Ol gility 1 Double click on the QIAgility icon on the desktop 2 Ifthe instrument is connected to the computer the software will proceed automatically to Normal Mode operation If the instrument is not connected to the computer or if the instrument is switched off the QlAgility User Manual 01 2009 6 1 Operating Procedures software will run in Virtual Mode See Section 5 5 for more details about Virtual Mode operation QlAgility Pure Precision sess New Recent Protocols ml HotStarT agl_signed3 Open Cancel 3 A splash screen will open To create a new run file select Empty project PCR Setup Wizard or Optimisation Wizard and then click on the Open button to continue See Sections 5 13 1 5 13 2 and 5 13 3 for more details about these options To use a saved run file or to modify a saved run file click on the Recent tab A list of saved run files will be displayed Left click on a run file to select it and then click on the Open button To use a Q Protocol click on the Protocols tab A list of Q Protocols will be displayed left click on a run tile to select it and then click on the Open button Alternatively double click on the run tile to open it directly 4 The main software window will open See Section 5 6 for a description of the features of the main software window
48. manual PCR setup or when preparing master mix for PCR setup at a later time To change the master mix extra volume settings 1 Select Options Run Settings Set master mix extra volume 2 The Master Mix Extra Volume dialog box will appear BA Master Mix Extra Yolume Extra Masher Mis 18 required to account for evaporation and tip losses during construction and aliquatting The master mix extra volume i specified as minimum amount plus an additional amount per r action The total master mix extra volume prepared Lancel depends on the number of reactions and e rounded up to be an integral multiple of the per reaction master mix volume Minimum extra volume required E a pl Recommend at least 30 Perreaction extra volume required f a ul Recommend at least Tul per reaction QlAgility User Manual 01 2009 5 39 QlAgility Software Minimum extra Defines the additional volume of volume required master mix which is prepared Per reaction Defines the additional volume of volume master mix which is added for each reaction 3 Adjust the minimum extra volume and per reaction volume 4 Click on the OK button to return to the main software window 5 9 4 Set standard extra volume When preparing standard dilutions extra volume is required to account for evaporation and pipet loss Changing the standard extra volume from the default setting can be useful when preparing standard dilutio
49. of rows in the Reagents table will be adjusted accordingly 8 Enter the concentrations directly into the Reagents table 9 Click on the Next button 10 The Reagent selector window will open The reagents are listed in the Reagents panel in white boxes QlAgility User Manual 01 2009 5 135 QlAgility Software lese Joris for hese reagens G z Finagnnis Al Tip amp T AT ht ip Cul Tecan api be 5p Tacan Liga pis As l nahe chi pa mart Keagert 1 5 Reagert 1 10 Wi 6 Mix plate 51 Pest 1 15 81 Tip ftp Tecan D B Reaction D ggnl deep well CH Ri eagent bloc si 3 L AECH SCH CH S CH Ci Sample dpi PER tote Genre CE He apien 700g ACR tube Generic SCH ei dee ei a SH SCH van Back Hee 11 Each reagent must be assigned a location otherwise the 12 13 14 reagent import will be canceled To do this left click on a reagent and drag it to the desired well on a reagent plate Do this for all the reagents If the reagent locations do not matter click and drag the Auto white box to the desired reagent segment Reagents will automatically be assigned to a location Selected wells will be highlighted red Note Some reagent locations may already be in use by previously defined reagents If the name of the reagent used in the saved master mix setup is identical to reagents already set up these will automatically be allocated to
50. of tips to Available or tips to Unavailable Before using this option tips Available must be selected Unavailable Set all tips on Sets all of the tips to Available or current plates Unavailable to Available Unavailable Set all tips on Sets all tips to Available or Unavailable all plates to Available Unavailable 3 Select one of the options to make the selected tips Available or Unavailable Available 200 pl tips are 5 58 QlAgility User Manual 01 2009 QIAgility Software 5 11 5 11 1 shown in dark red on the software worktable Available 50 ul tips are shown in dark blue and Unavailable tips are shown in white 4 Only 1 group of tips can be selected at a time To make more than one group of tips Available or Unavailable repeat steps 1 3 for each group of tips Managing samples Managing sample banks A sample bank is a collection of wells on a given plate or plate segment that is grouped and treated as a single unit for liquid handling operations Individual Sample wells must be assigned to a sample bank before they are available for use in a reaction setup Reaction wells can also be assigned to a sample bank this enables a reaction to be used as a component of a second reaction Sample banks are managed using the Update Sample Bank dialog box The Update
51. position As the instrument is switched off the pipetting head will drops approximately 70 mm This will not damage the instrument but may result in a pipet tip being picked up 6 20 QlAgility User Manual 01 2009 Instrument Setup and Calibration 7 1 1 Instrument Setup and Calibration Before starting any runs the QlAgility must be calibrated This section outlines the calibrations that must be performed If the QIAgility is moved we recommend recalibrating the plate positions Unless the pipetting mechanism has been serviced or pipetted volumes are found to be inaccurate there is no need to recalibrate the volume Note If pipetted volumes are found to be inaccurate please contact QIAGEN Technical Services Setup tip ejector Before starting ensure that the worktable is clear except for the tip ejector Procedure 1 Select Options Robot setup Set up tip ejector Alternatively if tip ejector calibration is being performed for the first time click on the OK button in the following dialog box OOOO x You ll need to configure the tip ejector location before continuing Hit OK to start the procedure 2 Review the following message Cn x The location of the tip ejector must be calibrated to ensure proper operation of the instrument This must be done carefully to avoid damage to the instrument Warning the process for calibrating the location of the tip ejector temporarily disables the instru
52. protocole ait t effectu Toujours porter des lunettes de protection deux paires de gants et une blouse de laboratoire La personne responsable par exemple le Chef du laboratoire doit prendre les pr cautions n cessaires pour assurer la s curit de l environnement du poste de travail et pour tre s r que les op rateurs de l instrument sont suffisamment form s et non expos s des quantit s dangereuses de substances toxiques chimique ou biologique comme d fini dans Material Safety Data Sheets MSDS ou des documents OSHA ACGIH ou COSHH L vacuation des vapeurs et d chets doit tre conforme tous r glements et dispositions l gales au plan national d partemental et local concernant la sant et la s curit Moving parts W4 To avoid contact with moving parts during operation of the QlAgility the instrument must be operated with the hood closed If the in built hood sensor is not functioning correctly contact QIAGEN Technical Services Bewegliche Ger teteile Um jeglichen Kontakt mit beweglichen Ger teteilen w hrend des Laufes zu vermeiden darf der QlAgility nur benutzt werden wenn die Klappen f r den Proben und Cartridge Einsatz geschlossen sind Sollten die Sensoren nicht ordnungsgem funktionieren kontaktieren Sie bitten den Technischen Service von QIAGEN QlAgility User Manual 01 2009 WARNING A WARNING A Safety Information El ments mobiles Afin d
53. reaction setup Required volumes for reaction setup 5 14 Selecting the COM port QlAgility User Manual 01 2009 5 124 5 124 5 124 5 133 5 139 5 140 5 142 5 143 5 143 Contents 3 Contents 5 15 Service register 5 144 6 Operating Procedures 6 1 6 1 Starting the software 6 1 6 2 Using the UV lamp 6 3 6 3 Operating the HEPA filter 6 4 6 4 Executing a run 6 5 6 4 1 Q Protocols 6 5 6 4 2 Selecting a saved run file 6 7 6 4 3 Creating a new run file 6 8 6 4 4 Preparing the worktable 6 8 6 4 5 Starting a run 6 10 6 5 Pausing aborting a run 6 11 6 6 Exception handling 6 11 6 7 Reports log files 6 13 6 7 1 Pre run report 6 13 6 7 2 Post run report 6 15 6 7 3 Log files and support packages 6 16 6 8 Importing and exporting reaction sample data 6 18 6 9 Shutting down the software and the instrument 6 18 7 Instrument Setup and Calibration 7 1 7 1 1 Setup tip ejector 7 1 7 1 2 Calibrate plate positions 7 4 7 1 3 Calibrate plate heights 7 7 7 1 4 Calibrate tip offsets 7 11 7 1 5 Calibrate volumes 7 13 8 Maintenance Procedures 8 1 8 1 Regular maintenance 8 2 8 1 1 Cleaning the QlAgility 8 2 Contents 4 QlAgility User Manual 01 2009 Contents 8 2 Periodic maintenance 8 2 8 2 1 Decontaminating the QlAgility 8 2 8 2 2 Replacing the HEPA filter 8 3 9 Troubleshooting 9 1 9 1 System setup 9 1 9 2 Operation 9 2 9 3 Warnings and errors 9 5 9 3 1 Warning and error messages 9 5 9 3 2 Instrument error codes 9 8 9 4 Self diagnos
54. remaining standards 21 Click on the Next button to continue 22 The Sample Editor screen will appear BCE setup wizard Sample editor E b x Sampie Felim That pag it used bo p t up Harp bonk To ack ar mr ramele bark cick on ee or EE Be hark To edi an miting hank pau wih bo eit and ckck on To iera a bank Mhiri Ihre bank you tt bo eraai arad Ch oe ee highlight the bark ark To Sa kk on Head lo Cornu peu with to delete and cick on Delete ER Ai Tip 2008p Tecan ph Ai Tip fpl Tacan iip F ET Bix pla Ei Tip lpl Tecan tip RE Reaction 7000p deep Ri Reapen Ci Sample 700p PCR tub C2 Reaction G t PCR bu P22 ee at LE LIT Wir Daae Dank Flers Bank Haw Dank Ed Bank Beck Res 5 130 QlAgility User Manual 01 2009 QIAgility Software Delete Bank Deletes selected sample bank Rename Bank Opens a dialog box from where the sample bank name can be changed Click on the OK button to continue New Bank Displays the Update Sample Bank dialog box which enables a new sample bank to be created See Section 5 11 1 Edit Bank Displays the Update Sample Bank dialog box which enables an existing sample bank to be moditied See Section 5 11 1 23 Existing sample banks will be listed on the left side of the dialog box Use the buttons beneath the list to manage the sample bank list Alternatively left click on a plate with Sam
55. safety mechanism A master mix is a pooled group of reagents that can be added to a reaction plate Master mix is always added to a reaction first because it normally constitutes the largest volume of the reaction The Master Mix Block is intended to hold diluent and master mix on the instrument worktable The menu bar contains 5 menus File Control Wizards Options and Help All software functions can be controlled from these menus Indicates whether the instrument is operating in Normal Mode or Virtual Mode For Normal Mode operation the instrument must be switched on and connected to the computer In Normal Mode operation run files can be executed A button located at the back of the QlAgility It allows the user to switch the QIAgility on and off Q Protocols are run files which have been developed by QIAGEN to directly facilitate specific PCR applications Q Protocols are installed in the QProtocols subfolder A reaction is the destination for the samples master mixes and reagents Reactions can be assigned to a sample bank this enables a reaction to be a component of a different reaction A reaction that is a component of another reaction is an Intermediate reaction QlAgility User Manual 01 2009 10 1 Glossary Term Reagent Reagent Block Right hand pane Run file Tip Tip chute Tip Rack Holder Tip receptacle box
56. starting a run file It contains the following information M Run file M Software version M Instrument details E Run time estimate M Protocol information In addition the pre run report also contains detailed information about Assay Setup Robot table setup Reaction steps Task list and Program Settings The following options are available from the toolbar at the top of the pre run report en Prints the pre run report Pririt iz Saves the pre run report Assign a file name Pau select a location and then click on the Save button LA Opens a new e mail message which SEN enables the pre run report to be e mailed E Saves the pre run report as a Word MSWord document Assign a file name select a location and then click on the Save button th rt Close Closes the pre run repo QIAgility User Manual 01 2009 6 13 Operating Procedures Generating the pre run report To generate a pre run report L Open the run file for which the pre run report will be generated If necessary adjust the run file according to your needs Select Wizards Generate report The pre run report will be displayed Alternatively the pre run report can be generated when starting a run To do this 1 2 3 Select the icon from the toolbar The Save file dialog box will open Select a location in which to save the run file and then click on the Save button
57. the Shift key to select multiple reactions Click on the Up or Down buttons to move the selected reaction s up or down in the Reaction List Enables a Special reaction to be set up and added to the Reaction List Selects all of the reactions in the Reaction List Highlights master mixes and reagents which are involved in a selected reaction in green Click on the icon again to remove the highlights QlAgility User Manual 01 2009 5 87 QlAgility Software Plate ID Import Export Clear Well Display Order 5 88 Highlights diluent standards and sample banks which are involved in a selected reaction in orange Click on the icon again to remove the highlights Highlights destination reaction wells which are involved in a selected reaction in blue Click on the icon again to remove the highlights Enables a plate ID to be entered This can be entered manually or using a bar code reader Enables interactive input of reaction ID bar codes Click to open the Barcode Entry dialog box Enables reaction data to be imported Click to open the Import Names dialog box Enables reaction data to be exported Click to open the Export Reaction Info dialog box Clears any user assigned reaction IDs and concentration values This determines the sequence in which wells are displayed in the sample data grid i e Label Sequence or Pipetting
58. the QlAgility move the package to the site of installation and check that the arrows on the package point upwards In addition check whether the package is damaged In case of damage contact the transporter of the package The QIAgility packaging is supplied with 2 tiltwatch indicators and 2 shockwatch indicators Inspect these indicators the tiltwatch indicators should be silver and the shockwatch indicators should be white If any of the shockwatch tiltwatch indicators are red broken or missing contact the transporter of the package See the underside of the lid of the box tor a guide to removing the QlAgility from the box 4 2 QlAgility User Manual 01 2009 Installation Procedures When lifting up the QlAgility slide your fingers under both sides of the instrument and keep your back straight WARNING Risk of personal injury and material damage W A The QlAgility is too heavy to be lifted by one person To avoid personal injury or damage to the instrument do not lift the instrument alone After unpacking the QlAgility check that the following documents are supplied E Packing list M QlAgility Software CD E Factory volume calibration report Read the packing list to check that you have received all items If anything is missing contact QIAGEN Technical Services Check that the QlAgility is not damaged and that there are no loose parts If anything is damaged contact QIAGEN Technical Services Make su
59. the target reaction plate well tub Defines the well in the selected reaction plate to which waste will be moved Use a new tip Instructs the instrument to use a new tip to for each move each sample sample Re use tips Instructs the instrument to reuse tips when moving samples to the waste well 6 Select a sample bank to be moved to waste from the drop down menu 7 Click on the button to select the target reaction plate The Plate well Selector window will appear 5 112 QlAgility User Manual 01 2009 QIAgility Software 5 12 7 8 Left click on a reaction plate to select it The Remove Waste dialog box will reappear Note If there is only one Reaction plate this plate will be selected by default To return to the Remove Waste dialog box left click on the selected plate 9 Define the well tub 10 Select Use a new tip for each sample or Re use tips 11 Click on the OK button to return to the main software window The remove waste command will be added to the Reaction List Importing and exporting reaction and sample data Import IDs using a bar code reader Bar code sample IDs can be imported using bar code readers that can connect to a computer via a USB or keyboard wedge A keyboard wedge is an input device that is inserted between the keyboard plug and the computer keyboard socket For the best results the bar code reader system should be able t
60. then drag to increase or decrease the size of the right hand pane in a vertical or horizontal direction Minimize Minimizes the right hand pane Maximize Maximizes the right hand pane Close Closes the right hand pane Next No function Tip Please refer to Section 5 12 1 for detailed information about the Tip right hand pane Standard Please refer to Section 5 12 2 for detailed information about the Standard right hand pane QlAgility User Manual 01 2009 5 29 QlAgility Software Reagent Please refer to Section 5 12 3 for detailed information about the Reagent right hand pane Master mix Please refer to Section 5 12 4 for detailed information about the Mix right hand pane Sample Please refer to Section 5 12 5 for detailed information about the Sample right hand pane Reactions Please refer to Section 5 12 6 for detailed information about the Reaction right hand pane Progress report Please refer to Section 5 12 8 for more detailed information about the Progress report right hand pane 5 7 Managing users User groups with differing access privileges can be created using the User Management menu There are 3 groups of user Administrator Designer and Operator Administrator An Administrator is a member of the standard Windows Administrators group and has full administrative access in the log in domain The Enable Acces
61. to get a setting closer to the tube base run but insufficient without touching volume of master mix was delivered to the last reactions aliquoted b Pipetting head Ensure that the volume calibration data is correct aspirating larger and has been configured properly volumes than it should and consuming all master mix before all reactions are made c Source reagent Ensure that the height calibration of all reagent remains in the tube wells used for construction of the master mix is set after completion of correctly Use manual height calibration to get a the run but the setting closer to the tube base without touching master mix has run out before all reactions aliquoted d Master mix is Increase the master mix extra volume viscous and sticks to configuration See Section 5 9 3 tips causing large losses during aliquoting Uneven levels in reaction tubes Air bubbles trapped The liquid level sensor functions equally well on in sample tubes or air bubbles or the liquid surface Centrifuge the master mix tubes sample plate to remove air bubbles 9 2 QlAgility User Manual 01 2009 Troubleshooting Comments and suggestions Software locks or crashes Screen savers and Disable screen savers and power save modes on power save modes the computer not disabled on the computer Z axis not rising after power has been switched on a Power cords not Ensure that all power cords are securely plugged securely plugged in i
62. typical PCR reactions with samples standards and master mixes to be set up The wizard allows the user to set up reagents and then use these to prepare master mixes The wizard can also be used to set up master mixes without setting up reactions This section outlines the PCR Setup Wizard screens that will guide the user through the setup Instructions are displayed on each screen 5 124 QlAgility User Manual 01 2009 QIAgility Software Note Depending on the type of run being set up only some of the screens will be used l To set up a PCR reaction using the PCR Setup Wizard Select Wizard PCR Setup Wizard or select PCR Setup Wizard from the splash screen that appears when the software is started 2 The QlAgility Setup Wizard will appear PCR setup wizard infection This Wiradi Lake pou through esch ol the single sepa in Geen mg eating wath tamples and a Masiet Moc Thit werrand guider pau thr est a Mader Mic donc ample acai raie con nier dette oh Wiha eg uau Rep the wiza mn Enden care of 7 Jm pel up mages and mader mex wari bo wsi wg bes reat d Les tun reel GG wert bopati the whole pp keen indice Go waren r Option _ fe ani bo el up on a sree matai res Dori use a perel I Iwan Lo roe Standards alles mur FF tement slip nan temple banks Net 3 Select the desired options and then click on the Next button
63. user Any previous version will be replaced All parameters except tip availability are saved Select this option to start a run See Section 6 4 5 Pauses the instrument during a run A dialog box will appear Click on the Continue Run button to continue the run or click on the Abort Run button to abort the run See Section 6 5 Initiates the instrument homing routine After this routine the instrument arm will return to its resting position Allows the user to enter and save comments for a run file in plain text Any comments will be displayed in a message box when the run tile is opened This icon is not enabled when a Q Protocol is loaded Opens a pdf file of the QIAgility User Manual version 1 0 Enable the user to highlight the source and destination wells on the software worktable Opens the UV Lamp Control dialog box H a UV lamp is not installed and enabled in the software this icon is shown in gray See Section 6 2 QlAgility User Manual 01 2009 QIAgility Software 5 6 3 L Switches the HEPA filter on and off The fan color alternates between green on and red off If a HEPA filter is not installed this icon will be shown in gray See Section 6 3 Indicates a problem with the run Errors must be resolved and acknowledged before the run can continue Opens the Service Register See Sections 6 6 and 9 3 1 for more details Opens a protocol description for a Q Prot
64. viter tout contact avec les l ments mobiles du QlAgility lorsqu il est en marche toujours fermer les portes de l instrument pour les chantillons et pour la cartouche Si les d tecteurs ne fonctionnent pas correctement contacter le Support Technique QIAGEN Risk of overheating w5 To ensure proper ventilation maintain a minimum clearance of 10 cm at the sides and rear of the QlAgility Slits and openings that ensure the ventilation of the QlAgility must not be covered berhitzung des Ger tes Zur Sicherstellung einer ausreichenden Bel ftung des QlAgility muss ein Mindestabstand von 10 cm an den Seiten und an der R ckseite des Ger tes eingehalten werden L ftungsschlitze und ffnungen des Ger tes nicht abdecken Risque de surchauffe Laisser un espace d au moins 10 cm sur les c t s et l arri re du QlAgility pour assurer une ventilation efficace Les grilles et prises d or assurant la ventilation du QlAgility ne doivent pas tre couvertes Risk of personal injury and material damage W The QlAgility is too heavy to be lifted by one person To avoid personal injury or damage to the instrument do not lift the instrument alone Verletzungsgefahr und Besch digung des Ger tes Der QlAgility ist zu schwer um von einer Person gehoben zu werden Um Verletzungen des Benutzers oder eine Besch digung des Ger tes zu vermeiden ist davon abzusehen das Ger t alleine zu heben QlAgility User Manual 01 2009
65. volume if Multi eject was selected The extra volume is dependent on the settings 6 Select the Tip Ejection Mode Multi pickup Re use tips or Use new tips 7 f Multi eject was selected the Multi Eject Settings option will be available See Section 5 9 10 for more details about how to configure multi eject options 8 Select the sample bank to be copied from the drop down menu 9 Click on the button to select the target reaction plate The Plate well Selector window will appear 10 Left click on a reaction plate to select it The Bank Duplication dialog box will reappear Note If there is only one Reaction plate this plate will be selected by default Left click on the selected plate to return to the Bank Duplication dialog box 11 Define the First well and the Volume 12 Click on the Add button to configure the first sample bank copy 13 If required repeat steps 9 12 to configure more copies The software will automatically calculate the Total Volume QlAgility User Manual 01 2009 5 103 QlAgility Software 14 Note To remove a copy left click on a copy in the Reaction plates list and then click on the Remove button Click on the OK button to return to the main software window The Reaction List will be updated with the sample bank duplication step Add sample dilution step This
66. wells to this sample bank proceed as for Modifying an existing sample bank Modifying an existing sample bank 1 To select all of the wells within a plate left click on a plate with Sample or Reaction function To select a group of wells within a plate left click on the plate and then drag Selected positions will be highlighted red Right click on the plate to view the plate operations menu Select Remove selected wells from sample bank The Update Sample Bank dialog box will open Select Existing Bank and then select a sample bank from the list It desired left click and drag on the plate schematic in the lower portion of the dialog box to modify the original well selection Alternatively options in the Sample Selection panel and Filter Selection panel can be used to select wells To add selected wells to the existing sample bank click on the Add Selection and Close button To remove QlAgility User Manual 01 2009 5 63 QlAgility Software 5 12 5 12 1 5 64 selected wells from the existing sample bank click on the Remove Selection and Close button View and edit information using the right hand pane Before setting up a reaction list all plate functions must be configured This can be done using the right hand pane The right hand pane refers to the area on the right hand side of the software workspace Left click on a plate in the main software
67. 0 sample 5 82 standard 5 65 tip 5 64 Index 2 RS 232 interface 4 6 S Safety 1 1 chemicals 1 3 electrical 1 2 mechanical hazards 1 4 proper use l 1 Sample tubes 3 8 Servicing 8 1 service register 5 144 Software 5 1 QProtocols folder 5 9 empty project 5 139 folders 5 8 Hardware Wizard 5 10 installation 5 1 main software window 5 13 managing users 5 30 menu bar 5 13 mode indicator 5 25 multi eject options 5 48 Optimisation Wizard 5 133 PCR Setup Wizard 5 124 plate buttons 5 28 plate function 5 54 plate type 5 53 reaction list 5 93 required volumes 5 143 right hand pane 5 29 5 64 sample banks 5 59 service register 5 144 software worktable 5 26 tip availability 5 57 tip usage 5 46 toolbar 5 23 virtual mode 5 12 QlAgility User Manual 01 2009 Index Storage conditions 1 Support packages 6 16 Symbols 1 12 T Technical assistance 2 2 Tip ejector 3 5 Tip rack holders 3 9 Tip receptacle box 3 3 Transport locks 4 4 Transportation conditions 1 Troubleshooting 9 1 self diagnostic tools 9 10 U Unpacking 4 2 USB interface 4 6 UV lamp 6 3 V Virtual Mode 5 144 W Warnings 1 1 6 11 9 5 Waste disposal 1 3 3 Wizards Hardware Wizard 5 10 QlAgility User Manual 01 2009 Optimisation Wizard 5 133 PCR Setup Wizard 5 124 Worktable 3 6 X X axis 3 5 Y Y arm 3 6 Y axis 3 5 Z Z axis 3 5 Index 3
68. 6 2 QlAgility User Manual 01 2009 Operating Procedures 6 2 Using the UV lamp Warning An electronic interlock ensures that the instrument hood is closed during UV lamp operation Under no circumstances should this interlock be disabled Before operating the UV lamp remove all worktable accessories This ensures that the worktable has maximum exposure To operate the UV lamp 1 Remove all plates and accessories from the worktable Note The tip ejector must be present 2 Close the instrument hood ou 4 The UV Lamp Control dialog box will appear Lid status Lamp status Activate lamp for Start Click on the icon on the toolbar U Lamp Control Close Status Lid status Closed or not installed Lamp status Inactive OFF Timed Control Activate UY lamp for 00 15 00 E Close software when UY finishes Enable Lamp Disable Lamp r Manual Control Indicates whether the instrument hood is Closed or not installed or Open Indicates whether the lamp is Inactive OFF or Active ON Enables the user to set UV lamp exposure times of between 1 second and 30 minutes using the arrows Initiates UV lamp operation QlAgility User Manual 01 2009 6 3 Operating Procedures 6 3 6 4 Close sottware Shuts down the QIAgility Software when UV when UV lamp operation is complete finishes
69. A We manzetion ss sample bp sample normalization into a reaction plate f Select the sampla bank and the duent Divert Sample bank Lu pweg rs Select the dition parameters to use Final volume 100 vl Desked concentration 77 Lowest norr2eso sample conc 10 00 Mix cork 5 N Pipette product to a secondary plate Advanced options D Allow contamination uses less tips contaminates sample with diluent 7 Auto adust small volumes to enable to move liquid NOTES Concen ators lot samples at source plate C1 wels A1 ae lower then lina dessad concentration 11 For these cases oniy sample iqud val be moved Tips Requred 5 x 50 pl 6 x 200 pl Largest available bp size 200 ul QlAgility User Manual 01 2009 5 109 QlAgility Software Diluent Sample bank First well Final volume Desired concentration Mix count Use secondary target First well Secondary volume Allow contamination 5 110 Defines the diluent to be used for the sample normalization Defines the sample bank to be used for the sample normalization Opens the Plate well Selector screen which enables the target reaction plate and the secondary target reaction plate to be selected Defines the first well of the reaction plate into which the sample normalization will be targeted Defines the final volume Defines the concentration to normalize to Defines the number of times to mix Instruc
70. Class A digital device pursuant to part 15 of the FCC Rules These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment This equipment generates uses and can radiate radio frequency energy and if not installed and used in accordance with the instruction manual may cause harmful interference to radio communications Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at his own expense QIAGEN GmbH Germany is not responsible tor any radio television interference caused by unauthorized modifications of this equipment or the substitution or attachment of connection cables and equipment other than those specitied by QIAGEN GmbH Germany The correction of interference caused by such unauthorized modification substitution or attachment will be the responsibility of the user QlAgility User Manual 01 2009 Appendix A Declaration of conformity Name and address of the company QIAGEN GmbH QIAGEN Strasse 1 40724 Hilden Germany We herewith declare under our sole responsibility that the product QIAgility Cat no 9001730 31 meets all applicable requirements of the following European Directives Low Voltage Directive LVD 2006 95 EC Electromagnetic Compatibility 2004 108 EC Directive EMC Hombrechtikon January 1 2009 A L ck
71. Contents Contents 1 Safety Information 1 1 1 1 Proper Use 1 1 1 2 Electrical safety 1 2 1 3 Chemicals 1 3 1 4 Waste disposal 1 3 1 5 Mechanical Hazards 1 4 1 6 Translations of warnings and cautions 1 4 1 7 Symbols on the QIAgility 1 12 2 Introduction 2 1 2 1 About this user manual 2 1 2 2 General information 2 2 2 2 1 Technical assistance 2 2 2 2 2 Policy statement 2 3 2 2 3 Version management 2 3 2 3 Intended use of the QIAgility 2 3 22301 Requirements for QlAgility users 2 4 3 General Description 3 1 3 1 QlAgility principle 3 1 3 2 External features of the QlAgility 3 2 3 2 1 Front view of the QlAgility 3 2 3 2 2 Side view of the QlAgility 3 3 3 2 3 Rear view of the QlAgility 3 4 3 3 Internal features of the QlAgility 3 4 3 4 Liquid level tracking 3 9 3 5 Computer 3 10 QlAgility User Manual 01 2009 Contents 1 Contents 4 Installation Procedures 4 1 4 1 Requirements 4 4 2 Unpacking the QlAgility 4 2 4 3 Installing the QlAgility 4 4 4 4 Setting up the QIAgility 4 8 4 4 1 Position calibration 4 9 4 4 2 Height calibration 4 9 4 4 3 Tip offset calibration 4 9 4 4 4 Volume calibration 4 9 4 5 Packing the QIAgility 4 10 5 QlAgility Software 5 1 5 1 Software installation 5 1 5 2 Folders 5 8 5 2 1 QProtocols folder 5 9 5 3 Hardware Wizard 5 10 5 4 Starting the software 5 11 5 5 Virtual Mode 5 12 5 6 Main software window 5 13 5 6 1 Menu bar 5 13 5 6 2 Toolbar 5 23 5 6 3 Mode indicator 5 25 5 6 4 Software work
72. EEE recycling requirements and where a replacement product is being supplied by QIAGEN provides free recycling of its WEEE marked electronic equipment in Europe If a replacement product is not being purchased from QIAGEN recycling can be provided upon request at additional cost To recycle electronic equipment contact your local QIAGEN sales office for the required return form Once the form is submitted you will be contacted by QIAGEN either to request follow up information for scheduling collection of the electronic waste or to provide you with an individual quote QlAgility User Manual 01 2009 A 3 Appendix A A 4 FCC declaration The United States Federal Communications Commission USFCC in 47 CRF 15 105 declared that the users of this product must be informed of the following facts and circumstances This device complies with part 15 of the FCC Operation is subject to the following two conditions 1 This device may not cause harmful interference and 2 this device must accept any interference received including interference that may cause undesired operation This Class A digital apparatus complies with Canadian ICES 0003 The following statement applies to the products covered in this manual unless otherwise specitied herein The statement for other products will appear in the accompanying documentation NOTE This equipment has been tested and found to comply with the limits for a
73. Ignore errors during run Run settings Set master mix extra volume Run settings Set standard extra volume Run settings Set tip usage options 5 20 Enables a number of run settings including pipetting options e g pipetting speed tip reuse extra volumes and level sensor settings to be adjusted These settings are stored with the run file and allow the application to be reproduced on another instrument See Section 5 9 Enables the volume of air that the pipetting head takes up before aspirating liquid to be configured The air is blown out upon ejection ensuring that all liquid is ejected See Section 5 9 1 Enables adjustment of the pipetting speed i e the aspirate eject speed See Section 5 9 2 Enables the method of tracking liquid level to be selected There are 3 options Do not use Detect liquid level using sensor and Use Liquid Level estimate See Section 5 9 7 Enables the software error level to be selected There are 3 options Interrupt run on all errors Interrupt run on serious errors and Ignore all errors See Section 5 9 8 Enables the additional volume of master mix to be defined See Section 5 9 3 Enables the additional volume of standard to be defined See Section 5 9 4 Enables configuration of tip usage See Section 5 9 9 QlAgility User Manual 01 2009 QlAgility Software Run settings Enables the user to c
74. Important Tubes supplied by different manufacturers may have slightly different dimensions despite a similar appearance Such differences can significantly affect the calibration settings in particular the plate height calibration We recommend that once a particular tube type is chosen the user always purchases that consumable from the same manufacturer to avoid frequent recalibration 3 8 QlAgility User Manual 01 2009 General Description 3 4 Conductive Filtered Tips and Tip Rack Holders Tip Rack Holders can hold 200 ul or 50 ul Conductive Filtered Tips on the worktable Supplied tips are carbon impregnated See Section 6 4 4 for details about how to insert tips into a Tip Rack Holder Liquid level tracking The QlAgility can track the liquid level using 1 of 2 methods liquid level sensing or liquid level estimate Liquid level sensing For maximum accuracy and precision the QIAgility is equipped with a liquid level sensor This feature enables the instrument to automatically detect when the pipet tip makes contact with the liquid as the tip descends When aspirating the tip is placed below the liquid surtace at the minimum insertion depth required to collect the aspirate volume When dispensing the tip is placed at the liquid surface and retracted as liquid is ejected This minimizes contact between the tip and the liquid reducing liquid carry over The liquid level sensor relies on conductive tips to detect t
75. Information CAUTION ACHTUNG ACHTUNG weist auf Situationen und Umstdnde hin die zu einer Besch digung des Ger tes f hren k nnen Um einen Ger teschaden zu vermeiden muss die genannte Anleitung unbedingt befolgt werden N here Angaben zu der Art der Gef hrdung und der Vermeidung solcher Situationen werden in einem Textfeld wie diesem gemacht CAUTION CAUTION CAUTION ATTENTION Le terme CAUTION Attention est utilis pour signaler les situations susceptibles de provoquer des d t riorations de l instrument ou d autre mat riel Les d tails sur ces circonstances figurent dans un encadr semblable celui ci Damage to the instrument Avoid spilling water or chemicals onto the QIAgility Damage caused by water or chemical spillage will void your warranty Besch digung des Ger tes Vermeiden Sie es Wasser oder Chemikalien auf dem QlAgility zu versch tten Durch versch ttetes Wasser oder versch ttete Chemikalien verursachte Ger tesch den sind nicht durch die Garantie abgedeckt Deterioration de l appareil Eviter de renverser de l eau ou des substances chimiques sur le QlAgility Tout dommage caus par de l eau ou des produits chimiques mettra fin la garantie Damage to the instrument C2 Direct sunlight may bleach parts of the instrument and cause damage to plastic parts The QlAgility must be located out of direct sunlight Besch digung des Gerdtes Direktes Sonnenlicht kann Teile des
76. K tab to update the table Note If the default volume for a reagent is O ul the reagent can still be used in the master mix component selection but it will not be shown in the reaction configuration QlAgility User Manual 01 2009 5 71 QlAgility Software 4 When a reagent name is entered the associated well will appear orange on the plate on the software worktable If the reagent name remains blank the associated well will appear gray and it will not be possible to use this reagent in a master mix or reaction 5 12 4 Master Mix Master mixes can be prepared using the QlAgility or a premade master mix can be used Master mixes can be added to reaction wells By detault master mix is pipetted into a reaction well first because it normally constitutes the greatest volume of the reaction To prepare a master mix using the QIAgility individual reagents and their volume per reaction must be defined The order in which the reagents are added to the master mix can also be defined The software calculates the volume of reagent and diluent required to make the correct volume of master mix If premade master mix is used the user only needs to define the volume of master mix per reaction Note Commercially available master mixes are not premade master mixes because they require addition of primers A commercial master mix and the individual primers must be defined as reagents in the software and then combined into a mas
77. Master Mix panel QlAgility User Manual 01 2009 5 79 QlAgility Software Look in 5 PresetMasterMix Di e DICH ES 2 Buffer Dual Labeled Probe Fe KE 2x Buffer Dye My Recent KE Labelled Dual Probes Documents KE Realtime PCR Dye KE Realtime PCR Dual labelled Probe E Standard PCR Desktop My Documents SE My Computer K e UMET File name v Places Files of type Master mix preset DI Cancel l 2 Select a file and then click on the Open button 3 The Reagent Selector window will appear The reagents are listed in the Reagents panel in white boxes KSE Plirnan select thee baratron of thane ruagrnia AE iip Coie Comforts Gp CGEM AE Dig ied nee e GRACE Mi red tapered Bi Sarpe ii imi Lepezed bbe Germi BE Tip bel Condkectnee Im GAREN si d aD af vi vi CE Pech pm POR Iuba Generi CA Reactie ig PCR ture Eemere sie 10 SCH 2 O wh Bei 4 Each reagent must be assigned to a location otherwise the reagent import will be canceled To do this left click on a reagent and drag it to the desired well on a reagent plate Do this for all the reagents If the reagent locations do not matter click and drag the Auto white box to the desired reagent segment Reagents will automatically be assigned to a location Selected wells will be highlighted red Note Some reagent locations may already be in use by previously detined reagent
78. N 200yl 8 x QIAGEN 500yl Internal Vial Free Standin 17 Generic 5ml Tubes 24 Generic 1 5ml Tapered Tubes 24 Generic 2ml Tubes Select Plate Type r Plate Usage Options Pipette Order Vertical DI Segmentation 4 x 8 Well Segments DI Labelling and Well Display Order Ordered by Character Label DI r Selected Plate Information Standing 8 x QIAGEN 1 5ml Tapered Tubes Pipette Vertical Segmentation 4 x 8 Well Segments Labelling Ordered by sl Plate ID StdReagent_new Segment Set ID 16 Manufacturer QIAGEN Consumable Part Number Required Adaptor Reagent Block 16x0 2ml PCR 8x2ml 1_5ml Flat T apered Adaptor Part Number 9241724 Reagent 4 Ale zero 1 ase Me P A ase ase co kg ate ase 0 L Bie B20 E u EL B40 FO IG ese B65 oo pre Bse He ri Description 16 x QIAGEN 200ul 8 x QIAGEN 2ml Free Filter to V BIAGEN V Other T Tips I Favorites Add Favorite Remove Favorite More Info Enables the plate type to be selected from the drop down menu e g Rotor Gene Standard 96 Well Plates which match the selection will be listed in the Plate panel Plate Lists plates which match the plate type selection in the Select Plate Type drop down menu Select a plate from this list to view an image of the plate a plate schematic and Selected Plate Information Pipette Order Enables the pipet order to be sele
79. Panel The Control Panel window will open 2 Double click on the Add or Remove Programs icon 3 Select QlAgility from the list of installed programs and then click on the Remove button To uninstall the software via the Programs menu 1 Select Start Programs QlAgility Uninstall 2 Click on the Yes button to continue Note When the software is uninstalled calibration settings run settings and run files will not be deleted QlAgility User Manual 01 2009 5 7 QlAgility Software 5 2 Folders When the software is installed a number of folders and subfolders are created Please select a Folder location where the technical support diagnostic package will be saved EME Qlagility a CA AccDefs Data IS Help 5 Libs PlateDefs PlateIma PresetMasterMix QProtocols IS Security IE Settings P Sarketnefs Pin gt HE Data Run files are saved in this folder Data Logs Log files are saved in this subfolder Data Pre run and post run reports are saved in Reports this subfolder Data Diagnostic support packages are saved in SupportPack this folder ages Help Contains a pdf of the QIAgility User Manual version 1 0 QProtocols Q Protocols are stored in this folder see Section 5 2 1 for more details about this folder 5 8 QlAgility User Manual 01 2009 QIAgility Software 5 2 1 I
80. Pit Muggli Director Business Excellence QIAGEN Instruments AG QlAgility User Manual 01 2009 A 5 Appendix A This page left intentionally blank A 6 QlAgility User Manual 01 2009 Appendix B Appendix B ABI 7000 7500 SDS master mix naming conventions Absolute Quantification For absolute quantification the ABI software requires each reaction to be associated with a detector reporter and quencher To achieve this master mixes used in the exported reactions must be named in the QlAgility software according to the convention D_R_Q D_R_Q Indicates a string of characters which excludes Is a separator D Is a placeholder for detector R Is a placeholder for reporter Q Is a placeholder for quencher Indicates an optional component Indicates O or more items For example Mix C EBV FAM TAMRA specifies a mix with detector for EBV using FAM reporter and TAMRA quencher The Mic C portion of the name is unused by the SDS software The absolute quantification function exports a single file XXX TXT where XXX is the filename Allelic Discrimination For allelic discrimination the ABI software requires each reaction to be associated with a marker identifying a pair of QlAgility User Manual 01 2009 D Appendix B B 2 detector reporter quencher sets To achieve this master mixes used in the exported reactions must be named in the QlAgility software acc
81. QlAgility User Manual 01 2009 5 125 QlAgility Software Eon gun each piyin ippa and function angert sample mantion Ip In cach rode Left cirk on a plis bn aper hg ple ihan change configuration by ether a ngit chck of uce butions ai top mgh Set plate tune balore netectng function a eat Te D Ea z CR WWW HEURE EN DIT I PESTE er 10 d BA Tip n Tecan tip mga CO EE we 6 EE SE EE asc MO SC KE O CR Semow amreR ume cm CZ Feact ITO PRUDA Generic 2 eg TEE o O O gt BEE S Sessocecenee Wed E hate hh n 6 ns AR e Sepsesssooss 2 seseosoveues m st sf e go 0 O0 oo on MN OO oo o oO Bes mie Set Plate Opens the Plate Configuration dialog box which provides options to change the plate type See Section 5 10 1 for more details about how to change the plate type using the Plate Configuration dialog box Set Function Opens a submenu which provides options to change the plate function See Section 5 10 1 for more details about the available plate functions 4 Left click on a plate to select it Click on the Set Plate button 5 The Plate Configuration dialog box will open Change the plate type as outlined in Section 5 10 1 6 Repeat steps 4 5 for all plates on the worktable 7 Left click on a plate to select it Click on the Set Function button submenu will appear T
82. Sample Bank dialog box can be accessed from the plate operations menu or from the Sample right hand pane See Section 5 12 5 for more detailed information about managing sample banks using the Sample right hand pane Right click on a Sample or Reaction plate to view sample bank options in the upper panel of the plate operations menu Select any of these options apart from Toggle sample bank list and Set preload volume to directly display the Update Sample Bank dialog box QlAgility User Manual 01 2009 5 59 QlAgility Software Add selected wells to sample bank Add First n wells on plate to sample bank Add all wells on plate to sample bank Add list of wells on plate to sample bank Remove selected wells from sample bank Toggle sample bank list Set preload volume Set liquid level mode for segment VW Toggle image Toggle zoom Delete calibration data Change plate type Change accessory Change plate function VW Add selected Opens the Update Sample Bank dialog wells to sample box and enables selected wells to be added bank to a new or existing sample bank Add first n Opens the Update Sample Bank dialog wells on plate box and enables consecutive wells on a to sample bank plate to be added to a new or existing sample bank Add list of wells Opens the Update Sample Bank dialog on plate to box and enables a list of wells to
83. The QlAgility must only be operated by qualified personnel who have been appropriately trained Servicing of the QlAgility must only be performed by QIAGEN Field Service Specialists Verletzungsgefahr und Besch digung des Ger tes Die unsachgem e Bedienung des QlAgility kann zu einer Verletzung des Benutzers oder zur Besch digung des Ger tes f hren Die Bedienung des QlAgility darf nur durch qualifiziertes Personal das entsprechend geschult wurde erfolgen Die Wartung des QlAgility darf nur durch Mitarbeiter des QIAGEN Kundendienstes durchgef hrt werden Risque de dommages corporels et mat riels L utilisation non convenable du QlAgility peut causer des blessures ou des d t riorations de l instrument Le QlAgility ne doit tre utilis que par du personnel qualifi qui a t form de fa on appropri e Seul un ing nieur du service apr s vente QIAGEN est autoris effectuer des travaux d entretien sur le QlAgility Safety Information WARNING Electrical hazard W2 Any interruption of the protective conductor earth ground A lead inside or outside the instrument or disconnection of the protective conductor terminal is likely to make the instrument dangerous Intentional interruption is prohibited Lethal voltages inside the instrument When the instrument is connected to line power terminals may be live and opening covers or removing parts is likely to expose live parts Gef hrdung durch Elektrizit t
84. This bar indicates whether the instrument is operating in Virtual Mode or Normal Mode OlAvaility simulated QIAgility Indicates that the instrument is operating in simulated Virtual Mode QlAgility Indicates that the instrument is operating in Normal Mode Liquid level tracking option This bar indicates whether the liquid level sensor is enabled Double click on this bar to change between Tip sensor Estimate and Not Used Liquid Level Tip Sensor Tip sensor Indicates that liquid level sensing is enabled Estimate Indicates that the liquid level estimate function is enabled Not Used Indicates that both liquid level sensing and liquid level estimate functions are disabled Tip reuse option This bar indicates the tip reuse mode Double click on the bar to open the Tip Usage dialog box See Section 5 9 9 for more details about setting tip usage options Tip re use DH times QIAgility User Manual 01 2009 5 27 QlAgility Software User logged in This bar displays the user that is currently logged in to the software Plate buttons Plate buttons are located in the top right corner of the schematic plates on the main software window They provide information about the plates and appear when the cursor is moved over a plate The warning button is an exception it will appear if the plate has not been position or height calibrated and will remain vis
85. Toolbar Sample Software worktable 10 2 Description A reagent can be combined with other reagents to make a master mix or added individually to a reaction Reagents are always dispensed to reaction wells before samples The Reagent Block is intended to hold reagents and standards on the instrument worktable The right hand pane refers to the area at the right side of the software workspace It provides access to options which relate to different plate functions When a run is in progress a progress report is displayed in the right hand pane A run file defines the reaction setup Defines the function of a plate as a Tip Rack Holder Tips in the Tip Rack Holder must be set to available or unavailable Used tips are ejected through the tip chute into a tip receptacle box at the side of the instrument A Tip Rack Holder supports tips on the instrument worktable The tip receptacle box collects used tips at the side of the instrument The toolbar consists of a series of icons from which a range of software functions can be accessed A sample is always added to a reaction last Samples must be assigned to a sample bank before they can be used in a reaction setup The software worktable visually simulates the instrument worktable The 6 plate positions are labeled Al A2 B1 B2 C1 and C2 Positions for the Master Mix Block and Reagent Block are labeled MI and R1 When a run is in progress the location of the pipe
86. al concentration Maximum working volume achieved Status OK or Error Options to Print Save E mail or Export the report into a Word document are available via the toolbar at the top of the Post run Report The Post run report is automatically saved in a subdirectory called Reports in the current run file save directory The default directory is C Program Files QlAgility Data QlAgility User Manual 01 2009 6 15 Operating Procedures 6 7 3 6 16 Log files and support packages Log files A new log file is generated when the software starts when a run starts or when a log file reaches 16 MB in size The 8 most recent logs are stored Log files are saved under selected installation directory Data Logs e g C Program Files QIAgility Data Logs To view a log file 1 Select Help Display log file 2 The log file will be displayed 3 Items listed in red indicate an error ltems listed in green indicate the start shutdown of the software and the start end of a log file QIAGEN agility 4 9 9 8 Log File created 04 11 2008 ee Togga Debug Mescag t Support packages On completion of a run a support package zip file is constructed and saved This support package contains the log file for the run The system saves the 50 most recent support packages QlAgility User Manual 01 2009 Operating Procedures
87. ally calculated based on the number of samples in the sample bank and the number of replicates When constructing reactions this option instructs the instrument to alternate sample wells with water When selected the operation prepares successive reactions using a sample from the bank then diluent then the next sample from the bank and so on This function is visible only when enabled in the Advanced Settings menu in the Options menu When selected the reaction constructed for each sample is placed into the same relative location from the start of the reaction plate as the sample from the start of the sample plate determined according to pipetting order QlAgility User Manual 01 2009 QlAgility Software Mix on Instructs the instrument to perform a mix ejection cycle upon ejecting the sample and defines the number of mix cycles to perform Mixing is only performed when the final reaction component is added and only when there is more than 1 component in the reaction Use Instructs the instrument to normalize normalization sample concentrations Auto Adjust Instructs the instrument to round up sample small Volumes volumes that are less than the minimum volume that can be pipetted i e 1 ul to the minimum volume i e 1 ul Where the operation would require less than the pipettable volume of diluent no diluent is transferred only sample is moved In all such cases the final volume is preserved
88. amp Use reagents Select to use reagents Other options in the Reagent right hand pane will become available 5 70 QlAgility User Manual 01 2009 QlAgility Software Clear Names Removes default reagent names from the Reagent Configuration table Set All Volumes Click to enter a new default volume for all reagents Click on the OK button to continue Name Defines the name of the reagent Def Vol Defines the volume of reagent to be added directly to the final reaction If the reagent is used in a master mix this per reaction volume can be changed in the master mix component selection Viscous Enables a reagent to be defined as viscous If a reagent is defined as viscous a lower pipetting speed will be used Mix count Defines the number of times the reagent will be mixed at the start of the run This ensures that reagents are homogeneous Setting up reagents 1 Left click on a plate or well with Reagent function in the main software window The Reagent right hand pane will appear 2 Select Use Reagents A detault reagent setup will appear in the Reagent Configuration table 3 Enter information into the Name Def Vol Viscous and Mix Count columns To do this left click on the individual cells and enter the new information For the Viscous column check the box to toggle between Yes and No Then click on the O
89. ard Data table will automatically be updated with default dilution ratios and concentrations Enter the concentration of the first standard Press Enter to update the Standard Data table QIAgility User Manual 01 2009 5 67 QlAgility Software 6 Individually click on cells in the Standard Data table in the Concentration column to enter the concentrations of the premade standard dilution series 7 After entering each concentration click on the OK tab to automatically update the dilution ratios Concentrations can also be entered using the Custom Concentration dialog box see below Note Concentration values are assumed to be entered in a single unit common to all values in the run The unit itself can be defined as needed for the application Entering concentrations using the Custom Concentration dialog box 1 Click on the Set Custom Conc button in the Standard right hand pane The Custom Concentration dialog box will appear x x Al 1 Restore Defaults 2 Individually click on cells in the table in the Concentration column and enter the concentrations of the premade standard dilution series 3 After entering each concentration click on the OK tab to update the table It desired click on the Restore Defaults button to return to the original default concentrations A Click on the OK button Preparing a standard
90. ata for each reaction contains a user selectable sample identifier and a user selectable concentration Data can be grouped into pages according to the master mix and or reaction identification See Appendix B A Setup Table Format file which can be used with the ABI 7000 7500 SDS software v1 2 3 for absolute quantification Master mixes must be named in the QlAgility software according to special conventions which allow the identification of Detector Reporter Quencher entities required by the ABI SDS software See Appendix B A Setup Table Format file which can be used with the ABI 7000 7500 SDS software v1 2 3 for allelic discrimination Master mixes must be named in the QlAgility software according to special conventions which allow the identification of Marker entities required by the ABI SDS software See Appendix B A csv Sample Info Text file which can be imported into the QlAxcel software The data is organized in a 8 x 12 grid that contains a user selectable identifier for each well of the 96 well plate 4 Choose an output format The output formats available depend on the Export Mode that was selected Sample Label Determines how the sample is to be named when the data is imported into the Rotor Gene software QlAgility User Manual 01 2009 QlAgility Software Concentration Determines the concentration value to be Option associated with the reaction for import into the Rotor Gene sof
91. ation for a standard dilution series each of these locations operates independently of other dilution series Standard dilutions are set up using the Standard right hand pane To view the Standard right hand pane left click on any plate or well with Standard function QlAgility User Manual 01 2009 5 65 QlAgility Software Standard right hand pane Use standard Use pre mixed standard series Standard name No of dilution concentrations Concentrations of first standard Enable mixing during dilution 5 66 Standard Options ETTET Use gretreond shared taraa F r Sarnen seed Standard Geer Site Irch ee Wl mc gr share SEsrabarel D geen Dees Corsair of beet dandani I Sel Custom Cone Erbie ger dap Geer be Ho od imma io me cer ac dest 5 B Change tea ae each duton FF Mare akama ea L in bekon Standard Data Fobo prepaure shandond ia rei pd in earen All wells ee empi JD Concertation Winter Semele Tout ee jo u DI DIE DIE Select to use a standard This makes other options in the Standard right hand pane available Select if using a premade standard dilution series The Set Custom Conc button will become available Displays the default name of the standard dilution series If desired click in the box and enter a different name Defines the number of dilution concentrations Defines the concentrat
92. bebe GL Sample Gi et Sangle H1 GL Dane A C1 Sampie BIEC bebe L C1 Sangi D CT Beie E ZOO LECH Sid 5 82 QlAgility User Manual 01 2009 QlAgility Software Delete Bank Rename Bank New Bank Edit Bank Plate ID Import Export Clear lt select sample bank gt Deletes the selected sample bank Deleting a sample bank will not affect sample names sample IDs or concentrations Opens a dialog box in which the sample bank name can be changed Click on the OK button to continue Displays the Update Sample Bank dialog box which enables a new sample bank to be created See Section 5 11 1 Displays the Update Sample Bank dialog box which enables an existing sample bank to be moditied See Section 5 11 1 Enables a plate ID to be entered This can be entered manually or using a bar code reader Opens the Barcode Entry dialog box which enables interactive input of sample ID bar codes Opens the Import Names dialog box which enables sample data to be imported from a file Opens the Export Samples dialog box which enables sample data to be exported to another file Deletes any user assigned sample names sample IDs and concentration values Sample IDs are reset to blank and concentrations are reset to 0 A sample bank can be selected from the drop down menu QIAgility User Manual 01 2009 5 83 QlAgility Software 5 84 Well Display Ord
93. bed in Section 5 4 2 Change the COM port to COM4 as described in Section 5 14 3 Shut down the software as described in Section 6 9 4 4 Setting up the QIAgility Note If the Hardware Wizard appears when the computer is switched on see section 5 3 for more details 1 Ensure that the instrument hood is closed 2 Set the power switch of the QlAgility to the on position and switch the computer on The pipetting head should move upwards If this does not happen please consult the Troubleshooting section of this user manual 3 Double click on the icon on the desktop This launches the QIAgility Software Alternatively select Start Programs QlAgility QIAgility Note If the instrument is not switched on the software will be operated in Virtual Mode For more information see Section 5 5 4 The following splash screen will appear Select the New tab QlAgility Pure Precision 33355 New Recent a Empty project ini PCR Setup Wizard i Optimisation Wizard 4 8 QlAgility User Manual 01 2009 Installation Procedures 4 4 1 4 4 2 4 4 3 4 4 4 5 Select Empty Project and then click on the Open button Alternatively double click on Empty Project 6 The following message box will appear OE x i Youlll need to configure the tip ejector location before continuing Hit OK to start the procedure 7 Click on the OK button to proc
94. c shock Do not open any panels on the QlAgility Risk of personal injury and material damage Only perform maintenance that is specifically described in this user manual Servicing The QlAgility is supplied with a warranty that lasts for 1 year beginning on the date of shipment The warranty includes all repairs due to mechanical breakdown Application development software upgrades accessories and disposable items are not included in the warranty QIAGEN offers comprehensive Service Support Agreements including Warranty Extensions Full Cover Support Agreements and instrument application training including on site installation Service Support Agreements maximize productivity and ensure high performance trom your instrument In addition service histories are fully documented and all parts are certified and guaranteed Contact your local QIAGEN Field Service Specialist or your local distributor for more information about flexible Service Support Agreements from QIAGEN QlAgility User Manual 01 2009 8 1 Maintenance Procedures 8 1 8 1 1 CAUTION A WARNING A 8 2 8 2 1 8 2 Regular maintenance Cleaning the QlAgility Damage to the instrument C3 Do not use solvents or reagents containing acids alkalis or abrasives to clean the QIAgility Risk of electric shock Do not open any panels on the QlAgility Risk of personal injury and material damage Only perform maintenance that is speci
95. centration left click on a cell in the Sample Name Sample ID or Conc column Directly enter the desired information 5 12 6 Reactions Pipetting operations in a given run are defined by a Reaction List Reaction lists can be created and moditied using the Reaction right hand pane QlAgility User Manual 01 2009 5 85 QlAgility Software To view the Reaction right hand pane left click on a reaction plate The buttons located below the Reaction List can be used to configure the list The Reaction Data panel lists the wells and contents of the selected reaction plate It also enables reaction data to be imported from a spreadsheet and exported to another file See Section 5 12 7 for more detailed information about importing and exporting information into the Reaction right hand pane Reaction right hand pane Add Edit Aa Let Pipette 5 ul of Sample Dark 1 bi Cio 35 el plate veica CE Pre Ell Pretic 5 ul of Sample Bark 2 Mis C In 35 ell plate ee C2 Pr CS zs lz toe ss 2 2 SSES FoTeToO w Well ID compas tube ID and constituent Piste ID aamgin Wha eg a1 a ing ar ra a a MN e Essen Cen Vel Chepley lecken TC babal Saperne D Pipeliing Saaquence 3925p Mee C2 pl Sample i C1 22S d Met 5 pl Semele Di C1 29 26 ul Mot C Spl Sample C1 ECI 24 25 qi Mee C 5 pl Sample D C1 26125 yl McC Spl Samp El C1
96. cientists as well as to the researchers at QIAGEN We therefore encourage you to contact us if you have any suggestions about product performance or new applications and techniques For technical assistance and more information please see our Technical Support Center at www giagen com goto TechSupportCenter or call one of the QIAGEN Technical Service Departments or local distributors see back cover or visit www qiagen com 2 2 QlAgility User Manual 01 2009 Introduction 2 2 2 2 2 3 2 3 Policy statement It is the policy of QIAGEN to improve products as new techniques and components become available QIAGEN reserves the right to change specitications at any time In an effort to produce useful and appropriate documentation we appreciate your comments on this user manual Please contact QIAGEN Technical Services Version management This document is the QIAgility User Manual version 1 0 Intended use of the QIAgility The QlAgility is designed to perform automated PCR setup and liquid handling actions The QlAgility is intended for molecular biology applications This product is neither intended for the diagnosis prevention or treatment of a disease nor has it been validated for such use either alone or in combination with other products The system is intended for use by professional users such as technicians and physicians trained in molecular biological techniques and the operation of the QIAgility
97. ck whether these are the correct tip types and whether sufficient tips are available If not add more tips to the worktable and make these available in the software See Section 5 10 2 for more details about how to do this The following picture outlines how to insert tips into Tip Rack Holders TANT 4 Place the correct plates on the worktable 5 Load the correct plate height and plate position calibrations for each plate and Tip Rack Holder See Sections 5 8 2 7 1 2 and 7 1 3 for more details about how to do this 6 Place the correct tubes in each plate on the worktable 7 Add the correct volumes of reagent diluent standard samples and if used premixed master mix into the correct tubes on the worktable Note To view the required volume of liquid place the cursor over the source well A hover box will appear which displays the required volume of liquid that the software has calculated This volume includes the extra volume which allows for liquid recovery limitations and losses due to evaporation and tip contact during pipetting Alternatively view the pre run report Es L 9 0 Zu Bu Zu Zu 8 FF F ell K in Reagent block standard 200 flat tapered Et Fil D 1 5m tapered hinged tube Reagent Before run manually load 20 0 NIE 30 8 Close the instrument hood QlAgility User Manual 01 2009 6 9 Operating Procedures 6 4 5 Starting a run l Click on the icon
98. cols Q Protocols are locked Edit access is only permitted to update the lab notebook set tip availability modify sample banks and assign plate IDs barcodes and well IDs barcodes to sample reaction wells defined in the run A loaded Q Protocol cannot be saved as a Q Protocol It can be saved as a locked User Developed Protocol or an unlocked normal run file If further adjustments are required the Q Protocol must be unlocked and saved as a normal run file If the user attempts to overwrite an existing Q Protocol the following message will appear QE U x C Program Files QIAgility QProtocols HotStarTaq1_signed3 QA5 is a QIAGEN Protocol run and cannot be overwritten Using a Q Protocol 1 Start the QlAgility software as outlined in Section 5 4 Note If the QlAgility software is already operating press the L icon in the toolbar 2 The following splash screen will appear QlAgility User Manual 01 2009 6 5 Operating Procedures QlAgility Pure Precision sees New Recent Protocols ml HotStarT agl_signed3 o on Cancel 3 Select the Protocols tab All Q Protocols that are saved in the appropriate folder i e QProtocols will be displayed 4 Select the desired Q Protocol Click on the Open buton 6 A description of the Q Protocol will appear A si x iha bat air 7 Review the description and then click on the Close button 8 If necessary modify the
99. ct the sample bank from the Samples panel Select the master mix Enter the number of replicates in the Target wells panel Click on the OK button Sample bank with no master mix i 2 3 Select the sample bank from the Samples panel Set the sample volume in the Volume panel Enter the number of replicates in the Target wells panel Click on the OK button Sample bank with reagents not used in master mix 1 2 3 4 Select the sample bank from the Samples panel Select the reagents from the Unmixed reagents panel Enter the number of replicates in the Target wells panel Click on the OK button Sample bank with master mix and reagents not used in a master mix l Select the sample bank from the Samples panel 2 Select the master mix 3 Select the reagents from the Unmixed reagents panel QlAgility User Manual 01 2009 5 141 QlAgility Software 4 Enter the number of replicates in the Target wells K pane 5 Click on the OK button No template control with master mix l 2 3 4 Select Water from the Samples panel Select the master mix Enter the number of replicates in the Target wells panel Click on the OK button Alternate samples or standards with no template control l 2 gt A Select the sample bank from the Samples panel Se
100. cted from a drop down menu Available options vary depending on the selected plate type Segmentation Enables the number of segments on the plate to be selected trom a drop down menu Available options vary depending on the plate type QlAgility User Manual 01 2009 QIAgility Software Labelling and Well Display Order Filter to Add Favorite Remove Favorite More Info This determines the sequence in which wells are displayed in the sample data grid i e Label Sequence or Pipetting Sequence Each plate type has a specific pipetting order and specitic label order Where these are different e g vertical pipetting order and horizontal label order the sequence in which wells are listed in the grid changes according to the well display order selection This function is useful for example when it is convenient to dispense liquids by column vertical pipetting order but to export the data by row horizontal label order Enables the list of plates in the Plate panel to be filtered Select QIAGEN Other Tips and or Favorites If QIAGEN is selected only QIAGEN plate types will be displayed in the Plate list Adds a selected plate type to a list of favorite plate types Removes a selected plate type from a list of favorite plate types Opens the Plate Information dialog box which displays more intormation about a selecte
101. ction and select Set Concentrations Well The Well column indicates the label of the reaction well as determined by the plate type Final Contents The Final Contents column describes the final composition of the liquid in the well as determined by a complete simulation of the run Note When pipetting operations add liquids to a well and later remove them the final well contents may be empty This QlAgility User Manual 01 2009 5 89 QlAgility Software is different to the data presented when hovering the cursor over a reaction well on the software worktable In this case only liquids added to the well are shown ID The ID column shows a combination of identifiers associated with each reaction well This includes a Reaction ID which can be assigned as a fixed attribute of the well It also includes a list of the IDs of samples present in the well on completion of the run as determined by simulation of the pipetting operations The label ID and contents IDs are combined together as a Full ID using a character as separator with the user assigned label ID listed first Concentration The Concentration column displays a concentration value associated with a reaction well When a reaction contains just one sample or standard and the starting concentration of that sample has been defined the final concentration of that sample in the reaction well is dis
102. ctions Alternatively the dilution series can be set up from a list of concentrations To do this 1 Select Use standard and Use pre mixed standard series 2 Enter the list of concentrations either using the Custom Concentration dialog box or by entering the values directly into the Standard Data list 3 Dilution ratios will be automatically calculated 4 Deselect Use pre mixed standard series See Section 5 9 4 for more details about setting the standards extra volume QlAgility User Manual 01 2009 5 69 QlAgility Software 5 12 3 Reagents The default location for reagents is on the right side of the Reagent Block Some plates have several segments and therefore have more than one option for the location of reagents Reagents can be added directly into reaction tubes or can be used to make up a master mix which can then be added to reaction tubes To improve precision and accuracy it is recommended that reagents are added to a master mix rather than pipetted individually When the per reaction volume of reagent is lt 1 ul i e outside the QlAgility pipetting range the reagent must be added to a master mix Reagents are set up using the Reagent right hand pane To view the Reagent right hand pane left click on any plate or well that has Reagent function Reagent right hand pane a He He He He He Ha He Tes a fp Q
103. ctory and safe operation of the QlAgility E Connect the line power cord to a line power outlet that has a protective conductor earth ground M Do not adjust or replace internal parts of the instrument E Do not operate the instrument with any covers or parts removed M If liquid has spilled inside the instrument switch off the instrument disconnect it from the power outlet and contact QIAGEN Technical Services 1 2 QlAgility User Manual 01 2009 Safety Information If the instrument becomes electrically unsafe prevent other personnel trom operating it and contact QIAGEN Technical Services The instrument may be electrically unsafe when M The line power cord appears to be damaged M It has been stored for a prolonged period of time in conditions which are outside of the Storage Conditions outlined in Appendix A E It has been subjected to severe transport stresses 1 3 Chemicals WARNING Hazardous chemicals W3 Some chemicals used with this instrument may be A hazardous or may become hazardous after completion of the protocol run Always wear safety glasses gloves and a lab coat The responsible body e g laboratory manager must take the necessary precautions to ensure that the surrounding workplace is safe and that the instrument operators are not exposed to hazardous levels of toxic substances chemical or biological as defined in the applicable Material Satety Data Sheets MSDSs or OSHA ACGIH t
104. d eject each pooling liquid separately This allows pooling of component volumes each up to the largest tip size on the worktable Sample contamination may occur Use new tips Instructs the instrument to use a new tip for each pooled liquid per sample in the sample bank This option avoids contamination of sample wells but tip consumption is higher than with other options QIAgility User Manual 01 2009 5 99 QlAgility Software Premix count First well Replicates Sample bank Volume Add Remove Samples Mix count Mix volume Defines the number of mixes to be performed when aspirating samples to be pooled This option is only available when individual samples are moved separately Opens the Plate well Selector screen which enables the target reaction plate to be selected Defines the first well of the reaction plate into which the sample bank will be pooled Defines the number of replicates Defines a component sample bank to be added to the target reaction wells in a pooling step Defines the volume of each sample in the sample bank to be added during a pooling step Adds the defined pooling step to the Samples list Removes the detined pooling step from the Samples list Defines the list of pooling steps Defines the number of mix operations to be performed when the final component is added to each pooled reaction Specifies the volume to be aspirated and ejec
105. d plate type Changing the plate type Before starting a run the correct plate type must be selected in the software The physical plate type in use at a given location on the worktable must match the plate type selected for this location in the software This ensures that the software uses the correct calibration settings for that plate QlAgility User Manual 01 2009 5 53 QlAgility Software To change the plate type in the software proceed as follows l 6 Position the cursor above the plate that is to be changed Right click on the mouse The plate operations menu will appear Select Change plate type from the plate operations menu The Plate Configuration dialog box will appear Select a plate type from the Select Plate Type drop down menu The Plate list will be automatically updated Select a plate from the Plate list Note If you cannot find a plate type that matches or is very similar to the plate that you are using please contact QIAGEN Technical Services Click on the OK button to continue Changing the plate function Before starting a run the correct plate function must be selected for each plate on the worktable Some plates e g Reagent Blocks have more than 1 segment Different plate functions can be selected for different segments of the same plate There are 7 plate functions Sample Reagent Mix Reaction Standard Di
106. debie Gp ome 200 pl IMPOSSIBLE OPERATION QlAgility User Manual 01 2009 QlAgility User Manual Multi eject Diluent Multi eject Settings Sample Multi eject Settings Re use tips Use new tips Enable mixing during dilution No times to mix Diluent Sample bank 01 2009 QlAgility Software Instructs the instrument to use 1 tip to aspirate the total volume of sample and to use a different tip to aspirate the total volume of diluent The instrument will then multi eject to the target wells to construct all dilutions Opens the MULTI EJECT dialog box which enables configuration of diluent multi eject options See Section 5 9 10 for more details about how to configure multi eject settings Opens the MULTI EJECT dialog box which enables configuration of sample multi eject options See Section 5 9 10 for more details about how to configure multi eject options Instructs the instrument to reuse a single tip for all dilutions per sample Instructs the instrument to use a new tip for each dilution Enables mixing during dilution Defines the number of times to mix Defines the diluent to be used for dilution Defines the sample bank to be used in the dilution Opens the Plate well Selector screen which enables the target reaction plate to be selected 5 105 QlAgility Software First well Defines the first well of the reaction plate into which the dilution wi
107. des information about the QIAgility in the following sections Safety Information Introduction General Description Installation Procedures QlAgility Software Operating Procedures Instrument Setup and Calibration Preventive Maintenance Troubleshooting ie ee gee EE Ags 0 Glossary Appendices Index The appendices include the following M Technical data E Warranty terms QlAgility User Manual 01 2009 2 1 Introduction 2 2 2 2 1 Terms used in this manual The following terms for controlling the mouse are used in this manual Left click Click with the left mouse button Right click Click with the right mouse button Double click Click twice with the left mouse button Select In the toolbar select the xxx submenu from XXX xxx the XXX menu Examples are File Exit and Options New General information Technical assistance At QIAGEN we pride ourselves on the quality and availability of our technical support Our Technical Services Departments are staffed by experienced scientists with extensive practical and theoretical expertise in sample and assay technologies and the use of QIAGEN products If you have any questions or experience any difficulties regarding the QlAgility or QIAGEN products in general do not hesitate to contact us QIAGEN customers are a major source of information regarding advanced or specialized uses of our products This information is helpful to other s
108. dilution series using the QlAgility 1 Left click on a plate or well with Standard function in the main software window The Standard right hand pane will appear 5 68 QlAgility User Manual 01 2009 QlAgility Software 2 Select Use standard If desired click in the Standard name field and enter a different name for the standard dilution 3 Enter the desired number of dilution concentrations The Standard Data table will automatically be updated with default dilution ratios and concentrations 4 Enter the concentration of the first standard Press Enter to update the Standard Data table 5 Ifa dilution series with varying ratios is required the dilution ratios can be moditied To do this click on a cell in the Standard Data table and enter a different dilution ratio Click on the OK tab to automatically update the concentration The water volume sample volume and total volume columns are automatically updated when the standard is used in a reaction 6 Select Enable mixing during dilution and enter a value for the No of times to mix diluent and standard It is recommended that a minimum of 5 mixes is entered 7 Standards are typically prepared using the same tip If desired each dilution can be prepared using a new tip To select this option select Change tips after each dilution 8 Specify the Minimum volume required if unused in rea
109. documentation have been developed entirely at private expense They are delivered and licensed as commercial computer software 2 Licence xl accept the agreement do not accept the agreement lt Back Cancel 6 Accept the terms of agreement and click on the Next button to continue 5 2 QlAgility User Manual 01 2009 QIAgility Software E setup otaa HN Select Destination Location Bey Where should Ql gility be installed Q Setup will install Ol gility into the following folder To continue click Next If you would like to select a different folder click Browse C Program Files Ql aility Browse At least 39 1 MB of free disk space is required lt Back Cancel 7 To install the software under the default path click on the Next button To install the software under a different directory browse for the directory and then click on the Next button Note If a previous software version is already installed the Select Destination Location screen will not appear The following message box will appear instead 2 j Aprevious installation of the QIAgility software has been found Do you wish to upgrade 8 To uninstall a previous software version click on the Yes button The calibration settings and run files will be retained To maintain the previous version of the sottware click on the No button and browse for a different installati
110. does not share a wall socket with other laboratory equipment and that the QIAgility is plugged directly into its own wall socket Important The wall socket should be easily accessible Risk of overheating W5 To ensure proper ventilation maintain a minimum clearance of 10 cm at the sides and rear of the QIAgility Slits and openings that ensure the ventilation of the QIAgility must not be covered QlAgility User Manual 01 2009 4 1 Installation Procedures CAUTION Damage to the instrument C2 cause damage to plastic parts A Direct sunlight may bleach parts of the instrument and The QlAgility must be located out of direct sunlight Power requirements The QlAgility operates at M 100 240 V 250 VA 50 60 Hz 5 A fuse Ensure that the voltage rating of the QlAgility is compatible with the AC voltage available at the installation site Main supply voltage fluctuations must not exceed 10 of nominal supply voltages Grounding requirements To protect operating personnel and for correct functioning of the liquid level sensor QIAGEN recommends that the QlAgility is correctly grounded earthed The instrument is equipped with a 3 conductor AC power cord that when connected to an appropriate AC power outlet grounds earths the instrument To preserve this protection feature do not operate the instrument from an AC power outlet that has no ground earth connection 4 2 Unpacking the QIAgility Before unpacking
111. down all other software 3 Install the QlAgility Software See Section 5 1 for detailed information about how to install the software Note Some virus protection software is known to interfere with QlAgility Software and will cause the software to run very slowly Connecting the computer to the QlAgility Note Before connecting the QlAgility to the computer for the first time ensure that the QIAgility Software has been installed The QlAgility has two interface options for connection to the computer RS 232 and USB The laptop which is supplied with the QlAgility must be installed via the USB interface If a different computer is used either the RS 232 or the USB interface can be used depending on the configuration of the computer Note Connect the computer to the QlAgility either via the USB or via the RS 232 interface Do not make both connections at the same time To connect via the USB interface E Connect the USB cable between the USB port on the instrument and the USB port on the computer To connect via the RS 232 interface M Connect the 9 pin serial cable between the RS 232 port on the instrument and the RS 232 port on computer QlAgility User Manual 01 2009 Installation Procedures Installation of UV lamp To install the optional UV lamp connect the UV lamp into the UV lamp socket at the rear of the instrument The UV plug is black with 4 pins Warning An electronic interlock ensures that the instrum
112. e or to open a Q Protocol Enables an existing run file to be opened Select the run file and then click on the Open button This file can be used as it is or modified to create a new run file Saves the run file under the current file name or under a new file name selected by the user Any previous version will be replaced All parameters except tip availability are saved QlAgility User Manual 01 2009 QlAgility Software Lab notebook Allows the user to enter and save comments for a run file in plain text Any comments will be displayed in a message box when the run file is opened Protocol Opens a description of the Q Protocol description template which is currently loaded This option is only available when a Q Protocol or User Developed Protocol is loaded Unlock Unlocks the protocol which is currently protocol loaded This option is only available when a Q Protocol or User Developed Protocol is loaded 1 8 Lists the 8 run files which have been used most recently Left click to select and open one of these run files Exit Closes the QlAgility Software Control menu The Control menu provides options to send the instrument to its home position start a run or pause abort a run Control Wizards Option Send robot home Start Pause abort Send robot Initiates the instrument homing routine After home this routine the Y arm will return to its resting position Start Select t
113. e access hatch using a 2 5 mm Allen key Remove the access hatch Unscrew the 4 thumb screws Remove the H Frame Remove the HEPA filters Replace the HEPA filters and reassemble QlAgility User Manual 01 2009 8 3 Maintenance Procedures This page left intentionally blank 8 4 QlAgility User Manual 01 2009 Troubleshooting 9 Troubleshooting 9 1 System setup Comments and suggestions Instrument does not turn on a Power cord not Check the power connection connected b Fuse blown Replace the fuse Computer software cannot communicate with system a USB or RS 232 Check the connection of the USB or RS 232 cable cable not connected See Section 4 3 between the computer and the instrument b Incorrect COM port Check the COM port setting If the instrument is settings connected to the incorrect COM port the software will start in Virtual Mode See Sections 4 3 and 5 14 QIAgility Software does not launch a QlAgility Software Install the QlAgility Software See Section 5 1 not installed b Old version of The QlAgility Software operates with Windows XP Microsoft Windows Professional See Section 3 5 QlAgility User Manual 01 2009 9 1 Troubleshooting 9 2 Operation Comments and suggestions Running out of master mix a Master mix remains Ensure that the height calibration of the master in the tube after mix tube is set correctly Use manual height completion of the calibration
114. e g d setup exe 3 Select Install Operating Software on the splash screen This will initiate the installation process 4 The QlAgility Setup Wizard will appear This wizard will guide you through the installation Instructions are displayed on each screen of the wizard Note We recommend using the default settings for all screens QlAgility User Manual 01 2009 5 1 QlAgility Software dl Setup QIAGility BEE 215 sl Welcome to the QIAgility Setup Wizard This will install QIAGEN Ql gility v4 09 09 10 on your computer It is recommended that you close all other applications before continuing Click Next to continue or Cancel to exit Setup 5 Click on the Next button to continue with the installation process The License Agreement screen will appear fl Setup QIAgility License Agreement Please read the following important information before continuing Please read the following License Agreement You must accept the terms of this agreement before continuing with the installation Licence Agreement 1 In the following QIAGEN refers to QIAGEN GmbH and its affiliated companies and Software means the programs and data supplied on this physical medium eg CD ROM or over the Internet with these conditions If you are unsure of any aspect of this agreement or have any questions they should be emailed to support qiagen com The Software and any accompanying
115. e to a different serial port 9 3 Warnings and errors 9 3 1 Warning and error messages Warnings and errors are indicated by the symbol in the toolbar In addition warning blue or error red messages are listed in the pre start checklist Click on the icon to view a message describing the error or warning QlAgility User Manual 01 2009 9 5 Troubleshooting ET ns Em ven ap range Red messages are errors ond eg prevent the run from gem Problem deleted af plate Sb roll plale buncunl all amp Ce 348 pelle myued ralh vue D n valable me Preble detected al plate b well labo hanal AA Ce IH well venpagd sale only Sb ze astdaldn in c qment Hating from well Al There are not enough wells in the output plate to proceed Neduce the cede ol ampere rrrzmedatar Ver eestor beet bi oduc Vee sole el rrepgeral onal god ghal E Cancel Pre Flun Flepon GF Warnings are noncritical The run can commence with active warning messages but this may lead to erroneous results Note Warnings and errors are logged in the post run report and in any support packages Warnings Not enough There is an insufficient supply of 50 ul tips small tips Not enough There is an insufficient supply of 200 ul large tips tips Well too full Too much liquid will be ejected into a well Well too small A well cannot contain sufficient liquid to supply the run Eject volume A volume of less than 5 ul is programmed too low t
116. ebook 1 HotStarTaqi O45 2 QuantiFAST SYBR 7 Q45 3 BYDY 8 0A5 Exit Ctrl Q 2 Select one of these files 6 4 3 Creating a new run file There are 2 wizards PCR Setup Wizard and Optimisation Wizard which can be used to create a new run file Alternatively a new tile can be created by selecting Empty Project when the software is started Note Once a run file has been created it can be checked using Virtual Mode operation See Section 5 4 and 5 5 for more details about Virtual Mode operation See Sections 5 13 1 5 13 2 and 5 13 3 for information about how to create a new run tile either using a wizard or using the Empty Project function 6 4 4 Preparing the worktable After loading the desired run file the worktable must be prepared The pre run report provides details about the location and amount volume of consumables and liquids that are required on the worktable tor completion of the loaded run file To view the pre run report select Wizards Generate report See Section 6 7 1 tor more details about the pre run report Note Before preparing the worktable ensure that the tip receptacle box has sufficient space to accommodate additional used tips that will be produced from the run 1 Prepare the reagents and samples 6 8 QlAgility User Manual 01 2009 Operating Procedures 2 Open the instrument hood 3 If tips are available on the worktable che
117. eed to tip ejector calibration See Section 7 1 1 for more details about how to do this Note Tip ejector calibration must be performed before any other calibrations 8 Perform the remaining calibrations in the order listed in Sections 4 4 1 4 4 4 Position calibration Please refer to the detailed description of position calibration n Section 7 1 2 Height calibration Please refer to the detailed description of height calibration n Section 7 1 3 Tip offset calibration Please refer to the detailed description of tip offset calibration in Section 7 1 4 Volume calibration For installation the user should perform Option 1 trom the Volume Calibration Wizard Please refer to the detailed description of volume calibration in Section 7 1 5 QlAgility User Manual 01 2009 4 9 Installation Procedures 4 5 Packing the QIAgility WARNING Risk of personal injury and material damage W2 A The QlAgility is too heavy to be lifted by one person To avoid personal injury or damage to the instrument do not lift the instrument alone If you need to transport the QlAgility package the instrument as follows 1 Open the hood and remove all plates and tips from the worktable 2 Shut down the QlAgility Software and switch off the QlAgility as outlined in Section 6 9 3 installed disconnect the UV lamp and HEPA filter from the instrument 4 Reinstall the transport locks see Section 4 3 5 Disco
118. efault calibration settings 4 See the following sections for detailed information about Options 1 3 Option 1 Use Option 1 to manually adjust the P axis unit value for specific volumes This method is used to enter the values supplied on the factory volume calibration report Increasing the P axis value increases the volume aspirated or dispensed Conversely decreasing the P axis value decreases the volume aspirated or dispensed 1 Select Option 1 from the Volume Calibration Wizard dialog box 2 The Volume Calibration Wizard Manual Calibration dialog box will appear 7 14 QlAgility User Manual 01 2009 Instrument Setup and Calibration BH Volume Calibration Wizard Manual Calibration Enter calibration values manually Value P axis units nominally 26 4 1363 19 2687 75 4013 53 5322 7 Save Back Next Click in the appropriate cell in the Value P axis units column to manually change the P axis units Click on the Next button QIAGEN x K Settings changed save w Click on the Yes button to continue QIAGEN x e J Settings Saved Click on the OK button The Volume Calibration Wizard History of Calibration Data dialog box will appear QlAgility User Manual 01 2009 7 15 Instrument Setup and Calibration BF Volume Calibration Wizard History of Calibration Data History of calibration data Curre
119. ell QlAgility User Manual 01 2009 5 81 QlAgility Software 5 12 5 Samples To be used in reactions samples must be organized into groups called Sample Banks Each sample can be assigned a name an ID e g a barcode and a starting concentration This information can be imported from an external file e g an Excel spreadsheet Samples in the same Sample Bank are treated identically during a reaction A sample may be present in more than one sample bank Sample banks can be continuous groups of wells or a combination of individual wells but they cannot span multiple plates or plate segments See Section 5 12 7 for more detailed intormation about importing and exporting data into the Sample right hand pane Diluent water can be used as a sample for nontemplate controls Standards are treated in the same way as samples Sample banks can be moditied or created using the Sample right hand pane To view the Sample right hand pane left click on a Sample well Sample right hand pane Sample Darke tebect a campi bank to heghight rote Latest Water and Sample Dark 1 15 ver Dank Sample Dark 2 16 weile Bank Sample Bank 3 8 veel heleta Bark Berana Bank Hew Blank ER Bark E ampie Cha kor 35 eve plate vertical G01 0 EE ie We Drei Qader Label Engenni OF Posting Sequence Be AT fh 1 Sample BI at Sek C1 GC Zeie Di ot Song EI 0
120. ell in the Vol per Reaction and enter a new volume Click on the OK tab The water diluent volume is automatically adjusted to make up the QlAgility User Manual 01 2009 5 77 QlAgility Software difference between the combined reagent volume and the volume of master mix per reaction Note Water will always be added unless the reagent volumes add up to the desired master mix volume 10 Click on the OK button to continue Added reagents will be listed in the Machine mixed Master Mix panel in the order in which they will be added to the master mix 11 Click on the Close button The corresponding well in the Master Mix Block will now be colored yellow To prepare another master mix left click on a different well in the Master Mix Block and repeat the above procedure Changing the reagent insertion order Diluent water is usually the component with the largest volume and is therefore by default added to the master mix first However the insertion order can be adjusted Note It is recommended that any reagents that contain detergent are added last This limits the risk of froth forming on the surface of the master mix To change the reagent insertion order 1 Click on the Adjust Insertion Order button in the Mix right hand pane 2 The Master Mix Reagent Insertion Order dialog box will appear BH master Mix Reagent Insertion Order Use the up and down controls
121. ent hood must be closed for operation of the UV lamp Under no circumstances should this interlock be disabled Installation of HEPA filter To install the optional HEPA filter connect the HEPA filter into the HEPA filter socket at the rear of the instrument The HEPA plug is silver with 5 pins Installation of AC power cord Important The QlAgility Software must be installed on the computer before the QlAgility is switched on Connect the QlAgility to the power outlet as follows 1 Ensure that the power switch of the QlAgility is set to the off position 2 Check that the voltage rating on the label at the back of the QlAgility matches the voltage available at the installation site 3 Plug the power cord into the main power input socket 4 Plug the power cord into a grounded power outlet Important The wall socket should be easily accessible 5 Atthis stage do not switch the instrument on COM port configuration The COM port used to connect the computer to the QlAgility must be correctly configured in the software to enable the software to communicate with the QlAgility instrument By default the software is configured to use COM1 and this corresponds to the first RS 232 port on the system To use the supplied laptop with the USB interface the COM port must be reconfigured to COMA QlAgility User Manual 01 2009 4 7 Installation Procedures To do this 1 Start the software in Virtual Mode as descri
122. er Copy all Paste to current cell Row height Export This determines the sequence in which wells are displayed in the sample data grid i e Label Sequence or Pipetting Sequence Each plate type has a specitic pipetting order and specific label order Where these are different e g vertical pipetting order and horizontal label order the sequence in which wells are listed in the grid changes according to the well display order selection This function is useful for example when it is convenient to dispense liquids by column vertical pipette order but to export the data by row horizontal label order Select to copy the Sample Data list The data can be pasted into an Excel file Pastes a list of Yes No values from a spreadsheet into the Sample Data column Enables row height to be adjusted A submenu will appear Select Grow to increase the row height or select Shrink to decrease the row height Select to export the Sample Data list to another file A submenu will appear Select either Export to CSV or Export to Excel Managing sample banks via the Sample Banks panel The Sample Banks panel located at the top of the Sample right hand pane displays a list of current Sample Banks Click on the New Bank or Edit Bank buttons to open the Update Sample Bank dialog box Sample banks can be
123. es a selected reaction in the Reactions list 1 position up the list Moves a selected reaction in the Reactions list 1 position down the list 26 Select a master mix from the drop down menu 27 Select a standard or sample from the second drop down menu and define the number of replicates in the field below 28 Click on the button to define the Target plate 29 Click on the Add button The reaction will now be added to the Reactions list 30 Repeat steps 26 29 for all required reactions 31 Click on the Next button 5 132 QlAgility User Manual 01 2009 QIAgility Software 5 13 2 32 The following message will appear OO 3 1 Wizard completed You can enter this wizard again from the Wizards menu and A make changes if necessary 33 Click on the OK button to return to the main software window Optimisation Wizard The Optimisation Wizard enables matrix combinations of reactions based on different concentrations of reagents to be set up For example to optimize a probe and primer forward and reverse combined a reaction could be set up with 3 different concentrations of the probe and with 3 different concentrations of primer i e a total of 9 reactions Several optimizations are possible using the Optimisation Wizard Note The user must provide all required concentrations of all the variables that are to be optimized This section o
124. es the highest accuracy and precision but requires a large number of tips Run duration will be increased Tips will be reused where possible More than one aspirate eject cycle will be performed using the same tip Run duration will be decreased but accuracy and precision will be compromised Defines the maximum number of times tips are reused This option is only available when tip reuse has been selected Select to allow multiple liquid ejections from a single aspirate QlAgility User Manual 01 2009 5 47 QlAgility Software Allow multi Allows multi ejection into wells which dispensing to already contain liquid This is only allowed non empty where cross contamination would not occur wells by tips contaminated with existing target well contents without contaminating source wells Multi Eject Opens the MULTI EJECT options for Settings Application Settings dialog box which enables multi eject options to be configured Note These options are disabled if a Q Protocol is loaded and locked 3 Select Use each tip for one operation only or select Re use tips where possible from the drop down menu 4 Iftip reuse has been selected define the Maximum times to re use tips Note Tip reuse lowers accuracy and precision due to retention of liquid on the tip interior and exterior It is therefore recommended that a tip is reused a maximum of 8 times 5 If desired select the mult
125. esented The Preserve source well indices function changes the reaction well allocation strategy used by the software for the corresponding liquid handling operation Normally this function is disabled and the software allocates reaction wells sequentially from the first available well in the target plate not used by previous reaction setup operations in the run When activated the software attempts to use the well index in the reaction plate corresponding to the well index of the sample in the source plate for the reaction made using that sample The software applies special rules to allow reactions which Preserve source well indices and those which do not to coexist in the same run In short for each reaction plate the sottware determines the highest index reaction well required by a Preserve source well indices liquid handling operation and treats the next well as the first available for all other reaction construction operations which do not Preserve source well indices in that plate Require extra volume in intermediate wells When activated a tick is visible By detining sample banks in reaction plates it is possible to construct new reactions from others previously constructed The wells in such sample banks are considered to be intermediate reaction wells By default the software does not account for dead volumes of the intermediate wells when checking for underflow conditions In practice this can result i
126. evel See Section 3 4 QlAgility User Manual 01 2009 QlAgility Software 5 9 8 Use liquid level Instructs the instrument to use liquid level estimate estimate to track the liquid level See Section 3 4 Do not use The instrument performs pipetting liquid level operations at the height calibration position for the plate tube Note These options are disabled if a Q Protocol is loaded and locked Warning Do not use liquid level is not recommended for general use because liquid is more likely to be retained on the tip exterior Pipetting accuracy and precision may therefore be compromised when using this option This option is intended for use only in exceptional circumstances Note For correct function of the liquid level sensor it is essential that the plates that are physically located on the instrument worktable are correctly assigned in the software Note The Use liquid level estimate function relies on the assumption that source wells are initially supplied with the volume of liquid that has been calculated by the software Overfilling the source wells can cause excess liquid to be retained on the tip exterior Underfilling the source wells causes insufficient volumes to be aspirated and then pipetted A tick will appear next to the option that has been selected Set liquid level tracking error level If a tube contains insufficient liquid to complete a reaction setup an error message will appear
127. f tips to be used to calculate the average offset 7 Click on the Start button to start tip offset calibration 7 1 5 Calibrate volumes There is a direct relationship between the rotation of the motor shaft and the vertical movement of the pipet piston Volume calibration defines the number of units that the P axis motor must move to accurately deliver a given volume of liquid Volume calibration is performed using the Volume Calibration Wizard During installation of the QlAgility the QlAgility User Manual 01 2009 7 13 Instrument Setup and Calibration user should perform Option 1 from the Volume Calibration Wizard Opening the Volume Calibration Wizard 1 Open an Empty Project as outlined in steps 1 2 of Section 5 13 3 2 Select Options Robot Setup Calibrate Volumes 3 The Volume Calibration Wizard dialog box will appear Options 1 3 will be displayed BA Volume Calibration Wizard x m Introduction Volume calibration establishes the accuracy of the robot pipetting mechanism Specifically it defines the number of units the P axis motor must move to accurately deliver a given volume of liquid Please choose one of the following options Options Calibrate manually Robot performs no pipetting User enters P axis units directly for each calibration volume 2 View current calibration settings and review calibration history 3 Reset to d
128. fically described in this user manual Wipe the instrument with a damp cloth only The worktable inside the instrument should be cleaned using a moist soft cloth Tri Gene can be used on all surfaces Note Do not wipe the rails These rails support the pipetting head and allow it to slide backwards and forwards easily Wiping the rails will remove the grease and make them more susceptible to rust Periodic maintenance Decontaminating the QlAgility To remove DNA RNA from the worktable and to eliminate cross contamination the QIAgility must be routinely decontaminated Proceed as follows 1 Remove all loading blocks and the tip ejector chute from the worktable Wash these in detergent and rinse with clean water 2 Soak these components in Tri Gene for 15 30 min 3 Thoroughly rinse the components in nucleic acid free water 4 Briefly rinse with absolute ethanol and dry with a soft paper towel QlAgility User Manual 01 2009 9 Maintenance Procedures Spray the instrument worktable with Tri Gene and allow to stand for 15 30 min Wipe away with clean paper towels Spray the worktable the nucleic acid free water and dry with clean paper towels Repeat this 3 times Spray the worktable with Tri Gene and allow to air dry Return all components to the worktable and close the hood If fitted switch on the optional UV lamp for 15 min 8 2 2 Replacing the HEPA filter oS a Unscrew the 4 screws on th
129. filter is immediately applied to the current selection Adds selected wells to the sample bank The Update Sample Bank dialog box will then be closed Deletes selected wells from the sample bank The Update Sample Bank dialog box will then be closed Closes the Update Sample Bank dialog box Opens the Sample selection and Filter selection panels in addition to the Sample Bank Name panel Closes the Sample selection and Filter selection panels QlAgility User Manual 01 2009 QlAgility Software Create a new sample bank l To select all of the wells within a plate left click on a plate with Sample or Reaction function To select a group of wells within a plate left click on the plate and then drag Selected positions will be highlighted red Right click on the plate to view the plate operations menu Select Add selected wells to sample bank The Update Sample Bank dialog box will open Select New Bank and enter a name for the new sample bank If desired left click and drag on the plate schematic in the lower portion of the dialog box to modify the original well selection Alternatively options in the Sample Selection panel and Filter Selection panel can be used to select wells Click on the Add Selection and Close button The selected wells will now appear in color on the software worktable To add another group of
130. ft click on the sliders and drag to adjust the pipetting speed for a given liquid group Adjust the mixing speed in the same way Note When pipetting a viscous liquid it is recommended to select a slower pipetting speed than the default value Sample speed Defines the aspirate eject soeed when pipetting samples Reagent speed Defines the aspirate eject soeed when normal pipetting normal reagents Reagent speed Defines the aspirate eject speed when viscous pipetting reagents which have been defined as viscous 5 38 QlAgility User Manual 01 2009 QIAgility Software 5 9 3 Standards speed Defines the aspirate eject speed when pipetting standards Diluent and master Defines the aspirate eject soeed when mix speed pipetting diluent and master mix Intermediate Defines the aspirate eject soeed when reaction speed pipetting to and from reaction wells Mixing speed Defines the speed of all mixing operations A Click on the OK button to return to the main software window Set master mix extra volume Extra master mix is required to account for evaporation and pipet loss during reaction setup The master mix extra volume is defined by a minimum volume plus an additional volume per reaction The total volume is calculated by the software and rounded up to the next whole reaction Adjusting the minimum extra volume and per reaction volume trom their default settings can be useful when preparing master mix for
131. g Reagent name Non unique tip type for volume Problems with reagent naming in the Optimisation Wizard have occurred The correct tips for the required volume are not available 9 3 2 Instrument error codes All instrument errors are associated with an error number All error numbers start with 40000 If an instrument error occurs immediately save a support package and contact QIAGEN Technical Services See Section 6 7 3 for details about how to save a support package Instrument error codes FIFO over run error 2 Bad checksum error 3 Bad axis number used when an axis number is not supported by command 4 Instrument is sent an unknown command 5 Vacuum sensor cannot sense vacuum 6 An axis is not enabled 7 Tip sensor did not detect liquid 8 Tip sensor could not be reset 9 Home switch could not be found within limit 10 82C55 I O pins are unstable 11 An error has occurred in SPI coms 129 An invalid axis was specified 130 The instrument did not respond with the first reply 9 8 QlAgility User Manual 01 2009 Troubleshooting 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 QlAgility User Manual The instrument did not respond with a second reply The COM port has problems The micro firmware is mismatched An invalid COM port was chosen An attempt was made to move an axis beyond its limit Too many replies were specified in send Packet An
132. gated according to the combination of master mix and reaction ID with 1 page created tor and named after each unique grouping of master mix name and reaction ID All reactions are placed into a single page called Page 1 No identification is used blank The well label is used as the identifier The index of the well in the pipetting sequence is used as the identifier The index of the well in the horizontal sequenced grid export is used as the identifier Export button 6 Enter a file name and select the location to which the data will be exported 7 Click on the Save button to continue QlAgility User Manual 01 2009 QIAgility Software Data fields Data fields which are available for export and their export string designators are as follows Separator 0 Sample number 1 Sample location 2 Sample type 3 Known concentration 4 Sample and reagent name 5 Sample ID l Plate ID P In the export modes where the data can be freely defined the user must specify the data content by writing an export string During export these designators are substituted with actual corresponding data For example to generate a csv file which contains the sample number the sample location and the sample ID a valid format string would be 1 0 2 0 l The 0 between the individual data fields indicates that a separator is to be inserted A separator will result in a comma in
133. gility is supplied with 2 Master Mix Blocks which can hold M 5x5 ml free standing tubes M 1x5 ml free standing tubes and 4 x 1 5 ml tapered tubes 3 6 QlAgility User Manual 01 2009 General Description Reagent Block The Reagent Block is intended to hold reagents and standards on the worktable The Reagent Block can hold 8 x 1 5 ml tapered tubes 8 x 2 ml free standing tubes and 16 x 200 ul PCR tubes Adapters The QlAgility is supplied with 3 SBS adapters M 2 x Adapter 96 x 0 2 ml PCR Tubes E 1 x Adapter Flip Cap 32 x 1 5 ml Tapered Base The 96 well adapters are intended to hold strip tubes and unskirted and halt skirted PCR plates QlAgility User Manual 01 2009 3 7 General Description The 32 well adapter enables caps to be locked in position preventing interference with the pipet tip tube lifter plate can be placed underneath the block enabling easy removal of the tubes Sample tubes A range of tube types can be used with the QlAgility The following sample tubes are supplied with the instrument M 5 ml free standing tubes M 200 ul PCR tubes Note Supplied sample tubes are not guaranteed to be sterile Free standing tubes 5 ml are typically used to hold diluent and large volumes of master mix These tubes are normally supported in the Master Mix Block PCR tubes 200 pl are typically used to hold samples and reactions and are normally supported by the 96 well adapters
134. gt 2 Browse for a new folder location 3 Click on the OK button to continue The subdirectories will automatically be generated in the new file location 5 9 6 Configure system color To configure the system colors 1 Select System color configuration from Options Run settings 2 The Sample Color Configuration dialog box will open There are 3 tabs Sample Colours Liquid Colours and Selection Colours Sample Enables contiguration of sample colors Colours Liquid Colours Enables configuration of liquid reagent colors QlAgility User Manual 01 2009 5 41 QlAgility Software Selection Enables configuration of colors that Colours represent a liquid function and that represent members of a sample bank In addition colors used for selection and highlight indications can be configured Sample Colours SS Sample Colour Configuration Colour Ju a x Close Book Liquid Colours 5 42 QlAgility User Manual 01 2009 QIAgility Software BH sample Colour Configuration O xl No Liquid Empty Sample Empty Tip ai e mum e Water Mee Premis MasterMis Reagent Standard 1 Standard 2 Preload Liquid Waste tub well Selection Colours bag Sample Colour Configuration Selection eeng Je Indicate Target 8 Indicate Source Fescinliqi Reaction Sample Bank Reaction Ta
135. hange the default file Set default file location for all saved files See Section location 9 99 Run settings Saves current software run settings as the Save current new default settings This does not include settings as calibration settings default Run settings Resets software settings to the factory reset settings to defaults Click on the Yes button to factory default continue Run settings Provides options to change the default System colour colors which are used for all liquid groups configuration on the software worktable See Section 5 9 6 Run settings Enables or disables the shutdown beep A shutdown tick will appear when the shutdown beep is beep enabled Run settings Allows or inhibits operation of the Allow separately contigured Windows screensaver screensaver A tick indicates that the screensaver is not inhibited Run settings Enables or disables automatic generation Generate file of unique file names for reaction exports names for Unique tile names are based on the run file reaction export name time and date A tick will appear when this function is enabled Advanced Provides additional options for use in settings specialist applications Only change these settings under direct instructions from QIAGEN See Appendix C for more detailed information about these settings QlAgility User Manual 01 2009 5 21 QlAgility Software Change plate type Change accessory
136. hanged 4 Click on the Save button The current calibration settings are now saved on the Setup Disk and can be transferred to another computer 5 8 2 Load calibrations from setup disk To transfer calibration settings from a Setup Disk to a different computer 1 Select Options Calibration management Load calibrations from setup disk Select Calibration Settings File Look in Data DI eff My Recent SupportPackages Documents E Desktop My Documents My Computer K File name z Los CNET Files of type Robotics Calibrations xml DI Cancel PI SE J Open as read only dh 2 Select the file that contains the saved calibration settings Click on the Open button QlAgility User Manual 01 2009 5 35 QlAgility Software 3 Ifthe instrument has existing calibration settings the following dialog box will appear EE hl 4 calibration already exists for this robot Ql gility Do you wish to sf overwrite it De 4 Click on the Yes button to overwrite the existing calibration settings 5 8 3 Delete multiple calibrations To delete existing calibration settings 1 Select Options Calibration management Delete multiple calibrations 2 The Delete Multiple Calibrations dialog box will appear BF Delete Multiple Calibrations NOTE Delete Multiple Calibrations will delete ALL calibrations for the selected options below
137. he change in capacitance when the tip contacts the liquid inside a tube the smaller the volume of liquid inside the tube the lower the change in capacitance For correct functioning of the liquid level sensor it is essential that the plates that are physically located on the instrument worktable are correctly assigned in the software See Section 5 10 for details about how to do this If a liquid is nonconductive e g pure water oil the level sensor will not detect any change in capacitance QlAgility User Manual 01 2009 3 9 General Description 3 5 3 10 Note Addition of low concentrations of conductive substances e g salts to nonconductive liquids may enable liquid level sensing to be used Note To pipet from wells that contain less liquid than the level sensor limit it is necessary to switch the level sensor off or reset the error detection levels It may also be necessary to manually calibrate the plate height closer to the base of the tube Alternatively the liquid level estimate mode can be used Liquid level estimate This feature enables the instrument to estimate the liquid level using information from the run configuration The software tracks the movement of liquid between wells and estimates the liquid level during all liquid transfers This information is used to determine the optimal tip placement Levels of accuracy and precision comparable to those obtained with liquid level sensing are obtai
138. his can be used to transfer data to the QlAgility User Manual 01 2009 5 117 QlAgility Software Rotor Gene Q or other data storage systems e g LIMS environments To export sample or reaction data 1 Left click on a Sample or Reaction plate to view the right hand pane 2 Click on the Export button The Export Samples or Export Reaction Info dialog box will appear BH Export Samples s x r Export Mode Export Cancel Output Format Specifiers The following special sequences are used for specifying the format of each line of the Concentration if known e g for standards 44 Name Sample Reagent 45 ID PlatelD ZP 3 Select an Export Mode from the drop down menu CSV File Excel A csv text file with comma separators compatible between columns The data is fixed and contains the number location sample name reagent name sample type concentration and target volume Rotorgene v4 4 A sam sample file which is compatible with the Rotor Gene 2000 3000 software version 4 6 5 x The data is fixed and contains location sample name and sample type 5 118 QlAgility User Manual 01 2009 QIAgility Software Rotorgene v4 6 A smp sample file which is compatible or later with the Rotor Gene Q software version 4 6 or later The data contains the sample concentration and a user selectable sample identifier which can be ei
139. his option to start a run See Section 6 4 5 for more details about starting a run QlAgility User Manual 01 2009 5 15 QlAgility Software Pause Abort Pauses the instrument during a run A dialog box will appear Click on the Continue Run button to continue the run or click on the Abort Run button to abort the run See Section 6 5 for more details Wizards menu The Wizards menu provides access to the PCR setup wizard and Optimisation wizard It also enables the user to import sample names export reaction data or generate pre run reports Wizards Options Help PCR setup wizard Optimisation wizard Import sample names Ctrl I Export reaction data Ctrl E e Generate report Ctri R PCR setup wizard Optimisation wizard Import sample names 5 16 Launches the PCR Setup Wizard This wizard can be used to create new run files See Section 5 13 1 for further details Launches the Optimisation Wizard This wizard enables specialized PCR functions to be set up For example this wizard can be used for optimization of a PCR run e g primer concentration See Section 5 13 2 for further details Opens the Import Names dialog box which enables sample and reaction data to be imported from a file to a selected sample or reaction plate See Section 5 12 7 for further details QlAgility User Manual 01 2009 QIAgility Software Exp
140. hose used during height calibration Select plate to test in Plate function Mix v Mix plate 5 tube positions M1 SE Select tip types to profile wi Start test Test how many tips per tip type fi Ele Start Abort Reset All Plate function Defines the function of the plate in which tip offset calibration will be performed QlAgility User Manual 01 2009 Instrument Setup and Calibration Opens the Plate well Selector screen which enables selection of the location of the plate in which tip offset calibration will be performed Select tip types Lists the tip types to be calibrated 200 ul to profile conductive tips are selected by default Test how many Defines the number of replicates that will be tips per tip type performed for the calibration of the selected tip type Start Starts the tip offset calibration Abort Aborts the current tip offset calibration Reset All Resets the tip offset calibration settings to the factory default values 3 Select the correct plate function from the drop down menu of the plate in which tip offset calibration will be performed 4 Click on the button The Plate well Selector screen will open Left click on a plate to select the location of the plate in which tip offset calibration will be performed 5 Ensure that the correct tip type is selected in the Select tip types to profile panel 6 Define the number o
141. how to do this In addition see Section 5 13 4 for examples of how to set up typical reactions 8 To save the run file select File Save As Enter a name for the run file and select a location in which to save it 9 Click on the Save button 5 13 4 Example reactions This section outlines the protocols for setting up a number of typical reactions Open the Reaction right hand pane as outlined in Section 5 12 6 and then use one of the following example reactions Master mix with no sample Master mix with sample bank Sample bank with no master mix Sample bank with reagents not used in master mix Sample bank with master mix and reagents not used in a master mix No template control with master mix Alternate samples or standards with no template control Empty wells Master mix with no sample IR 5 140 Select No samples empty wells from the Samples panel Select the master mix Enter the number of replicates in the Target wells panel The number of replicates will equal the number of wells in the reaction plate Click on the OK button QlAgility User Manual 01 2009 QlAgility Software Master mix with standard 1 2 3 4 Select the dilution series from the Samples panel Select the master mix Enter the number of replicates in the Target wells panel Click on the OK button Master mix with sample bank 1 2 3 4 Sele
142. i re de l appareil Type plate on the back of the instrument Plakette auf der R ckseite des Ger tes QlAgility User Manual 01 2009 Warnung vor einer Gefahrenstelle Symbole de danger CSA listing mark for Canada and the USA CSA Zeichen f r Kanada und die USA Marquage CSA pour le Canada et les Etats Unis Manufacturer Hersteller Fabricant WEEE mark for Europe WEEE Zeichen f r Europa Safety Information Marquage WEEE pour l arri re de l Europe l appareil Biohazard symbol chute and on the front edge of the worktable Im Spitzen Warnung vor Biogef hrdung Abwurfschacht und am vorderen Rand der Arbeitsplatte Dans le canal Symbole de danger d ejection des biologique cones et a l avant de la table de travail Type plate on FCC mark of the United the back of the States Federal instrument Communications Commission Plakette auf FCC Markierung der USA der R ckseite Validierung durch die Federal des Ger tes Communications Commission Marquage FCC des Etats l arri re de Unis validation par la l appareil Federal Communications Commission Type plate on C Tick mark for Australia the back of the supplier identification instrument N17965 N15148 1 14 QlAgility User Manual 01 2009 Safety Information Plakette auf der R ckseite des Ger tes Plaque l arri re de l appareil Type plate on the back of the instrument Plakette auf der R ckseite des Ge
143. i ejections and multi dispensing options If Allow multi ejections from a single liquid pickup is selected the Multi Eject Settings button becomes an option Click on this button to configure multi eject options See Section 5 9 10 for more details 6 Click on the OK button to return to the main software window 5 9 10 Configure multi eject options 1 Select Options Run Settings Set tip usage options 2 The Tip Usage dialog box will appear See Section 5 9 9 for more details about configuring tip usage options 5 48 QlAgility User Manual 01 2009 QlAgility Software 3 Select Re use tips where possible or Use each tip for one operation only and then click on the Multi Eject Settings button 4 The MULTI EJECT dialog box will open B MULTI EJECT options for Application Settings j x m Multi Eject Options negt nn m Initial Ejection Volume Apply Default Initial Ejection Volumes Default Initial Ejection Yolume using a 50 pl Tip 1 pl Default Initial Ejection Yolume using a 200 pl Tip 4 pl Specify Initial Ejection Volume Se Cancel Additional Extra Volume f B pl NOTE Select the amount of additional extra liquid to aspirate Setting this to zero may reduce precision Use air on multi eject Apply Default Initial Ejection Volumes Specify Initial Ejection Volume Additional Extra Volume Select to blow out
144. ialog box In addition the component will be colored in green as a reminder of a future service Note Once a service has been acknowledged and saved it cannot be edited Note A component can be serviced at anytime it does not need to be colored red in the Service Register dialog box for a service to be performed n QlAgility User Manual 01 2009 Operating Procedures WARNING A WARNING A 6 1 Operating Procedures This section describes how to operate the QlAgility Before proceeding we recommend that you familiarize yourself with the features of the QlAgility by referring to Sections 3 2 and 3 3 The QIAgility hood must remain closed during operation of the instrument Only open the hood when the instrument is not operating or when instructed to do so by the software Note Opening the hood during operation of the QlAgility will cause the system to pause The instrument will complete the current movement which may take up to 10 seconds Risk of personal injury and material damage W7 Do not attempt to move the QIAgility during operation Moving parts W4 To avoid contact with moving parts during operation of the QlAgility the instrument must be operated with the hood closed If the in built hood sensor is not functioning correctly contact QIAGEN Technical Services Starting the software Note Before starting the software ensure that the instrument hood is closed and that the QIAgility
145. ible until all of the calibrations for that plate have been completed E Prompts the user to proceed to plate i calibration Opens the Set Alignment Warning l en dialog box if plate position calibration has not been completed and opens the Contigure Plate Heights dialog box if plate height calibration has not been completed El Enlarges the view of the plate Click again to return to the normal view Zoom Displays details about the current plate Click on the OK button to return to the Info main software window Toggles between an image of the current Toggle plate and the plate schematic 5 28 QlAgility User Manual 01 2009 QlAgility Software Right hand pane The right hand pane refers to the area at the right side of the software workspace It provides access to options which relate to different plate functions i e tip reaction master mix reagent and sample There is no right hand pane for diluents because the diluent does not have a definable function In addition when a run is in progress a progress report is displayed in the right hand pane The l icon is available at the top left of the right hand pane when Minimize or Restore has been selected from the same icon in the menu bar Left click on the El icon to access the following options Restore Reduces the size of the right hand pane Move Enables the right hand pane to be moved Size Click on the right hand pane and
146. ility Robotics Control Software Ol gility Plate Library Files 8 16 Channel Robot Support Files USB Drivers Plate Image Files ei e 11 Review the displayed details Click on the Install button Setup QIAgility Te Fa Installing N Please wait while Setup installs QlAgility on your computer A nn Extracting files C Program Files Ql gility Helppdfs Ql ailityM anual pdf 12 The QIAgility Software will now be installed onto your computer This could take a few minutes 13 The following warning message will appear QlAgility User Manual 01 2009 5 5 QlAgility Software Software Installation The software you are installing has not passed Windows Logo testing to verify its compatibility with Windows XP Tell me why Biss Continuing your installation of this software may impair or destabilize the correct operation of your system either immediately or in the future Microsoft strongly recommends that you stop this installation now and contact the software vendor for software that has passed Windows Logo testing 14 For correct installation of USB drivers click on the Continue Anyway button i Setup QIAgility Please read the following important information before continuing When you are ready to continue with Setup click Next DlAaility Software Release Notes This document describes successive releases of the Ql gility sofware outlining changes made s
147. ince the previous release The releases are listed in inverse chronological order most recent release first and least recent last Each description includes information about the reason for the release a statement about compatibility and recommendations for use with available robotic instruments and details of major enhancements and defect fixes Date 6 Nov 2008 sa pee sl 15 Review the displayed information and then click on the Next button to continue with the software installation 5 6 QlAgility User Manual 01 2009 QIAgility Software fl Setup QIAgility E 5 xi Completing the QIAgility Setup Wizard Setup has finished installing GlAgility on your computer The application may be launched by selecting the installed icons Click Finish to exit Setup T Launch Ql aility 16 To directly launch the QlAgility Software select Launch QlAgility and then click on the Finish button If you do not want to launch the QlAgility software immediately click on the Finish button to complete the installation process Note Adobe Acrobat Reader v7 0 7 is also included on the QIAgility Software CD and is available for installation Uninstalling QlAgility software Two methods can be used to uninstall the software The recommended method is to uninstall the software via the Settings menu To uninstall the software via the Settings menu 1 Select Start Settings Control
148. ing this function may increase the amount of liquid carried on the exterior of tips Allow volumes gt tip capacity special operations When activated a tick is visible By default all of the liquid handling functions available from the Special button presented on the Reaction right hand pane work only with volumes up to the largest capacity tip supported on the QlAgility i e 200 pl Activating this option allows those functions to work with volumes larger than 200 ul Reactions are mixed by default When activated a tick is visible This function sets the detault setting of the Mix on ejection option presented on the Mix Settings section of the Reaction Configuration dialog box shown when editing PCR setup liquid handling operations displayed using the Add button of the Reaction right hand pane When activated the Mix on ejection option is checked by default when deactivated this option is unchecked by default QlAgility User Manual 01 2009 Appendix C Allow preserved well indices When activated a tick is visible This function affects the options listed in the Target Wells section of the Reaction Configuration dialog box shown when editing PCR setup liquid handling operations displayed using the Add button of the Reaction right hand pane When activated the Preserve source well indices option is presented when deactivated this option is not pr
149. ion of the first standard Enables mixing during dilution QlAgility User Manual 01 2009 QlAgility Software No of times to Defines the number of times to mix diluent mix diluent and and standard standard Change tips Instructs the instrument to change tips after after each each dilution dilution Minimum Sets the minimum volume of standards to volume create if the standards are not used in any required if reactions This allows the user to create one unused in set of standards that can be used for reactions multiple subsequent runs The minimum volume will be the volume entered plus the volume that is defined in the Standard extra volume field in the Run settings menu Set Custom Opens the Custom Concentration dialog Conc box which enables the concentration of dilutions to be defined Click on a cell in the table to directly enter a concentration Alternatively click on the Restore Defaults button to return to the default concentration values Click on the OK button to continue Using a premade standard dilution series l Left click on a plate or well with Standard function The Standard right hand pane will appear Select Use standard and Use pre mixed standard Series If desired click in the Standard name field and enter a different name for the premade standard dilution series Enter the number of dilution concentrations The Stand
150. ity If the instrument is switched on and is connected to the computer the software will proceed automatically to Normal Mode operation If the instrument is not connected to the computer or if the instrument is switched off the software will operate in Virtual Mode Gi icon on the desktop or select QlAgility User Manual QlAgility Software QlAgility Pure Precision 35353 QlAgility Version 4 9 9 9 1 6 61 Please wait Initializing serial connection on COM1 Updates and additional resources available at http Hi giagen com Warning This computer program is protected by copyright law and international treaties Unauthorized reproduction of this program or any portion of it may result in severe civil and K Ki criminal penalties and will be prosecuted to gt the maximum extent possible under the law 2 To force Virtual Mode operation click on the Force Virtual Mode button See Section 5 5 tor more detailed information about Virtual Mode operation 5 5 Virtual Mode Virtual Mode enables run files to be developed and simulated without actually performing the pipetting operations on the instrument This is particularly useful for checking new run files In Virtual Mode all software functions are enabled Run files which are developed in Virtual Mode can be saved and then run in Normal Mode Note Any modifications made to calibrations i
151. k on the Special button Select Add pause arbitrary SS The Configure Pause dialog box will appear Pause Pause time 00 00 30 Fre Cance 6 Adjust the pause time using the arrows h min s Note The Pause time can be between 1 s and 96 h 7 Click on the OK button The reaction list will be updated QIAgility User Manual 01 2009 5 97 QlAgility Software Add sample bank pooling step This function combines different sample banks pooling them into reactions This can generate significant tip savings but may result in contamination of sample banks depending on the tip usage configured for the operation Just 96 tips can be used to pool 3 x 96 well sample plates each defined as separate sample banks In comparison 288 tips would be used for the same operation when using Add mn reset eject position When using the Add sample bank pooling step option with the default tip usage setting the instrument picks up a tip takes an aliquot from the first plate takes an aliquot from the second plate and then takes an aliquot from the third plate The three samples are then pipetted into the reaction plate The second and third sample plates are therefore contaminated In contrast there is no sample plate contamination when using Add reset eject position To set up sample bank pooling using the Add sample bank pooling step option
152. ktable has been cleared 7 Click on the Yes button The automated calibration procedure will start 8 Once the X and Y axis positions have been located the following message will appear 9 Check the pipetting hub position If it is located correctly click on the Yes button to continue The Z axis position will now be located The Tip Ejector Calibration dialog box will reappear Proceed to step 14 7 2 QIAgility User Manual 01 2009 Instrument Setup and Calibration Tip Ejector Calibration r Automated Tip Ejector Calibration This function automatically determines the tip ejector location During the process the body of the pipetting head is touched against the tip ejector Please clear the pipettor hub remove all items from the worktable and ensure the tip ejector is secured Keep the lid open Warning beware personal safety Locate Ejector Y axis Position rs x axis Position D T1 Tip Ejector Height i 34 Locating Y axis found Y axis 75 Locating X axis found X axis 11 Locating Z axis found Z axis 194 Tip ejector location calibration complete 10 If the pipetting hub is not correctly located click on the No button The following dialog box will appear Tip Ejector Calibration r Automated Tip Ejector Calibration This function automatically determines the tip ejector location During the process the body of the pipetting head is touched
153. lect the master mix Check the Alternate sample wells with water box Click on the OK button Empty wells i Select No samples empty wells from the Samples panel 2 Enter the number of empty wells in the Target wells panel 3 Click on the OK button 5 13 5 Checking the reaction setup A reaction setup can be checked in 2 ways d 5 142 Run a simulation of the reaction setup in Virtual Mode See Sections 5 4 and 5 5 for more information about Virtual Mode operation Place the cursor over a source well to check the destination well s of the source well The destination wells will be highlighted For instance if the cursor is placed over a master mix well the wells on the reaction plate that will contain that master mix are highlighted QlAgility User Manual 01 2009 QIAgility Software 5 13 6 5 14 Required volumes for reaction setup The software automatically calculates the volume of standard diluent reagents and master mix required for a reaction setup To view the volume of liquid required generate the pre run report This report will list the required volumes See Section 6 7 1 tor more information about the pre run report Alternatively position the cursor above a source well i e diluent reagent master mix or standard A hover box will appear that reports the volume required This volume includes an extra volume to account for the dead v
154. ll be targeted Sample volume Defines the volume of the sample bank that will be used in a dilution Diluent volume Defines the volume of diluent that will be used in a dilution Add Adds the dilution step to the Dilutions list Remove Removes a dilution step from the Reaction plates list 6 Select the Tip Ejection Mode Multi pickup Re use tips or Use new tips 7 If Multi eject was selected the Diluent Multi eject Settings and Sample Multi eject Settings options will be available These options can be used to configure the multi eject options of the sample and diluent See Section 5 9 10 for more details about how to configure multi eject options 8 Select the diluent and the sample bank that will be used in the dilution from the drop down menus 9 Click on the button to select the target reaction plate The Plate well Selector window will appear 10 Left click on a reaction plate to select it The Sample Dilution dialog box will reappear Note If there is only one Reaction plate this plate will be selected by default Lett click on the selected plate to return to the Sample Dilution dialog box 11 Define the First well 12 Define the Sample volume and the Diluent volume and then click on the Add button 13 If required repeat steps 8 12 to configure more dilutions Note To remove a copy left click on a
155. logs which are produced by the software during normal operation When the software is installed the user access control is disabled and all users have at least Designer access privileges If user access control is disabled by an Administrator all users will return to having at least Designer access privileges Note Access privileges are included only to support a particular usage policy for the software and are not intended to prevent accidental or intentional circumvention of the policy or misuse of the software QlAgility User Manual 01 2009 5 31 QlAgility Software Note Upgrading the software does not affect user access control groups 5 7 1 Enable access control 1 Select Options User management Enable access control 2 Atick will appear next to the Enable access control option when this option is enabled 5 7 2 Create user groups To create a user group 1 Select Options User management Users amp Groups Note If Designer or Operator groups do not exist on the domain a message will appear to the operator Click on the Yes button the groups will automatically be created 2 The User Admin dialog box will appear ES SUPPORT AH Ga dal Less Groupes eal Sei 3 Select the user from the Users panel 4 Select the group that you want to assign the selected user to i e Administrators QlAgility Designer
156. luent and Tip Sample A sample is always added to a reaction last Samples must be assigned to a sample bank before they can be used in a reaction setup Reagent reagent can be combined with other 5 54 reagents to make a master mix or added individually to a reaction Reagents are always dispensed to reaction wells before samples QlAgility User Manual 01 2009 QlAgility Software Mix Reaction Standard Diluent Tip A master mix is a pooled group of reagents that can be added to a reaction plate Master mix is always added to a reaction first because it normally constitutes the largest volume of the reaction A reaction is the destination for the samples master mixes and reagents Reactions can be assigned to a sample bank this enables a reaction to be a component of a different reaction A reaction that is a component of another reaction is called an Intermediate reaction A standard is a dilution series with known concentrations Standards are treated like samples Diluent is used to dilute the master mix dilute samples and create standard dilution series It is assumed to be PCR grade water A diluent can only be assigned to a single well segment Only 1 diluent tube can be assigned in a run file The plate contains a Tip Rack Holder and tips Tips must be set to available or unavailable To change the plate function 1 Right click on the plate or the segment
157. managed via this dialog box See Section 5 11 1 for more QlAgility User Manual 01 2009 QIAgility Software detailed information about how to do this Alternatively double click on a sample bank to view the Update Sample Bank dialog box Left click on a sample bank to view the associated sample list in the Sample Data panel Modifying sample banks via the Sample Data panel 1 Select the sample bank to be edited from the lt select sample bank gt drop down menu in the Sample Data panel 2 An additional column will appear in the sample list 3 To add or remove a sample from a sample bank left click on a cell within this column A checkbox will appear in the cell 4 To add a sample to the sample bank list check the box to change the contents of the cell to Yes To remove a sample from the sample bank list check the box to change the contents of the cell to No Note Samples that are assigned to the selected sample bank are highlighted white and samples that are not assigned to the selected sample bank are displayed in gray Alternatively it is possible to copy and paste a column of Yes No values from a spreadsheet Right click in the cell of the desired starting row then select Paste to current cell Samples are given default sample names based on their position in the sample plate To change the sample name to input a sample ID or to input a starting con
158. ment lid interlock This allows the robot arm and pipettor to move when the lid is open Exercise caution to ensure your personal safety and avoid injury Are you sure you want to continue 3 Click on the Yes button to continue with tip ejector calibration 4 The Tip Ejector Calibration dialog box will appear QlAgility User Manual 01 2009 7 1 Instrument Setup and Calibration Tip Ejector Calibration r Automated Tip Ejector Calibration This function automatically determines the tip ejector location During the process the body of the pipetting head is touched 2 against the tip ejector Please clear the pipettor hub remove all items from the worktable and ensure the tip ejector is secured Keep the lid open Warning beware personal safety Locate Ejector Y axis Position fo X axis Position fo T Tip Ejector Height fo H Abort Test Finished 5 Click on the Locate Ejector button QIAGEN x 9 j Warning To avoid causing damage to the instrument please 1 Ensure that all plates tubes accessories adaptors and tip racks have been removed from the robot worktable 2 Ensure that the pipettor hub is not holding any tip 3 Ensure that the tip ejector is securely mounted to the worktable 4 Ensure that the lid is open For the duration of the calibration procedure Beware personal safety Continue 6 Open the instrument hood and ensure that the wor
159. n Virtual Mode will not affect calibrations on the actual instrument When the instrument is running in Virtual Mode the following message will be displayed at the top of the main software window indicating that the software is running in Virtual Mode Untitled 0AS QIAgility YIRTUAL MODE File Control Wizards Options Help Tl RE enee 5 12 QlAgility User Manual 01 2009 QIAgility Software 5 6 Main software window The main software window provides an interface for the creation of run files The main features are as follows M Menu bar M Toolbar M Mode indicator M Software workspace onduntiwe PRR Geet ea ea GOGO OOO Oo Seo POO Oe ee eo Seo OOO LE eo Ooo COO 08 LE u Ze Ooo COO O08 u Le Soo Goo ee ee Soo boo eee eo RB GoD oD0000 G00 Conductive tip CAGE mama ma man CEE E EEEE EEEE SOP PTET eee SOP E E E E E EEE Ceeeeeeeseeg SC ZZ u 2 2 Zu Zu 202 ee E ht 2 2 2 2 2 ttt et een no aha eerie ET TR em u SOG 0 0 6 0 0 OGG OO GOGO Oo Ooo SS OF GG58 556 EEE Ze Lu oo Een re ooo 900000000000 Conduetire tip CAGE ET ins Sun Socoscoscoss Eos Bo Ce CEE SZ en CLETETTETT ET pe Ce CR ae H OOO O0O000 0000 GoD ODOR ODO OG G0 GD oo Goo OO 0000000 GS eS GO Ci C1 noch Fr Eed Rtl Eer ee DL Ce ee ee i be bee eee ee Soo ooo ooo ooo Sob G6G 8860 86 6 Coon OO GORDO OGC Soon
160. n then try switching the instrument on again b An internal fault on Contact QIAGEN Technical Services the instrument has occurred Replicates do not provide high reproducibility a Incorrect volumes Insert the correct volumes for each reagent entered for each reagent b Master mix Increase the number of mixes or use the Wait for insufficiently mixed confirmation after creating mix option and manually mix the master mix c Less than 5 ul DNA It is recommended to use at least 5 ul DNA template used in template is used in reactions reactions d Air bubbles trapped Centrifuge the sample plate to remove air in sample tubes bubbles Software is very slow a Virus scanners Disable virus scanners on the computer running on the computer b Long reaction list A long reaction list will cause the software to significantly slow down QlAgility User Manual 01 2009 9 3 Troubleshooting Comments and suggestions Instrument pipets in mid air or pipets no liquid Level sensor Static electricity on the plasticware may be malfunction interfering with operation of the liquid level sensor Generate a support package and contact QIAGEN Technical Services Liquid in source well but received Ran out of Liquid error message a Incorrect tip The instrument may have been configured to pick configuration up tips that were not present in the Tip Rack Holder Ensure that tip configuration is correct b Incorrect pla
161. n addition these folders are important for operating the instrument AccDefs Libs PlateDefs Platelmg PresetMasterMix Settings SocketDefs TubeDefs Note Do not attempt to modify or delete these folders QProtocols folder Storing Q Protocols in this folder enables access to the gersunungsen software starts and also after clicking on the L icon QlAgility Pure Precision sees New Recent Protocols un HotStarT agl_signed3 pen Cancel Note If no Q Protocols are present in the QProtocols folder the Protocols tab will not be available If a specific Q Protocol is not saved in the QProtocols folder it will not be listed when the Protocols tab is selected QlAgility User Manual 01 2009 5 9 QlAgility Software 5 3 Hardware Wizard Found New Hardware Wizard Welcome to the Found New Hardware Wizard Windows will search for current and updated software by looking on your computer on the hardware installation CD or on the Windows Update Web site with your permission Can Windows connect to Windows Update to search for software Yes this time only C Yes now and every time connect a device No not this time Click Next to continue Cancel lt Back Nest gt 1 Select the desired option and then click on the Next button Found New Hardware Wizard S This wizard helps you install software for Ql aility If y
162. n shortages when aspirating trom intermediate reaction wells When this function is activated the software will generate warnings if QlAgility User Manual 01 2009 C 3 Appendix C C 4 aspirates from intermediate wells would cause the well volume to fall below its dead volume Advance Z axis whilst aspirating When activated a tick is visible This function modifies the aspirate operation to reduce contact between liquid and the exterior of the tip When activated aspirates are performed by advancing the tip downwards into the well while aspirating thereby approximately tracking the liquid surface during the operation Retract Z axis whilst dispensing When activated a tick is visible This function modities the eject operation to reduce contact between liquid and the exterior of the tip When activated dispenses are performed by retracting the tip upwards from the well while ejecting thereby approximately tracking the liquid surface during the operation Detect insufficient volume on aspirate When activated a tick is visible When using the level sensor during aspirate operations the software calculates the volume present in the well based on the position of the liquid surface and generates an error warning if the volume detected is less than the volume to be aspirated When activated this function suppresses this warning allowing the operation to proceed regardless Level sensor false trigger handling options
163. nables high precision pipetting 1 The QlAgility worktable is set up with a Master Mix Block a Reagent Block tips and plates tubes The instrument is then calibrated Note Tubes are placed into plates and are therefore treated as plates in the software 2 Run files are created and moditied using the easy to use QlAgility software The user can download Q Protocols from www giagen goto QIAgility and modify them according to their needs Wizards are also available to guide the user step by step through developing new run files 3 The progress of a run can be followed in real time The software highlights the position of the pipetting head on the screen as it moves 4 The QlAgility supports virtually all plate formats including Rotor Discs for the Rotor Gene Q therefore PCR reactions can be analyzed immediately using any PCR cycler QlAgility User Manual 01 2009 3 1 General Description 3 2 3 2 1 3 2 External features of the QIAgility Front view of the QIAgility EH Hood Tip chute El Feet Hood The hood of the QlAgility is manufactured from UV resistant acrylic Opening the hood enables access to the worktable During a run the hood isolates the worktable to maintain sample integrity and acts as a safety mechanism An in built sensor causes the instrument to pause if the hood is opened during a run The pause will be recorded in the post run report Warning Care should be taken when opening the h
164. ndow which enables a premixed master mix to be set up Defines the target plate that the reactions will be pipetted into Opens the Plate well Selector screen which enables selection of the target reaction plate QIAgility User Manual 01 2009 5 137 QlAgility Software Clear existing When selected the wizard deletes all reactions existing reactions in the run before generating the optimization reactions When this option is not selected the wizard appends the optimization reactions to the existing reaction list 16 Define the number of replicates for each reaction 17 Define the master mix to be used in the reaction 18 Click on the Create Premixed MM button The Plate well Selector window will appear Please select a masier mix locebon At Tip tpl Conduckren Lip AGEN 47 Tip bpl Conductive lip GACEN MA Send tapered tube D 0 SCH KT Sample L n Lapeer eed later Certes ic HX Tip gel Conductive lip HAGEN 1 Reagent block mt CE Reaction Piel PCR tube Generic CE Reaction pl POR tube Generic 19 Left click on a well in the Master Mix Block to select the location of the master mix 20 The following message box will appear RS sl Volume per sample not including additional reagents OK added by this wizard D Cancel 21 Enter the volume of master mix to be used per reaction 22 Click on the OK button 5 138 QlAgility User Manual 01 2009 QIAgility S
165. ned The pipet tip moves to a calculated position so that after aspiration the pipet tip remains below the liquid level Computer The QlAgility is operated via a computer A laptop with the correct specification for operation of the QlAgility and QlAgility Software is supplied as part of the QlAgility System However if a different computer is used to operate the QlAgility or to run the QIAgility Software then the following desktop or laptop hosting systems are recommended Desktop computer Windows XP Pro SP2 At least 2 6 GHz Pentium 4 CPU At least 512 MB RAM RS 232 serial port USB 1 1 port DVD CD ROM 80 GB tree hard drive capacity QlAgility User Manual 01 2009 General Description M Atleast 1024 x 768 screen resolution Laptop computer Windows XP Pro SP2 At least 1 6 GHz Pentium M CPU At least 512 MB RAM USB 1 1 port PCMCIA slot DVD CD ROM 80 GB tree hard drive capacity At least 1024 x 768 screen resolution The preferred platform is Windows XP Pro SP2 but if necessary the minimum computer requirements when using Windows Vista Business are Windows Vista Business Core 2 Duo CPU 1 GB RAM DirectX 9 capability RS 232 serial port and USB 1 1 port desktop USB 1 1 port and PCMCIA slot laptop DVD CD ROM 80 GB tree hard drive capacity At least 1024 x 768 screen resolution The computer connects to the QlAgility by one of the following interfacing options M USB computer USB
166. nnect the RS 232 or USB cable from the instrument to the computer and remove the AC power cord 6 Place the QlAgility into the packaging thoat it was originally shipped in 4 10 QlAgility User Manual 01 2009 QlAgility Software 5 1 QlAgility Software The easy to use QlAgility Software has been specially developed for use with the QIAgility instrument The software simulates the instrument worktable and enables the user to follow the progress of a run in real time by highlighting the position of the pipetting head on the worktable The software can also be run in Virtual Mode which enables run files to be simulated before use in Normal Mode The QlAgility Software is supplied without protocols Q Protocols can be downloaded trom www qiagen com goto QlAgility Wizards enable fast step by step setup of new run files which can be tailored to the needs of the user For convenience the software automatically calculates the required volume of each of the starting liquids e g master mix and samples In addition the software generates pre run and post run reports Software installation Install the QlAgility Software as follows 1 Insert the QlAgility Software CD into the CD ROM of the computer 2 The installer splash screen will be displayed after a few seconds If the splash screen is not automatically displayed click on Start Menu select Run and then enter CD DVD ROM drive setup exe
167. not apply any force by hand or otherwise in an upward or downward direction on the Y arm Click on the amp icon located on the software toolbar to pause the instrument before removing plates or tubes from the worktable 1 6 Translations of warnings and cautions This subsection contains translations of the warnings and cautions used in this user manual Each warning or caution has a reference number in square brackets at the top right of its box WARNING The term WARNING is used to inform you about situations that could result in personal injury to you or other persons Details about these circumstances are given in a box like this one 1 4 QlAgility User Manual 01 2009 WARNING QlAgility User Manual 01 2009 1 5 Safety Information WARNING WARNUNG WARNUNG weist auf Situationen und Umst nde hin die zu einer Verletzung des Benutzers oder anderer Personen f hren k nnen N here Angaben zu der Art der Gef hrdung und der Vermeidung solcher Situationen werden in einem Textfeld wie diesem neben der Warnung gemacht WARNING DANGER La formule WARNING DANGER est utilis e pour avertir des situations pouvant occasionner des dommages corporels l utilisateur ou d autres personnes Les d tails sur ces circonstances sont donn es dans un encadr semblable celui ci Risk of personal injury and material damage w1 Improper use of the QlAgility may cause personal injuries or damage to the instrument
168. not in contact with the plate Note If there is no tip attached the pipetting head can only move to a limited Z height 680 To obtain lower Z height positions the instrument must pick up a tip To do this click on the Get New Tip button Adjust the X position and Y position in the Plate Origin panel so that the pipetting head is directly above the center of the calibration well View the pipetting head from the front and from the side to ensure correct alignment Click on the Save button The current position is now saved as the calibrated value If desired click on the Check Pos button to confirm that the correct position has been saved To perform position calibrations on other plates repeat steps 3 7 When position calibrations are complete click on the Close button QlAgility User Manual 01 2009 Instrument Setup and Calibration 7 1 3 Calibrate plate heights Plate height calibration should be performed after plate position calibration It can be performed automatically or manually Automatic plate height calibration Before starting the procedure M Ensure that 50 ul tips are available that the Tip Rack Holder is calibrated and that the correct tips are set as available M Ensure that empty tubes are placed in the first 4 wells of each plate 1 Select Options Robot Setup Calibrate plate height 2 The Configure Plate Heights dialog box will appear
169. ns for manual PCR setup or for PCR setup at a later time To change the standard extra volume 1 Select Set standard extra volume from Options Run settings 2 The Standards Extra Volume dialog box will open Standards Extra Yolume E Ei Enter new standards extra volume pl This determines the additional volume made for each standard dilution trati d by the robot It d t affect EE EE he initial undiluted _ Cancel standard in a robot prepared standard series FO 3 Enter a new extra volume Minimum extra Defines the additional volume which is volume required prepared for each concentration of the standard dilution 4 Click on the OK button to return to the main software window 5 40 QlAgility User Manual 01 2009 QIAgility Software 5 9 5 Set default file location The default file location for all saved files is c Program Files QlAgility Data Run files are stored in this directory This directory contains three subdirectories Logs Reports and SupportPackages See Section 5 2 for more details about these subfolders To create a new default tile location 1 Select Options Run settings Set default file location Please select a default folder location for storage of runfiles reports logs and other user data 2 5 Qlagility a AccDefs CO Logs Reports SupportPackages DACH Help DACH Libs 4 PlateDefs 42 Platelmg 42 PresetMasterMix A NProtacale Pn
170. nsing QlAgility User Manual 01 2009 A 1 Appendix A Mechanical data and hardware features Dimensions Width 55 cm 21 6 in Depth 63 cm 24 8 in without cables 72 cm 28 3 in with cables Height 45 cm 17 7 in hood closed 86 cm 33 9 in hood open Mass 41 kg 90 2 Ib standard configuration Capacity Up to 96 samples per run Software QlAgility Software is supplied with the QlAgility System Default protocols are available for use with the QlAgility Software and can be downloaded from www giagen com goto QlAgility A 2 QlAgility User Manual 01 2009 Appendix A Waste Electrical and Electronic Equipment WEEE This section provides information about disposal of waste electrical and electronic equipment by users in the European Union The European Directive 2002 96 EC on WEEE requires proper disposal of electrical and electronic equipment when it reaches its end of life The crossed out wheeled bin symbol see below indicates that this product must not be disposed of with other waste it must be taken to an approved treatment facility or to a designated collection point for recycling according to local legislation The separate collection and recycling of waste electronic equipment at the time of disposal helps to conserve natural resources and ensures that the product is recycled in a manner that protects human health and the environment QIAGEN accepts its responsibility in accordance with the specific W
171. nt Settings F Nominal Yolume Ill Measured Volume fpl Value P axis units 49 85 74 52 152 38 284 6 552 53 1363 19 2687 75 4019 53 5322 7 Use displayed settings as new calibration Back Finish Generate Opens a report which summarizes the Report displayed calibration settings Use displayed Updates the default volume calibration with settings as new the displayed calibration settings calibration 8 Current Settings are displayed by default Saved calibration settings up to 9 can be accessed via the drop down menu Select one of these calibrations to display the associated calibration data in the table 9 To update the default volume calibration with the displayed calibration settings click on the Use displayed settings as new calibration button 10 If desired click on the Generate Report button to open a window that displays the current calibration settings in a table format 7 16 QIAgility User Manual 01 2009 Instrument Setup and Calibration Se AME ki is Close Print Save Email MSWord Calibration Data QlAgility Series Calibration Settings Current settings Target Vol ul Calibration Value 11 Click on the Close button to return to the Volume Calibration Wizard History of Calibration Data dialog box 12 Click on the Finish button to return to the main software window Option 2 Use Option 2 to view current calibra
172. o be ejected into a dry well Will The run contains reaction elements that will contaminate contaminate sample wells Volume too The run requires a volume of less than ul small to be pipetted 9 6 QlAgility User Manual 01 2009 Troubleshooting Multi eject The run is set up with multi eject functionality which can lead to reduced precision Master mix The master mix extra volume is set to extra volume prepare a total extra volume that is lower too small than the extra volume recommended to avoid shortages Standards An instrument prepared standard well has volume too a volume that is too large for a 200 ul tip high to mix effectively Speed not set A speed parameter has not been set Default settings will be used Air intake limits The maximum volume that can be pipetted is limited by the amount of preaspirated air Errors Not enough There are not enough output wells in the output wells reaction plate Too many The number of programmed standards standards exceeds the maximum number of standards The software can accommodate a maximum of 16 dilution series Invalid sample Sample banks are incorrectly configured contig Operation A reaction in the Reaction List cannot be impossible performed Dilution out of The sample and target concentration are range set to values that are not achievable Bad plate A plate configuration is not usable contig QlAgility User Manual 01 2009 9 7 Troubleshootin
173. o simulate user tabs or carriage returns appended to the bar code These simulated tabs or carriage returns automatically move the data input point cursor on the data table to the next input cell each time a bar code is read 1 Left click on a Sample or Reaction plate to view the Sample or Reaction right hand pane 2 Click on the M icon The Barcode Entry dialog box will open QIAgility User Manual 01 2009 5 113 QlAgility Software BH Barcode Entry m Barcode Data Sample Bank Name F Add to sample bank named CG Heu Ban Cancel OK 3 Scan the sample or reaction IDs IDs will automatically be added to the Barcode Entry table 4 To add samples or reactions directly to a sample bank select Add to sample bank named in the Sample Bank Name panel 5 Select either New Bank or Existing Bank If New Bank is selected enter a sample bank name If Existing Bank is selected left click on a sample bank to select it 6 Click on the OK button to return to the main software window Importing sample and reaction data from a file All sample and reaction data can be imported and exported from a variety of spreadsheets and text based files To import data from Excel files save the spreadsheet as a CSV Comma Delimited tile type 1 Left click on a Sample or Reaction plate to view the right hand pane
174. o update the plate function select Sample Reaction Reagent Standard or Mix 8 Repeat step 7 for all plates on the worktable 9 Click on the Next button to continue 5 126 QlAgility User Manual 01 2009 QlAgility Software ER sel vum ehe Reagen eniry Flesgert Endry AR QE RER aac PAP nm ANE ne E s pepe in lhe pes bisar ae aralabie here lo have thew cordes sup To sup pour magenta click ep Hee plate Holding the agents Dick Mess bn continu At Tip hehe Tecan tip A Tip Ta MI Mit plate 5 tule BA Tip pl Tecan tip AE Reaction 200041 deep well OR 10 Left click on a plate which has Reagent function The following dialog box will appear BF Please enter reagent details x ok A 10 Buffer Cancel Mol dNTP Primer fwd Primer rev Probe 1 Probe 2 Tag Clear all Clear all Clears all information in the Reagent column and updates all cells in the Viscous column to No 11 To change the reagent name left click on a cell in the Reagent column and then enter a new name To change a reagent from viscous to non viscous left click on a cell in the Viscous column check the box and then click on the OK tab Repeat this procedure to change a reagent from non viscous to viscous QlAgility User Manual 01 2009 5 127 QlAgility Software 12 Click on the OK button to continue
175. ocol Ke Q Unlocks a protocol I Indicates that the run file which is currently open is a locked Q Protocol Indicates that the run file which is currently Protocol open is a locked User Developed Protocol Mode indicator When the software is operating in Virtual Mode the following indicator is displayed Untitled QAS QIAgility YIRTUAL MODE File Control Wizards Options Help malaal l al ol cal When the software is operating in Normal Mode the following indicator is displayed Untitled QAS QLAgility S N 30305 File Control Wizards Options Help Eruul me sl nl a en QIAgility User Manual 01 2009 5 25 QlAgility Software 5 6 4 Software workspace The software workspace supports the following features Worktable Status bar Software version Instrument Liquid level sensing option Tip reuse option User logged in Windows Plate buttons Right hand pane Software worktable The software worktable visually simulates the instrument worktable The 6 SBS positions for plates are labeled Al A2 B1 B2 CI and C2 Positions for the Master Mix Block and Reagent Block are labeled M1 and R1 Status bar The status bar displays the current status of the instrument during a run or Software version This bar displays the current software version OlAgiity 4 9 9 8 5 26 QlAgility User Manual 01 2009 QIAgility Software Instrument
176. of the progress of the run will be displayed in the right hand pane See Section 5 6 4 6 10 QlAgility User Manual 01 2009 Operating Procedures 6 5 6 6 Pausing aborting a run A run can be paused and aborted at any time Pauses will be logged in the post run report If the run is aborted the instrument will discard the tip and return to its resting position To pause a run 1 Click on the amp icon in the toolbar or select Pause Abort from the File menu 2 The instrument will complete the current operation and will then pause The following dialog box will appear CS lt lt Operation paused at 07 11 2008 13 52 59 Continue 3 Click on the Continue Run button to continue the run or click on the Abort Run button to abort the run 4 The instrument hood must be closed to abort the run Note A run will also be paused when the instrument hood is opened Note The instrument does not stop immediately when the hood is opened Therefore wait until the Y arm has stopped moving and the warning screen is displayed before continuing Note An aborted run cannot be restarted from the point at which it was aborted Exception handling If an exception i e an error or warning occurs during a run an alarm will sound for 60 seconds and then at 30 second intervals A dialog box which contains information about the error will appear This box has 4 buttons Abort run
177. of a plate that is to be changed The plate operations menu will appear 2 Select Change plate function The available plate functions will appear as a submenu 3 Select a plate function A tick will appear next to the function that has been selected Note If the selected plate type is a Tip Rack Holder the only available function for the plate will be Tip QlAgility User Manual 01 2009 5 55 QlAgility Software Adding removing an accessory If required an accessory e g cooling block can be added under a plate Note Use of an accessory affects the plate height Plate height calibration must therefore be pertormed with the plate and accessory together To add or remove an accessory 1 Right click on the plate where the accessory is to be added removed The plate operations menu will appear 2 Select Change accessory The Select Accessory dialog box will appear BF select Accessory Plates with accessories have different calibration values to standard ok plates Manufacturer Eppendorf Part Number 3881 000 023 3 Select the required accessory trom the drop down menu An image of the accessory will appear Alternatively to remove an accessory select No accessory from the drop down menu 4 Click on the OK button to return to the main software window A plate which is associated with an accessory will now have a colored background in the main
178. of well detected at 648 based off the average of 4 samples Values el read 648 648 648 648 After compensation for this plate type the height will be set to 628 Save these settings Yes No 9 Click on the Yes button to accept the calibration if the averages for a plate are within 10 units of each other If the averages are not within 10 units of each other click on the No button to reject the current calibration and then repeat steps 5 8 Note Before repeating the calibration ensure that all tubes are sitting correctly and that the tips are not bent Note If there is significant variation across the 4 samples the following message box will appear Click on the OK or the Cancel button AEM i xj p Variation in height of 32 3 2mm detected which exnends the recommended tolerance of 15 15mm T is possible that net al tubes are saated properly on tha plan sa or a Up missed garg inte a lube property Continue mear or cancel this height calibration For bube S d ECH bube on plate Reagent block zondard 200 Flat tapered di Blt CE um 10 If more than one plate was selected in the Plates to Calibrate list the instrument will calibrate each plate in turn Repeat steps 6 9 for each plate 11 When all calibrations are complete click on the Close button Manual plate height calibration 1 Complete steps 1 4 of Automatic plate height calibration 2 Click on the Manual Setup
179. oftware CON x e 1 Wizard complete 23 Click on the OK button to return to the main software window 5 13 3 Using Empty Project 1 Select the icon from the toolbar The following splash screen will appear This splash screen will also appear when starting the software and can also be accessed by selecting File New QlAgility Pure Precision 35553 New Recent Protocols Empty project L PCR Setup Wizard GH Optimisation Wizard 2 Select Empty Project and then click on the Open button 3 Select the correct plate type in the software for each position on the worktable The plate types selected in the software must match the actual worktable setup See Section 5 10 1 for details about how to change plate types 4 Select the correct plate function for each plate on the worktable i e Diluent Reaction Reagent Standard Mix or Tip See Section 5 10 1 for details of how to change plate function Note Ensure that only plates that have been position and height calibrated are used QlAgility User Manual 01 2009 5 139 QlAgility Software 5 Set the tip availability for every plate that has Tip function See Section 5 10 2 for details about setting tip availability 6 Configure the samples diluent standards reagents and master mix See Section 5 12 7 Set up the reaction list See Section 5 12 6 for details about
180. olume that is dependent on the tube type ell in Reagent block standard 200 flat tapered Pi D 1 5m tapered hinged tube Reagent Before run manually load 20 0 ANT 30 Selecting the COM port 1 Select Options Robot Setup Select COM port 2 The Configure Serial Interface dialog box will open FF Configure Serial Interface E Ei Port Selection Serial Port tt Cancel 3 Select the desired COM port from the drop down menu and then click on the OK button Note For correct communication of the laptop supplied with the QlAgility with the instrument COM4 must be selected 4 The following message will appear SS 9 Software must be restarted for the change of serial port selection to take Ze effect Shutdown software now 5 Click on the Yes button to shut down the software QlAgility User Manual 01 2009 5 143 QlAgility Software 6 Restart the software 5 15 Service register The service register describes the current status of maintenance alert notification records that are associated with the instrument The software maintains a schedule of required service activities in the service register Maintenance activities that are scheduled for future dates are displayed as green records When a scheduled maintenance activity is due the record is displayed in red and a service alert notification is generated If the system has any unackno
181. omatic plate height checked items calibration operation Automatic plate height calibration is performed only for the selected plates Abort Aborts the current calibration activity Manual Setup Initiates the manual plate height calibration highlighted operation Manual plate height calibration is items pertormed only for the selected plate 3 Check the boxes next to the plates to be calibrated in the Plates to Calibrate list Alternatively click on the Select All button to select all of the plates Note Plates which have multiple segments e g Reagent Blocks are listed more than once but with different tube types Define the number of wells from which to take an average It is recommended that 4 wells are used to calculate the average Click on the Autodetect checked items button to initiate calibration rasen gt Ready to auto detect well heights Please ensure plate position are Fully GZ calibrated and empty tubes placed in the first 4 wells for each plate Ces Review the message and click on the Yes button to continue 7 8 QlAgility User Manual 01 2009 Instrument Setup and Calibration COS ix K Autocalibrating heights For 96 well plate vertical C1 tube type 200ul PCR tube care 7 Click on the OK button to continue 8 If Require confirmation from user was selected the following message will appear QIAGEN x Bottom
182. on Indicates the position of the pipetting head on the X axis During calibration the objective is to set this to match the center position of the calibration well Y position Indicates the position of the pipetting head on the Y axis During calibration the objective is to set this to match the center position of the calibration well Save Saves the current X and Y positions as the calibration location for the plate Revert to saved Restores the X and Y positions from the most recently saved values Raise tip Raises the tip Lower tip Lowers the tip Home Z Axis Raises the pipetting head to the top home position QlAgility User Manual 01 2009 7 5 Instrument Setup and Calibration 7 6 Check Pos Moves the pipetting head to the defined X and Y position to enable the user to visually inspect whether this corresponds to the center of the calibration well Get New Tip Collects a new 200 ul tip Eject Tip Discards the tip that is currently on the pipetting head Select a plate from the Plate Selection list Note Tip Rack Holders are listed as 96 well plates A schematic diagram of the selected plate is displayed on the right Position calibration is performed using a calibration well This well is highlighted red Use the Lower Tip and Raise Tip buttons in the Tip Control panel to move the pipetting head so that it is just above the plate surface Ensure that the tip is
183. on directory Click on the Next button to continue QlAgility User Manual 01 2009 5 3 QlAgility Software fl Setup QIAgility Regional Settings For correct customer service contact details to be provided the Ql gility software D needs to know the region of the world in which you are located Select Region Please select r lt Back Cancel 9 Use the drop down menu to select your region Click on the Next button to continue i Setup QIAgility loj xj Select Additional Tasks Ray Which additional tasks should be performed Q Select the additional tasks you would like Setup to perform while installing GlAaility then click Next Additional icons V Create a desktop icon Create a Quick Launch icon lt Back Cancel 10 Select the additional tasks and then click on the Next button Select Create a desktop icon to create a desktop icon to easily launch the software Select Create a Quick Launch icon to generate a quick launch icon 5 4 QIAgility User Manual 01 2009 QlAgility Software fl Setup QIAgility D ici xl Ready to Install Setup is now ready to begin installing Ql aility on your computer Click Install to continue with the installation or click Back if you want to review or change any settings Destination location C Program Files Ql gility Setup type Full installation Selected components QlAa
184. on the toolbar or select Control Start The Save as dialog box will appear To save the run file enter a name for the run file and click on the Save button If the run file has already been saved click on the Cancel button to continue The pre run Checklist dialog box will appear Checklist K iol x Please acknowledge the following messages and hit OK to continue Blue messages are warnings and must be checked to continue Red messages are errors and prevent the run from starting Messages Please make sure the tip discard chute is open and the tip disposal box is empty DJ Please confirm that tips tubes plates and liquids have been setup correctly as per the Pre Run Report U Tips During this run the robot will run out of 50 ul tips Check all boxes and hit OK to continue Please make sure the tip discard chute is open and the tip disposal box is empty Cancel Pre Run Report Gk If the run has been set up correctly the checklist will not list any warnings or errors other than those listed above If errors are listed user intervention is required before the run can be started Select the boxes next to the warnings to continue Click on the Pre Run Report button to view the pre run report Check the worktable setup Click on the OK button to start the run The location of the pipetting head will be highlighted on the sottware worktable in real time and a summary
185. ood during a run because it takes up to 10 seconds for the instrument to complete the current movement and for the pause to take effect Under no circumstances should this sensor be bypassed QlAgility User Manual 01 2009 General Description 3 2 2 Feet The feet have a non slip silicone base This ensures that the QlAgility is securely positioned Warning Do not attempt to slide the instrument on a bench without lifting as this may cause damage to the silicone base of the feet Side view of the QlAgility H Tip receptacle box Tip receptacle box The tip receptacle box collects discarded tips ejected from the tip chute at the side of the QlAgility Each QlAgility tip box can hold approximately 300 used tips If the tip box is gently shaken tips in the tip receptacle box settle and this allows approximately 100 extra used tips to be collected in the box QlAgility User Manual 01 2009 3 3 General Description 3 2 3 Rear view of the QlAgility H UV lamp socket DH RS 232 port H HEPA socket USB port Accessory DH Accessory power ratings H Accessory 2 H Main power input socket H Accessory 3 H Power switch Note Accessories 1 3 are not required for operation of the QlAgility Power switch The power switch has two positions M 0 power is switched off M power is switched on 3 3 Internal features of the QlAgility Sege KOT TETTEI _ ss gege e e e e gp ge 3 4 QlAgilit
186. or COSHH documents Venting for fumes and disposal of wastes must be in accordance with all national state and local health and safety regulations and laws OSHA Occupational Safety and Health Administration United States of America t ACGIH American Conference of Government Industrial Hygienists United States of America COSHH Control of Substances Hazardous to Health United Kingdom 1 4 Waste disposal Used labware and containers may contain hazardous chemicals Such wastes must be collected and disposed of properly according to local safety regulations For information about how to dispose of the QlAgility see Appendix A QlAgility User Manual 01 2009 1 3 Safety Information 1 5 Mechanical Hazards WARNING Moving parts W4 A Avoid contact with moving parts during operation of the QlAgility Under no circumstances should you place your hands under the pipetting arm when it is lowering Do not attempt to move any plates or tubes whilst the instrument is operating To ensure satisfactory and safe operation of the QlAgility Always use the packaging provided with the QlAgility when moving the instrument Only use recommended tips and Tip Rack Holders Keep the instrument hood closed whenever possible Do not disable the hood interlock When calibrating plates with the hood open always stand clear of the instrument when making adjustments Do not place any items on the arm of the instrument Do
187. ording to the convention M D R Q D RQ M is the marker name All other items are the same as for Absolute Quantification For example Mix D CMV_FAM TAMRA EBV JOE TAMRA specifies a mix with detector for CMV using FAM reporter and TAMRA quencher and detector for EBV using JOE reporter and TAMRA quencher Mix D represents the marker name in the SDS software The allelic discrimination function exports 2 files XXX TXT and XXXend TXT for endpoint analysis where XXX is the filename Note The Absolute Quantification and Allelic Discrimination export modes ignore reactions where the master mix name does not match the required format In the resultant files wells are only listed where their master mix contents are named so that they can match the required format QlAgility User Manual 01 2009 Appendix C Appendix C Advanced Settings Advanced run settings are available to adjust specific applications on the QlAgility These tunctions should be modified only under direct instructions from QIAGEN Tip pickup mode This defines the strategy used for collecting tips from the Tip Rack Holder Normal single stage or Three Stage can be selected Normal single Instructs the instrument to collect tips using stage a single downward movement This is the default setting Three Stage Instructs the instrument to collect tips in 3 separate downward movements 1
188. ort reaction Opens the Export reaction Info dialog data box which enables information about the contents of reaction wells from a selected reaction plate to be exported to another file See Section 5 12 7 for further details Generate Opens a window which contains the pre report run report for the loaded run file See Section 6 7 1 tor further details Options menu The Options menu includes options to manage user groups manage calibration settings and to configure pipetting and plate options Options Help I User Management Calibration Management Robot Setup Run Settings Advanced Settings rT F F F Change plate type Change accessory Change plate Function User Provides options to create user groups and management to enforce access restrictions on certain user groups See Section 5 7 for further details User Enables or disables access control If management access control is enabled a tick is Enable displayed Access control can only be Access Control enabled by an Administrator See Section 5 7 1 tor further details User Enables creation of user groups See management Section 5 7 2 for further details Users amp Groups QlAgility User Manual 01 2009 5 17 QlAgility Software User management change current user Calibration management Calibration management Save calibrations on setup disk Calibration management Load calib
189. ot exposed to hazardous levels of toxic substances chemical or biological as defined in the applicable Material Satety Data Sheets MSDSs or OSHA ACGIH t or COSHH documents Venting for fumes and disposal of wastes must be in accordance with all national state and local health and safety regulations and laws Gef hrliche Chemikalien Einige der in Verbindung mit diesem Ger t verwendeten Chemikalien sind gesundheitsgetahrdend oder k nnen nach Beendigung eines Protokoll Durchlaufes gesundheits gef hrdend werden Es sollten immer Sicherheitsbrille zwei Paar Handschuhe und ein Laborkittel getragen werden Der Betreiber der Anlage ist f r die Gew hrleistung der Sicherheit am Arbeitsplatz verantwortlich Er hat sicherzustellen dass die Bediener des Ger tes ausreichend geschult sind und nicht gesundheitsgef hrdenden Konzentrationen toxischer Substanzen chemischer oder biologischer ausgesetzt sind so wie dies in den Sicherheitsdatenbl ttern oder in anderen zu beachtenden Dokumenten festgelegt ist Bei der Behandlung von Abluft und bei der Abfallbeseitigung sind alle gesetzlichen Regelungen zur Gesundheit und Sicherheit auf nationaler regionaler und lokaler Ebene zu ber cksichtigen QlAgility User Manual 01 2009 1 7 Safety Information WARNING 1 8 A Substances chimiques dangereuses Certaines substances chimiques utilis es avec cet instrument peuvent tre dangereuses ou peuvent le devenir apr s que le
190. ot setup Enables calibration of length variation Calibrate tip between different tip types This calibration offsets is optional See Section 7 1 4 Robot setup Calibrates the pipetting head to the tip Setup tip ejector Enables correct tip ejection and ejector ensures that the vacuum hub is not damaged See Section 7 1 1 Robot setup Enables selection of the COM port which is Select COM used for communication with the QIAgility port See Section 5 14 Robot setup In Virtual Mode this option enables or Enable UV light disables a virtual UV lamp When enabled a tick will appear and the UV lamp bulb icon will be activated in the toolbar In Normal Mode this option is disabled If a UV lamp is physically detected by the instrument hardware this option will be ticked and the UV lamp bulb icon in the toolbar will be activated If no UV lamp is detected this option will not be ticked and the UV lamp bulb icon in the toolbar will be inactive See Section 6 2 Robot setup Opens the Service Register dialog box Service register This outlines the instrument service history The service history is updated by QIAGEN Technical Services See Section 5 15 QlAgility User Manual 01 2009 5 19 QlAgility Software Run settings Run settings Configure tip air intake Run settings Configure pipette speed Run settings Use liquid level when pipetting Run settings
191. oting 9 4 2 Electrical tests Check Communications USB or RS 232 cables bridge communication between the computer and the main controller of the instrument SPI bridges communication between the main controller and slave controllers i e accessories and axes controllers This test checks the integrity of both types of communications links in the system exercising the channel to 4 internal axes and any accessories if connected During this test a SPIERROR 11 error message is generated if the SPI link is unstable or a BADRXCHKSUM 137 error message appears if there is an unstable computer to instrument link If no error message appears during the test there is no problem with the communications links Liquid Sensor Test This test checks that the liquid sensor circuitry is functioning correctly so that it only triggers when the conductive tip touches the liquid QlAgility User Manual 01 2009 Glossary 10 Term Diluent Glossary Description Diluent is used to dilute the master mix dilute samples and Hood Master mix Master Mix Block Menu bar Mode indicator Normal mode Power switch Q Protocol Reaction create standard dilution series It is assumed to be PCR grade water A diluent can only be assigned to a single well segment Only 1 diluent tube can be assigned in a run file The instrument hood isolates the worktable maintaining sample integrity and acting as a
192. our hardware came with an installation CD lt 6 or floppy disk insert it now What do you want the wizard to do Install from a list or specific location Advanced Click Next to continue lt Back Cancel 2 We recommend that you select Install the software automatically 3 Click on the Next button to continue 5 10 QlAgility User Manual 01 2009 QIAgility Software 5 4 Hardware Installation 4 The software you are installing for this hardware Ql gility has not passed Windows Logo testing to verify its compatibility with Windows XP Tell me why this testing is important Continuing your installation of this software may impair or destabilize the correct operation of your system either immediately or in the future Microsoft strongly recommends that you stop this installation now and contact the hardware vendor for software that has passed Windows Logo testing Continue Anyway 4 Click on the Continue Anyway button Found New Hardware Wizard Completing the Found New Hardware Wizard The wizard has finished installing the software for E QlAgility e Click Finish to close the wizard 5 Click on the Finish button Starting the software Note Before starting the QlAgility Software ensure that the instrument hood is closed and that the instrument is switched On Double click on the Start Programs QlAgility QlAgil
193. ox left click on the selected plate 9 Define the First well 10 Define the Final volume the Desired Concentration and the Mix count 11 Define the remaining options in the Sample Normalization dialog box as required 12 Click on the OK button to return to the main software workspace The sample normalization will be added to the Reaction List Add remove waste pool bank members This function enables liquids from multiple sources to be moved into a waste well i e enabling pooling 1 Left click on a Reaction plate 2 The Reaction right hand pane will appear 3 Click on the Special button QlAgility User Manual 01 2009 5 111 QlAgility Software 4 Select Add remove waste pool bank members 5 The Remove Waste dialog box will open BH Remove Waste 3 lol x This feature removes waste moving all samples in a OK sample bank to a single tub well Select the sample bank Sample Bank 1 16 samples Sample volume 5 a pl Select the Waste well tub on a Reaction Plate ES well plate vertical C2 E well tub 141 z Use anew tip for each sample Re use tips Tip Settings NOTES Tips Required 16 x 50 pl Largest available tip size 200 pl ig Sample volume Defines the sample volume to be moved to waste Opens the Plate well Selector screen which enables selection of
194. played When a reaction contains more than one sample no final concentration value can be calculated so no value is displayed If desired the user can assign a concentration value to the reaction well User assigned concentrations are shown in blue This is useful for dilution of samples or stock wells which are supplied initially in reaction plates If a user assigned concentration is entered for a well which also has a valid calculated concentration the user assigned value is shown in red to indicate that it is overriding the software calculated value Note Concentration values are assumed to be entered in a single unit common to all values in the run The unit itself can be defined as needed for the application Reaction Configuration dialog box To open the Reaction Configuration dialog box click on the Add button from the Reaction right hand pane 5 90 QlAgility User Manual 01 2009 QlAgility Software EU S Rean Configuration pas of these sets Hadesa to this volume o TS Samele r E ces Pur mit befoan taking sampl M eb Total volume Fr E Which will be combined with ALL of these nda d bebes 7 een meer Number of wels k Mix Settings Mix on ejection FF fs pme r Nomak samples Into THIS caen plate Target reaction plate 86 wel plote honnordol 63 C2 Samples Allows selection of a sample bank from the drop down menu Pre mix before Select
195. ple or Reaction function The Update Sample Bank dialog box will appear Create sample banks as outlined in Section 5 11 1 24 Click on the Next button to continue 25 The Reaction Editor screen will appear Reaction dtot To comgpisia the ured combes the sampe and sand groupe valh the masie mest To add a mm sedecl a imunda me zer carci oF sangle Io odd to this max and select the Gate in which pou would like the reaction to take place Enin mee configuration Masten ma Standeeds sangies Tagel plate Me sl GeneOuc 72 loading plate 1 72 Add D H Eise Ranctinns cw Delle Il pl Back New QlAgility User Manual 01 2009 5 131 QlAgility Software Master mix Standards samples iteration s Target plate Add Copy Delete Up Defines the master mix that will be used in a reaction Defines the standard or sample that will be used in a reaction Defines the number of reaction replicates that will be performed Defines the target plate that the reaction will be pipetted into Opens the Plate well Selector screen which enables selection of the target reaction plate Adds a reaction to the Reactions list Enables a selected reaction to be copied within the Reactions list Options to Copy in place Copy to end of list or Cancel will appear Deletes a selected reaction in the Reactions list Mov
196. pooling step Add sample bank duplication step Add sample dilution step Add serial dilution step Add sample bank normalisation Add remove waste pool bank members Add pause 30 Adds a 30 second pause to the reaction list sec Add pause arbitrary Add reset eject position Adds a pause of defined length to the reaction list Configures the instrument to start pipetting into a reaction plate from its first well typically well Al This can be useful for pooling sample banks There is no contamination of source sample banks QlAgility User Manual 01 2009 5 95 QlAgility Software 5 96 Add pause until confirmation Add fan on Add fan off Add sample bank pooling step Add sample bank duplication step Add sample dilution step Add serial dilution step Add sample bank normalization Pauses the instrument for an unlimited period of time A dialog box will appear H desired enter a message that will appear on the screen when the instrument pauses Then click on OK to add the command to the reaction list When the instrument pauses user intervention is required to continue the reaction setup Click on the OK button to continue Turns the HEPA filter on Turns the HEPA filter off Opens the Sample Bank Pooling dialog box which enables sample banks to be pooled The user can control tip usage during the pipetting operation
197. r tes Plaque l arri re de l appareil On the front edge ofthe worktable Am vorderen Rand der Arbeitsplatte A l avant de la table de travail o C Tick Markierung f r Australien Lieferanten Identifizierung N17965 N15148 Marquage C Tick pour l Australie Identification du fournisseur N17965 N15148 RoHS mark for China the restriction of the use of certain hazardous substances in electrical and electronic equipment RoHS Markierung f r China Beschr nkung der Verwendung bestimmter gef hrlicher Stoffe in Elektro und Elektronikgerdten Marquage RoHS pour la Chine limitation de l utilisation de certaines substances dangereuses dans les quipements lectriques et lectroniques Crush point symbol Warnung vor Quetschgefahr Risque de contusions QlAgility User Manual 01 2009 1 15 Safety Information This page left intentionally blank 1 16 QlAgility User Manual 01 2009 Introduction 2 Introduction Thank you for choosing the QlAgility We are confident it will become an integral part of your laboratory Before using the QlAgility it is essential that you read this user manual carefully and pay particular attention to the satety intormation The instructions and safety information in the user manual must be followed to ensure safe operation of the instrument and to maintain the instrument in a safe condition 2 1 About this user manual This user manual provi
198. rations from setup disk Calibration management Delete multiple calibrations Robot setup Robot setup Calibrate plate heights Robot setup Calibrate volumes Enables the current user to be temporarily changed A dialog box will appear which enables an administrator to temporarily log in See Section 5 7 3 for further details Enables the transfer of calibrations and other software settings from one computer to another This is useful when the instrument is connected to a new computer See Section 5 8 Enables calibration settings to be saved using a range of storage devices e g USB stick See Section 5 8 1 Enables calibration settings to be loaded from a setup disk onto a computer See Section 5 8 2 Enables deletion of multiple calibration settings See Section 5 8 3 Provides options to calibrate the instrument These settings are maintained locally and are not associated with run files Defines the Z axis location i e height of the inside base of the tube or wells of a plate See Section 7 1 3 Calibrates the volume that is pipetted Ensures that the correct volume is accurately and precisely pipetted See Section 7 1 5 QlAgility User Manual 01 2009 QlAgility Software Robot setup Enables calibration of the position of each Calibrate plate plate Ensures that the pipetting head moves positions to the correct location for every well on a plate See Section 7 1 2 Rob
199. re Defaults 3 Enter the air volume in the boxes next to Samples Reagents Standards Diluent and master mix and Intermediate reactions Alternatively to return to the default air volume settings click on the Restore Defaults button QlAgility User Manual 01 2009 5 37 QlAgility Software Note Larger air volumes may be beneficial when pipetting viscous liquids Smaller air volumes may be beneficial when pipetting smaller volumes or when dispensing into small tubes 4 Click on the OK button to return to the main software window 5 9 2 Configure pipet speed To configure the pipet speeds 1 Select Options Run settings Contigure pipette speed 2 The Configure Pipetting Options dialog box will open BH Configure Pipetting Options E x m Sample speed Diluent and master mix speed OK 20 pl sec Current speed 150 pl sec 150 pl sec 20 pl sec Current speed 150 pl sec 150 pl sec _ m Reagent speed normal Intermediate reaction speed 20 pl sec Current speed 150 pl sec 150 pl sec 20 pl sec Current speed 150 pl sec 150 pl sec UE m Reagent speed viscous 20 pl sec Current speed 70 pl sec 150 pl sec r Standards speed Mixing speed eee 20 pl sec Current speed 150 pl sec 150 ul sec 20 yl sec Current speed 150 pl sec 150 yl sec possible mixing ensure that the J J mixing speed is set to maximum 3 Le
200. re that the QIAgility has equilibrated to ambient temperature before operating it Retain the packaging in case you need to transport or ship the QlAgility in the future Instructions for packing the QlAgility are outlined in Section 4 5 Using the original package minimizes damage during transportation of the QlAgility Carefully place the QlAgility onto the workbench where it will be used For site requirements please refer to Section 4 1 QlAgility User Manual 01 2009 4 3 Installation Procedures 4 3 Installing the QIAgility Releasing the transport locks Note The procedure for removing the transport locks is also written on the transport locks on the instrument 3 1 Unscrew the two screws 1 and 2 and remove the horizontal bar 2 Move the pipetting head to the right and remove the transport lock from the worktable 4 4 QIAgility User Manual 01 2009 Installation Procedures 3 Unscrew the Z axis locking screw When this screw is removed the pipetting head will drop 4 Store the transport lock and the Z axis screw with the rest of the packaging QlAgility User Manual 01 2009 4 5 Installation Procedures 4 6 Computer setup and installation of the QlAgility software For computer system requirements please see Section 3 5 1 Set up the computer as described in the computer installation instructions provided with the computer 2 Before installing the QlAgility Software shut
201. re the same length a slight enlargement in collar size makes the 200uL tip sit higher This makes the 200uL tip appear shorter on the robot The length offset accounts for this Length offset The tip offset calibration enables the software to automatically determine the correct height calibration for the QlAgility User Manual 01 2009 7 11 Instrument Setup and Calibration 7 12 200 ul tips based on the height calibration that was performed with 50 ul tips Before starting the procedure M Ensure that a plate with Reaction or Mix function with well sizes large enough to accommodate 50 ul and 200 ul tips is available this plate must be position and height calibrated M Place a tube in the first well of the reaction plate M Ensure that 50 ul and 200 ul tips are available that Tip Rack Holders are calibrated and that correct tips are set as available 1 Select Options Robot setup Calibrate tip offsets 2 The Configure tip offsets dialog box will appear BF Configure tip offsets x Tip Offset Close Tip offset calibration measures the apparent lengths of the _ selected tip types so that variations can be accommodated when pipetting Plate height calibrations are typically carried out with 50 ul tips When pipetting using other tip types such as 200 ul tips poor performance may occur due to differences in the on robot lengths of these tips relative to t
202. rget ae N Enables selection of a color LC Adds selected color Deletes selected colors QlAgility User Manual 01 2009 5 43 QlAgility Software Close Resets all sample colors Click on the Yes button to continue Refreshes the colors displayed on the software worktable according to the current settings Opens color theme Saves color theme Closes and applies updated colors 5 9 7 Adjust liquid level tracking options To adjust liquid level tracking options 1 Select Options Run settings Use liquid level when pipetting Configure tip air intake ES Configure pipette speed 5 Use liquid level when pipetting Ignore errors during run Set master mix extra volume Set standard extra volume Set tip usage options Set default File Inrafinn Tip Info To modify tip availability Do not use liquid level ow Detect liquid level using sensor Use liquid level estimate Tip Type Ay 2 Select 1 of the 3 options Do not use liquid level Detect liquid level using sensor or Use liquid level estimate The Use liquid level estimate function is intended for use when the level sensing function cannot be used i e if the liquid is covered with foil or if the liquid is non conductive Detect liquid level using sensor 5 44 Instructs the instrument to use the liquid level sensor to track the liquid l
203. rom one computer to another using a Setup Disk This is useful when the instrument is connected to a new computer The Setup Disk can be any storage device e g USB stick Note It is not necessary to use a Setup Disk when the software is updated to a new version Calibration settings will be retained Warning A Setup Disk that is created for one instrument should never be used with another instrument as this may result in damage to the instrument 5 8 1 Save calibrations on setup disk To create a Setup Disk 1 Select Options Calibration Management Save calibrations on setup disk Calibration Settings Select the robot for which you wish to export calibration QlAgility Save Cancel Select Connected Robot 2 The Calibration Settings dialog box will appear Ensure that the displayed serial number matches the serial 5 34 QlAgility User Manual 01 2009 QlAgility Software number of the instrument that is connected Click on the Save button to continue Save Calibration Settings As Save in SG Data DI Ari ES My Recent SupportPackages Documents Desktop My Documents BE My Computer Ki File name Calibration Settin ili gs Ql gility 30 10 2008 12 5 e Save g d Less HUEN Save as type Robotics Calibrations xml DI Cancel Places E 3 A default filename and location will be supplied If desired these can be c
204. s Explore save directory Display log file About QlAgility 5 6 2 Toolbar See Section 9 4 for more details This option should only be enabled under specific instruction from QIAGEN Allows the user to browse the number of movements each axis has performed since the last instrument service Launches a file Explorer window with the default file directory where run files are saved Displays the log file This file contains information about the run setup and all commands sent to the instrument from the computer The log file is updated as new runs are carried out with the oldest data being deleted See Section 6 7 3 Displays information about the QlAgility including the version number serial number and firmware number QIAGEN contact details which may be required to place orders or to request technical support are also displayed This section outlines functions that are available from the toolbar menu Opens the start up splash screen which displays options to create a new run file to open a recently used run file or to open a Q Protocol QIAgility User Manual 01 2009 5 23 QlAgility Software 5 24 Enables an existing run file to be opened Select the run file and then click on the Open button This file can be used as it is or modified to create a new run file See Section 6 4 2 Saves the run file under the current file name or under a new file name selected by the
205. s Control and Users amp Groups options are only available to administrators In addition an Administrator has all the access privileges of a Designer 5 30 QlAgility User Manual 01 2009 QlAgility Software Designer A Designer has read write access to all software functions and is able to design table layouts calibrate instrument settings define run settings set up reaction lists and import export data In addition a Designer has all the access privileges of an Operator Operator An Operator can view table layout run settings and reaction lists as read only but has limited edit access to instrument functions An Operator has edit access to update the lab notebook set tip availability assign plate IDs barcodes and well IDs barcodes to sample reaction wells defined in the run and to modity the set of wells associated with sample banks used in the run An Operator cannot modity reaction properties Note All user groups can modify saved run files If required standard Windows file system write protection mechanisms may be used to protect run file data The software does not provide a log in facility Users must log in to gain access to Windows The software identifies users from this initial log in This user identification function is always active and the user identification is documented in all pre run and post run reports as well as in diagnostic
206. s If the name of the reagent used in the saved master mix setup is identical to reagents already set up these will automatically be allocated to those positions 5 80 QlAgility User Manual 01 2009 QIAgility Software 5 To reset the location of any reagent double click on a reagent in the list then left click and drag again Alternatively click on the Reset All button to clear all reagent locations other than those that were defined upon entering the screen 6 Click the Next button to continue Copying a master mix When a master mix has been setup using the right hand pane the master mix can be copied to a different well which also has Mix function To copy a master mix 1 Right click on a well which contains a master mix 2 The plate operations menu will appear Q 7 EZ Copy mix setup Set liquid level mode for segment gt D Toggle image ar Toggle zoom ARC ae Delete calibration data zt Change plate type ast Change accessory asc Change plate function um 3 Select Copy mix setup The Copy Mix Setup dialog box will open EE xi Setup OK Copy mix setup from Mix D well D M1 Active Cancel 4 The Into field lists wells which have Mix function Select the well into which the master mix will be copied 5 Click on the OK button The master mix will now be copied into the selected w
207. serial dilution trom the drop down menus 8 Click on the button to select the target reaction plate The Plate well Selector window will appear 9 Left click on a reaction plate to select it The Serial Dilution dialog box will re appear 5 108 QlAgility User Manual 01 2009 10 11 12 QIAgility Software Note If there is only one Reaction plate this plate will be selected by default To return to the Serial Dilution dialog box left click on the selected plate Define the options as required in the Special settings for Dilutions panel Define a series of dilution ratios To do this enter a ratio and then click on the Add button Repeat this for every dilution ratio of the series Note To remove a dilution left click on a copy in the Dilutions list and then click on the Remove button Click on the OK button to return to the main software window The dilutions will be added to the Reaction List Add sample bank normalization This function equalizes the concentrations of the wells of a sample bank by dilution with a specified diluent The normalized samples are prepared in separate reaction wells l AE E E Left click on a Reaction plate The Reaction right hand pane will appear Click on the Special button Select Add sample bank normalization The Sample Normalization dialog box will appear d
208. space 5 26 5 7 Managing users 5 30 5 7 1 Enable access control 5 32 5 7 2 Create user groups 5 32 5 7 3 Change current user 5 33 5 8 Manage calibration data 5 34 5 8 1 Save calibrations on setup disk 5 34 5 8 2 Load calibrations from setup disk 5 35 5 8 3 Delete multiple calibrations 5 36 Contents 2 QlAgility User Manual 01 2009 5 9 Configure run settings 3 9 1 3 92 5 9 3 5 9 4 279 5 9 6 3 9 7 5 9 8 29 9 5 9 10 Configure tip air intake Configure pipet speed Set master mix extra volume Set standard extra volume Set default file location Configure system color Adjust liquid level tracking options Set liquid level tracking error level Set tip usage options Configure multi eject options 5 10 Define worktable setup 5 10 1 5 10 2 Plate operations Setting tip availability 5 11 Managing samples Seck 5 12 View and edit information using the right hand pane 5 12 1 5 12 2 5 12 3 5 12 4 3 123 5 12 6 5 12 7 5 12 8 Managing sample banks Tip Standards Reagents Master Mix Samples Reactions Contents 5 36 5 37 5 38 5 39 5 40 5 41 5 41 5 44 5 45 5 46 5 48 5 50 5 50 9 5 7 5 59 5 59 5 64 5 64 5 65 5 70 5 72 5 82 5 85 Importing and exporting reaction and sample data 5 113 Progress report 5 13 Programming run tiles 5 13 1 913 2 5 13 3 5 13 4 9 1329 5 13 6 PCR Setup Wizard Optimisation Wizard Using Empty Project Example reactions Checking the
209. t Allows the user to enter and save comments with the acknowledgment of a service Acknowledge Confirms that the selected service has been Service completed Exit Closes the Service Register dialog box To acknowledge a service 1 Select the component that has been serviced 2 Enter your user name in the Acknowledged By field 3 If desired enter further details about the service in the Comment field QIAgility User Manual 01 2009 5 145 QlAgility Software 5 146 Click on the Acknowledge Service button 5 A message will appear which summarizes the service 7 acknowledgment gar 9 Service notification will be acknowledged as completed with the following details we J Item Pipettor Due Date 21 Oct 2009 04 40 45 Period between services 12M Last service date 21 Oct 2008 04 40 45 from Installation Operations between services 300000 Operations at last service 0 from Installation Current operations 366013 usage count exceeded Acknowledge Date 17 Nov 2008 03 10 50 Acknowledged By Ql gility User Saving this service acknowledgement resets any service alert notification associated with the Pipettor and restarts the service schedule for this item Do you wish to save this service acknowledgement Click on the Save button to save the service acknowledgment The service that has been acknowledged will now be colored black in the Service Register d
210. t a sample bank name Sample bank names must be unique within the run Existing Bank Select to modify an existing sample bank Current sample banks that are defined for the selected plate segment are listed Banks defined Lists all sample banks that are defined in the elsewhere run Tile Select all Selects all of the wells within the plate Clear all Deselects all of the wells within the plate Range of wells Select to define a consecutive range of wells Specify the First well and then specify the Number of wells QlAgility User Manual 01 2009 5 61 QlAgility Software 5 62 List of wells Bank wells Specify concentration range Apply filter to selected wells Add Selection and Close Delete Selection and Close Cancel More Less Lists the range of wells e g Al B1 that is selected This list is automatically updated when the well selection is changed In addition a list can be directly entered into this field to select wells A list can consist of more than one description e g Al B2 C2 C6 Click to view the existing wells in the sample bank Wells are highlighted red Select to define a concentration range for the filter Specify the Min Concentration Max Concentration and whether to use selected wells INSIDE or OUTSIDE the detined concentration range Adds or removes samples from a sample bank based on a defined concentration range The
211. t available tip size 200 pl ha The Reaction right hand pane will appear Click on the Special button Select Add serial dilution step The Serial Dilution dialog box will appear BH Serial Dilution x Defines the diluent to be used in the serial dilution This sample bank must contain only one sample serial dilution 01 2009 Defines the sample bank to be used in the 5 107 QlAgility Software First well Min volume Enable mixing during dilution Change tips after each dilution No of times to mix Ratio Add Remove Opens the Plate well Selector screen which enables the target reaction plate to be selected Defines the first well of the reaction plate into which the serial dilution will be targeted Defines the minimum total volume for each dilution in the series Instructs the instrument to mix during dilution Instructs the instrument to change tips after each dilution When selected a new tip is used for aliquoting each diluent volume and each dilution sample When not selected a single tip is used to aliquot diluent and a new tip is used to aliquot the dilution samples Defines the number of times to mix Defines the sample diluent ratio for a given dilution Adds a given dilution to the Dilutions list Removes a selected dilution from the Dilutions list 7 Select the diluent and the sample bank to be used in the
212. te If the plate height calibration is too high the tip height calibration cannot reach low enough into the tube to aspirate all the fluid Ensure that plate height calibration is correct Error messages recorded in post run report but the run was completed a Volumes of reagents If liquid was not detected an error is recorded in or samples below _ the post run report the minimum volume which is required for liquid level sensing function Add an extra 20 ul volume as required Alternatively dilute samples and reagents and pipet larger volumes rather than pipetting small volumes of concentrated solutions A non readable error message is received when the software is started Correct plate Uninstall and then reinstall the software See definitions not Section 5 1 installed 9 4 QlAgility User Manual 01 2009 Troubleshooting Comments and suggestions Software does not start and the A required library file is not correctly installed or registered error message is displayed Present version of Reinstall the most recent version of the QlAgility the software software conflicts with an older version of the software Software running incorrectly with a Software error aborting error message Communications Ensure that no other devices e g modems are channel to the attempting to use the same serial port as the instrument being instrument interrupted Alternatively contigure the instrument to us
213. ted during the final mixing when the mix count is greater than O A value of O indicates that the software should choose an appropriate recommended value 6 Select Tip Ejection Mode Multi pickup Re use tips or Use new tips 5 100 QlAgility User Manual 01 2009 QlAgility Software 10 11 16 17 It Re use tips or Use new tips were selected define the Premix count Click on the button to select the target reaction plate The Plate well Selector window will appear Left click on a reaction plate to select it The Sample Pooling dialog box will reappear Note If there is only one Reaction plate this plate will be selected by default Left click on the selected plate to return to the Sample Pooling dialog box Define the First well and the number of Replicates Select a sample bank to be pooled from the Sample bank drop down menu Define the Volume to be added and then click on the Add button When Multi pickup is selected it is recommended to select Air gap from the drop down menu in the Samples panel Define the Volume to be added and then click on the Add button Repeat steps 11 14 for the remaining sample banks that will be pooled Define the Mix count and the Mix volume Click on the OK button to return to the main software window The
214. ter mix by the QIAgility By default master mixes are located on the Master Mix Block but they can also be located on other plates Master mixes are set up using the Mix right hand pane To view the Mix right hand pane left click on any well with Mix function 5 72 QlAgility User Manual 01 2009 QlAgility Software Mix right hand pane Min Sehen Ues Mate Ma ke Lis Tee traced Mtb Mo m Mater Hir rares T i gt Pr tr msd Maer Mii Machine mised Mather Mis Configure Mater Mix respect names ond default wolumes bom reagent ciet Vol of Masten Mir per comple 2525 pl Total vol of Hate Moco mae Del funskquotted Total reactions to prepare if sech fo B Estia urn M aa bor confmation afte ading ee FF wa lor confirmation Ste Gelrereg fred mer F Ho of times to mor esch reagent F B Ho of times to mir gt end 5 Lood SEET Adust Insertion Order See Mo plaie 5 h e parles Heed hisk Hd D Hesper bioch Lola H Head Link slack D Use Master Select to set up a master mix Options in the Mix Machine mixed Master Mix panel will be enabled Use pre mixed Select to use a premade master mix Master Mix Options in the Pre mixed Master Mix panel will be enabled Master mix Defines the master mix name name Volume per Defines the volume of master mix per sample reaction No oftimes to Defines the number of times to mix before mix before use use
215. the case of a csv file In an Excel spreadsheet a column break would be inserted QlAgility User Manual 01 2009 5 123 QlAgility Software 5 12 8 Progress report When a run is in progress the status of the run is summarized in the right hand pane Progress Start time 1 03 PM Current time 1 04 PM Estimated time of completion 1 44 PM 40 minutes remaining r Tasks E Adding 903 5 pl Diluent to MM RAN BP2 COMPLETE Adding 130 ul PreMaster Mix to MM RAN BP2 COMPLETE Adding 26 pl dNTP s to MM RAN BP2 COMPLETE Adding 6 5 pl Enzyme to MM RAN BP2 COMPLETE Adding 52 pl Primer for RAN BP2 to MM RAN BP2 COMPLETE Adding 52 ul Primer rey RAN BP2 to MM RAN BP2 COMPLETE Adding 903 5 pl Diluent to MM GAPDH COMPLETE Adding 130 pl PreMaster Mix to MM GAPDH COMPLETE Adding 26 pl dNTPs to MM GAPDH ACTIVE Adding 6 5 pl Enzyme to MM GAPDH Adding 52 pl Primer for GAPDH to MM GAPDH Adding 52 wl Primer rev GAPDH to MM GAPDH Adding 903 5 pl Diluent to MM TAF II 100 Adding 130 pl PreMaster Mix to MM TAF II 100 Adding 26 pl dNTP s to MM TAF II 100 Adding 6 5 pl Enzyme to MM TAF II 100 Adding 52 pl Primer for TAF II 100 to MM TAF II 100 Adding 52 ul Priomer rev TAF II 100 to MM TAF II 100 Adding 903 5 pl Diluent to MM Alpha Catenin Adding 130 pl PreMaster Mix to MM Alpha Catenin Soleo AE cif o habs nb 5 13 Programming run files 5 13 1 PCR Setup Wizard The PCR Setup Wizard enables
216. ther sample name or sample ID Custom A csv text file with comma separators comma between columns The data can be user separated defined Custom tab A txt file with tab separation between separated columns The data can be user defined Export directly Creates an xls spreadsheet file and if Excel into Excel 97 or is installed on the computer automatically later launches Excel with the imported data The data can be user defined Tube Map CSV A csv file with format fixed as well file location plate identifier sample identifier using the substitution pattern 2 0 P 0 l as described in Data fields in this section This describes the mapping of a tube well location plate and well label to its contents sample identification Roche MagNA A csv file with format fixed as the single Pure LC column sample identifier using the copy paste substitution pattern l as described below import file This describes the contents of each well to facilitate export to the Roche MagNA Pure LC instrument QlAgility User Manual 01 2009 5 119 QlAgility Software 5 120 Rotor Gene Q A smp sample file which is compatible v1 x 6000 v1 x with the Rotor Gene Q Rotor Gene 6000 amp 3000 v6 x AB17000 750 0 SDS absolute quantification AB17000 750 O SDS allelic discrimination QIAxcel Sample Into Text File 8x12 well grid and late revisions of the Rotor Gene 3000 software The d
217. those positions To reset the location of any reagent double click on a reagent in the list then left click and drag again Alternatively click on the Reset All button to clear all reagent locations other than those that were defined upon entering the screen Click on the Next button If only one reagent will be optimized i e if option was selected in step 3 proceed to step 15 If more than one reagent will be optimized i e option 2 or 3 was selected in step 3 repeat steps 7 13 and then proceed to step 15 l n 5 136 QlAgility User Manual 01 2009 QIAgility Software 15 The Optimisation Wizard Replicates dialog box will appear BE Uptimization Wizard Heplicates themen Speoly lhe number of represes Select Um mase ma pou would lve lu ure Select lha Tagal plate you proud Kelte vplumraleen lo vocu m Cisk Her bo CPL Opler How mary eck aie would you ike lo pioduce hb 5 weli required Masher mis Target plate How many replicates would you like to produce Master mix Create Premixed MM Target plate DS Crese Fremiend MM EE wen plans vertical D2 Ed FF Clear airing eactons Back Hent Defines the number of replicates for each reaction Defines the master mix to be used Opens the Plate well Selector wi
218. tic tools 9 10 9 4 1 Mechanical tests 9 11 9 4 2 Electrical tests 9 12 10 Glossary 10 1 Appendix A A 1 Technical data A 1 Environmental conditions A 1 Waste Electrical and Electronic Equipment WEEE A 3 FCC declaration A 4 Declaration of contormity A 5 Appendix B B 1 ABI 7000 7500 SDS master mix naming conventions B 1 Appendix C C 1 Advanced Settings C Appendix D D 1 Liability clause D 1 QlAgility User Manual 01 2009 Contents 5 Contents Index Index 1 Contents 6 QlAgility User Manual 01 2009 Safety Information 1 Safety Information Before using the QlAgility it is essential that you read this user manual carefully and pay particular attention to the safety information The instructions and safety information in the user manual must be followed to ensure safe operation of the instrument and to maintain the instrument in a safe condition The following types of safety information appear throughout this manual WARNING The term WARNING is used to inform you about situations that could result in personal injury to you or other Details about these circumstances are given in a box like this one CAUTION The term CAUTION is used to inform you about situations that could result in damage to the instrument or other A equipment Details about these circumstances are given in a box like this one The advice given in this manual is intended to supplement not supersede the normal safety requirements prevailing
219. tion Preparing a master mix for reaction setup 1 Left click on the well in the Master Mix Block that will contain the master mix The Mix right hand pane will appear Select Use Master Mix Enter a name for the master mix in the Master Mix name field Define the No of times to mix each reagent and the No of times to mix at end It desired select Wait for confirmation after adding final ingredient and Wait for confirmation after performing final mix These options are useful if extra reagents need to be manually added to the master mix or if the master mix needs to be vortexed Click on the Configure Mix button The Master Mix Component Selection window will appear Enter the master mix volume per reaction Enter the default sample volume The total reaction volume will then be calculated and displayed The total reaction volume cannot be edited Reagents are listed in the Component volumes panel To add reagents left click in a cell in the Use column then check the box to select Yes and then click on the OK tab Alternatively click on the Use all or Use none buttons to select all of the reagents or to deselect all of the reagents The default volumes in the Vol per Reaction column are the volumes that have been defined in the Reagent right hand pane To change these volumes left click on the corresponding c
220. tion settings and to replace the current default calibration settings with previously saved calibration settings 1 Select Option 2 from the Volume Calibration dialog box 2 The Volume Calibration Wizard History of Calibration Data dialog box will open 3 Proceed as for steps 8 12 of Option 1 Option 3 Use Option 3 to reset the volume calibration to the factory default calibration settings Current calibrations are automatically saved in the volume calibration history 1 Select Option 3 from the Volume Calibration dialog box QIAgility User Manual 01 2009 7 17 Instrument Setup and Calibration 2 The following message will appear CS ld 2 Reset volume calibration to Factory defaults Col e 3 Click on the Yes button 4 Click on the Cancel button in the Volume Calibration dialog box The volume calibrations will now be updated with the tactory detault calibration settings 7 18 QlAgility User Manual 01 2009 Maintenance Procedures WARNING A Maintenance Procedures The following maintenance procedures must be carried out to ensure reliable operation of the QlAgility E Cleaning the QlAgility E Minor corrective maintenance Following these procedures ensures that the QlAgility is free of dust and liquid spills Important Switch the instrument off and disconnect the line power cord from the power outlet before servicing Risk of electri
221. tip LAGE AX Tip riet Conductive tip OLAGERG e Mi Ser Lane ed D s DH Sample Mipi PCR puter Gemeri BE Tip ipl Conductive tip GOGEN HI Reagent eck e CH Sample ORs PCR ube Generis CE ferien Ciel PCR tube Generis ee ee ee ee Sa 8 Cancel Left click on a reaction plate to select it The Reaction Configuration dialog box will reappear Note If there is only one Reaction plate this plate will be selected by default To return to the Reaction Configuration dialog box left click on the selected plate Define the options in the Volume Target wells Mix Settings and Normalize samples panels as required Click on the OK button to return to the main software window Note See Section 5 13 5 for details about how to check the reaction setup 5 94 QlAgility User Manual 01 2009 QIAgility Software Using Special options in the reaction setup A number of Special options are available from the Reaction right hand pane To view these options left click on the Special button Note It is recommended that reactions that include Special options are simulated in Virtual Mode betore starting an actual run Reaction Plate ID INTE Wel Tal d cu an l Add pause 30 sec Add pause arbitrary Add reset eject position Add pause until confirmation Add Fan on Add Fan off Add sample bank
222. to adjust the order that reagents will be inserted into the Master Mix 20 ul Diluent 2 5 wl 10 Buffer 1 5 ul Mol 2 ul dNTP 5 78 QlAgility User Manual 01 2009 QIAgility Software Dn Moves the selected reagent down the list Up Moves the selected reagent up the list Close Closes the Master Mix Reagent Insertion Order dialog box 3 Left click on a reagent in the list Use the Dn and Up buttons to adjust the order of the reagents 4 Click on the Close button Preparing master mix without reaction setup Master mixes can be prepared without being assigned to a reaction To do this 1 Set up a master mix as described in the Preparing a master mix for reaction setup section 2 Define the total number of reactions to prepare using the Total reactions to prepare if unused option 3 If extra volume is required select Extra if unused Setting up a premade master mix 1 Left click on a well in the Master Mix Block The Mix right hand pane will appear 2 Select Use Master Mix and then select Use pre mixed Master Mix 3 Enter a name for the master mix in the Master Mix name field 4 Enter the Volume per sample and the Number of times to mix before use The corresponding well in the Master Mix Block will now be colored green Loading a saved master mix setup 1 Click on the Load button in the Machine mixed
223. to premix samples and then define taking sample the number of mixes This function instructs the instrument to mix each sample of the sample bank as it is aspirated for transfer to the reaction well Mixes and Defines the master mixes that will be added reagents in mix to the reaction All wells that have Mix wells function and that have been assigned a per reaction volume will be listed Selected master mixes will be added to the reaction Unmixed Defines the unmixed reagents that will be reagents added to the reaction All named reagents which have been assigned a per reaction volume will be listed Selected reagents will be added to the reaction QIAgility User Manual 01 2009 5 91 QlAgility Software Target reaction plate Sample volume Total volume Replicates Number of wells Alternate sample wells with water Preserve source well indices 5 92 Click on the button to open the Plate well Selector screen This screen allows the user to select the target reaction plate and well When Use normalization is selected this option defines the target volume for normalized samples in the reactions Defines the per reaction total volume The Total volume is automatically calculated based on the sample reagent and master mix volumes Defines the number of replicates to be performed for each sample bank Defines the total number of wells This number is automatic
224. ts the software to prepare a copy of the normalized samples in a second target plate Defines the first well of the secondary target plate into which the first normalized sample will be pipetted Specities the volume of normalized samples to be prepared in the secondary target plate Specifies that the tip used to pipet diluent will also be used to pipet source sample The tip will collect diluent then sample and will then eject the liquid into the target well QlAgility User Manual 01 2009 QIAgility Software Auto adjust Instructs the instrument to round up sample small volumes volumes that are less than the minimum to enable robot volume that can be pipetted i e 1 ul to to move liquid the minimum volume i e 1 ul In cases where the operation requires less than the pipettable volume of diluent no diluent is transferred only sample is moved In all such cases the final volume is preserved but the desired final concentration is not achieved 6 Select the diluent and the sample bank which will be used for the sample normalization from the drop down menus 7 Click on the button to select the target reaction plate The Plate well Selector window will appear 8 Left click on a reaction plate to select it The Sample Normalization dialog box will reappear Note If there is only one Reaction plate this plate will be selected by default To return to the Sample Normalization dialog b
225. tting head is highlighted on the software worktable QlAgility User Manual 01 2009 Glossary Term Description Standard A standard is a dilution series with known concentrations Standards are treated like samples Virtual Mode Virtual Mode enables run files to be developed and simulated without actually performing the pipetting operations on the instrument This is particularly useful for checking new run files In Virtual Mode all software functions are enabled Worktable The instrument worktable supports tips racks plates tubes the Master Mix Block and the Reagent Block QlAgility User Manual 01 2009 10 3 Glossary This page left intentionally blank 10 4 QlAgility User Manual 01 2009 Appendix A Appendix A Technical data QIAGEN reserves the right to change specifications at any time Environmental conditions Operating conditions Power 100 240 V 250 VA 50 60 Hz 5 A fuse Overvoltage Il category Air temperature 15 35 C 59 95 F Relative humidity 40 70 Altitude Up to 2000 m 6500 ft Place of For indoor use only operation Pollution level 2 Environmental 3K2 IEC 60721 3 3 class Transportation conditions Air temperature 25 C to 60 C 13 F to 140 F in manufacturer s package Relative humidity Max 75 noncondensing Storage conditions Air temperature 15 C to 30 C 59 F to 86 F in manufacturer s package Relative humidity Max 75 nonconde
226. tware Page Option Determines how the reaction data is to be grouped for analysis purposes after import into the Rotor Gene software Empty Label Determines how unpopulated reaction wells are named during export to the QlAxcel Sample Import Text file format Sample Label Full ID Comprises the identifier of the reaction well Reaction ID and all identifiers of contained samples Sample ID Sample ID A list of sample identifiers present in the reaction well Reaction ID The user assigned label associated with the reaction well Sample Name A list of sample names present in the reaction well Concentration Option Sample Source Uses the initial concentration value This is associated with the source sample or standard well Final Reaction Uses the final concentration value of the sample or standard after dilution with other ingredients This is associated with the reaction well QlAgility User Manual 01 2009 5 121 QlAgility Software 5 122 Page Option Master Mix Reaction ID Both None Empty Label None Label Label Number Well Number 5 Click on the Reactions are segregated according to the master mix present in the well with one page created for and named after each master mix Reactions are segregated according to the reaction ID user assigned label associated with the well with 1 page created for and named after each reaction ID Reactions are segre
227. ty must be set for every plate which has Tip function This enables the software to determine exactly where tips are available on the instrument worktable If this information is incorrect the run will not proceed correctly because the instrument may attempt to pick up a tip from a location where no tip is available To change tip availability 1 Left click on a plate that has Tip function to select all the tips within that plate Alternatively to select a group QlAgility User Manual 01 2009 5 57 QlAgility Software of tips left click on the plate and then drag Selected tips will be highlighted red Note To select individual tips left click on an individual tip and proceed as for a group or use the tip availability short cut Tip availability Hold down Alt and left click on individual short cut tips to switch the tip between available and unavailable 2 Right click on the plate Tip availability options will appear in the upper panel of the plate operations menu PEN 1 2 Set selected tips to Available Set selected tips to Unavailable vu Seb all tips on current plate to Awailable nu Set all tips on current plate to Unavailable Set all tips on all plates to Available Set all tips on all plates to Unavailable Toggle Image Toggle Zoom Delete Calibration Data Change plate type Change accessory Change plate Function Set selected Sets a group
228. ual 01 2009 9 75 QlAgility Software Default sample volume for this mix How much reagent to manually insert per reaction Default reaction volume Pause robot to manually load reagents after final ingredient added Additional ingredients are preloaded before the run Use all Use None Plate Tube Location Name 5 76 Defines the default sample volume for this mix Defines the volume of reagent that will be manually inserted into each reaction Defines the default reaction volume Instructs the instrument to pause after the final component of the master mix has been added This allows the user time to manually add more reagents to the master mix Defines whether additional reagents are added to the master mix before starting the run file Selects all of the reagents for use in the master mix All cells in the Use column will be populated with Yes Deselects all of the reagents for use in the master mix All cells in the Use column will be populated with No Defines the plate type that the reagent is located in Defines the tube type that the reagent is located in Defines the location of the reagent on the plate Defines the name of the reagent QlAgility User Manual 01 2009 QlAgility Software Use Defines whether the reagent will be used in the master mix Vol per Defines the volume of reagent that will be Reaction used in each reac
229. uired Min Defines the minimum concentration of the Concentration concentration range Max Defines the maximum concentration of the Concentration concentration rage Use selected Instructs the software to import data which wells INSIDE is within the defined concentration range range Use selected Instructs the software to import data which wells OUTSIDE is outside the defined concentration range range 10 The Import Preview panel displays the samples to be imported Click the Import button to import the data The imported data will be displayed in the right hand pane Note No data is imported from a row in which all fields are empty Note Existing data will be overwritten by any imported data that is located in the same well Note Multiple sample banks can be successively populated from the same import file To do this arrange the import file so that it has a column representing each sample bank Populate the rows in each column with a concentration value e g 0 to indicate membership of that sample in that bank Set the Row Filter to include rows with concentrations in the range 0 0 Set the Load Conc trom column and Sample Bank Name Click on the Import button Repeat for each sample bank column in the file Exporting sample and reaction data Sample and reaction data which is listed in the Sample and Reaction right hand pane can be exported in a number of formats T
230. utlines the Optimisation Wizard screens that will guide the user through the setup Instructions are displayed on each screen Note The Optimisation Wizard only provides steps to set Up an optimized matrix it does not provide steps for preparation of a master mix To set up a PCR reaction using the Optimisation Wizard 1 Select Wizard Optimisation Wizard or select Optimisation Wizard trom the splash screen that appears when the software is started 2 The Optimisation Wizard will appear QIAgility User Manual 01 2009 5 133 QlAgility Software 3 Select option 1 2 or 3 These options define the number of variables to be optimized 4 Click on the Next button to continue Reagent name Defines the name of the reagent 5 134 QlAgility User Manual 01 2009 QIAgility Software How much of this reagent would you like to use in the final reaction How many different concentrations would you like to use Set Locations Defines the volume of reagent to be used in the reaction Defines the number of different concentrations of reagent to be optimized Opens the Reagent selector window which enables selection of the location of reagents on the software worktable 5 Define the reagent name Define the volume of reagent to use in the final reaction 7 Define the number of different concentrations to use The number
231. ve the tip ejector location Cancel 20 Click on the OK button to save the tip ejector calibration 7 1 2 Calibrate plate positions Before using a plate on the worktable a position calibration must be performed Plate position calibrations can be saved and reused Important Tip Rack Holder calibrations must be performed before any other plate type can be calibrated Caution The Y arm will move during position calibration when the hood is raised Do not click on any software buttons while parts of your body are within the instrument worktable Before starting the procedure M Open the instrument hood 7 4 QlAgility User Manual 01 2009 Instrument Setup and Calibration M Place plates to be calibrated onto the worktable M Ensure that 200 ul tips are available in at least one Tip Rack Holder 1 Select Options Robot Setup Calibrate plate positions 2 The Set Alignment dialog box will appear Plate S lection C sr ral sm the Geeite boliji the PED wett Dore cat aA not che vertu GAS not calbeshed At Tip ul Conhictive CHA GLHR ni cabane O Enada Sch 7 eu u HE d Flac eeu HEDE Dono oe oo ooo Oo oo Coto oo oOo oc oo Oo Coto oo oo Dono od occ Oo oo dodo dodo occ o oo Coco oo oD 6 0 6 og Dono oo oo Plane Dig E mezani P D Este Touran or FE tete ante see u Dre Plate Selection Lists the plates that are located on the instrument worktable X positi
232. window to view information relating to plate function in the right hand pane A plate segment or well can have 1 of 7 functions Tip Standard Reagent Mix Sample Reaction or Diluent All functions except Diluent have an associated right hand pane See Sections 5 11 1 5 11 6 for more detailed information about these right hand panes When a run is in progress a progress report is displayed in the right hand pane See Section 5 12 8 Tip Tip availability is updated in real time while the software is operating and is recorded when software is shut down Tip availability should therefore be correct when the software is restarted However correct tip availability should always be checked before starting a run Two tip types can be used with the QlAgility 50 ul and 200 ul In the software worktable 50 ul tips are colored blue and 200 ul tips are colored red To view information about current tip availability tip requirements tip location and tip type left click on a plate with Tip function in the software worktable The Tip right hand pane will appear QlAgility User Manual 01 2009 QIAgility Software Tip right hand pane 5 12 2 Standards Standard dilutions can be prepared using the QlAgility or a premade dilution series can be used The default location for standards is at the left of the Reagent Block There may be more than one loc
233. wledged service alert notifications the icon in the toolbar is marked with a red exclamation mark Service alert notifications can be acknowledged by an operator using the Service Register dialog box To view the Service Register dialog box 1 Select Options Robot Setup Service register 2 The Service Register dialog box will appear 3 The component that requires a service most urgently will be preselected i e Pippettor or Hepa Filter Components that are colored red are due for a service and components that are colored green are due for a service at a future date 5 144 QlAgility User Manual 01 2009 QIAgility Software ur Service Register Item DueDate 21 Oct 2009 04 40 Hepa Filter Component Fipettor Due Date 21 Oct 2009 04 40 45 Reason Period between services 12M Last service date 21 Oct 2008 04 40 45 from Installation Operations between services 300000 Operations at last service 0 from Installation Current operations 366013 usage count exceeded Acknowledge Date fi 7 Nov 2008 02 53 35 Acknowledged By al cilty User Comment A H Acknowledge Service Exit Component Defines the selected component to be serviced Pipettor or Hepa Filter Due Date Defines the date that a service is required Acknowledg Displays the current date and time ment Date Acknowledged Displays the current user name by Commen
234. xtra per tip for Multi Eject Remove NOTES Total Sample volume required 0 pl Maximum total sample volume per tip 198 pl 200 pl Tip 2 pl Extra Volume Tips Required none Largest available tip size 200 pl IMPOSSIBLE OPERATION Multi eject Multi Eject Settings Re use tips Use new tips Sample bank 5 102 Instructs the instrument to use a single tip per sample to aspirate the total volume and to multi eject all duplications Opens the MULTI EJECT dialog box which enables configuration of multi eject options See Section 5 9 10 for more details about how to configure these options Instructs the instrument to use a single tip per sample to aspirate and eject each duplication volume separately Instructs the instrument to use a new tip for each sample and each duplication volume Defines the sample bank to be copied Opens the Plate well Selector screen which enables the target reaction plate to be selected QlAgility User Manual 01 2009 QIAgility Software First well Defines the first well of the reaction plate into which the sample bank will be copied Volume Defines the volume of the sample bank that will be taken Add Adds the duplication step to the Reaction plates list Remove Removes a duplication step trom the Reaction plates list Reaction plates Lists the duplication steps Total volume Defines the total volume which includes an extra
235. y User Manual 01 2009 General Description H X axis Worktable D Y axis D Master Mix Block Z axis H Reagent Block Pipetting head cover D Tip Rack Holders and tips DH Pipetting head D Y arm DH Pipetting hub H Tip ejector X axis The X axis directs the left right movement of the pipetting head Y axis The Y axis directs the forwards backwards movement of the pipetting head Z axis The Z axis directs the upwards downwards movement of the pipetting head Tip ejector The tip ejector facilitates tip removal from the pipetting head QlAgility User Manual 01 2009 3 5 General Description Pipetting head cover and pipetting head The pipetting head is located under the protective pipetting head cover The pipetting head consists of a motor driven backlash compensated pipetting mechanism This mechanism is similar to most hand pipets The pipetting head can be dismantled for servicing Y arm The Y arm supports the pipetting head Under no circumstances should the user apply force to the Y arm This may misalign the Y arm and cause pipetting errors Worktable The worktable has 6 SBS positions 127 76 x 85 48 mm in which Tip Rack Holders and plates are located In addition the worktable supports the Master Mix Block and Reagent Block The silver paint is epoxy paint which is hard wearing and UV resistant Master Mix Block The master mix block is intended to hold diluent and master mix on the worktable The QlA
236. y static electricity Recommended settings cause the pipettor to probe the surtace at least twice looking for successive level detections which are within a small tolerance before proceeding with dispensing QlAgility User Manual 01 2009 C 5 Appendix C This page left intentionally blank C 6 QlAgility User Manual 01 2009 Appendix D Appendix D Liability clause QIAGEN shall be released from all obligations under its warranty in the event repairs or modifications are made by persons other than its own personnel except in cases where the Company has given its written consent to perform such repairs or modifications All materials replaced under this warranty will be warranted only for the duration of the original warranty period and in no case beyond the original expiration date of original warranty unless authorized in writing by an officer of the Company Read out devices interfacing devices and associated software will be warranted only for the period offered by the original manufacturer of these products Representations and warranties made by any person including representatives of QIAGEN which are inconsistent or in conflict with the conditions in this warranty shall not be binding upon the Company unless produced in writing and approved by an officer of QIAGEN QlAgility User Manual 01 2009 D 1 Appendix D This page left intentionally blank D 2 QlAgility User Manual 01 2009 Index Index A
237. ype in this section Opens the Select Accessory dialog box which enables addition or removal of a special accessory trom the worktable See Adding removing an accessory in this section Enables the plate function to be changed A tick will appear next to the plate function that has been selected See Changing the plate function in this section 5 51 QlAgility Software Plate configuration dialog box BF Plate Configuration Select Plate Type Reagent Blocks D Hate Select the item that most closely matches the plate to be used 16 x Generic 1 5ml Tapered 8 x Generic 2ml Free Standing Tube 16 x Generic 200ul 16 x Generic 1 5ml Tapered Tubes 16 x Generic 200ul 16 x Generic 2ml Free Standing Tubes 16 x Generic 200yl 4 x Axygen 1 5ml Free Standing 2 x 500p Int 16 x Generic 200ul 4 x Axygen 1 5ml Free Standing 4 x 500yl Int 16 x Generic 200yl 4 x Generic 2ml Free Standing 4 x 500yl Inte 16 x Generic 200yl 8 x 500yl Internal Vial Free Standing 8 x Ger 16 x Generic 200ul 8 x Axygen 1 5ml Free Standing 8 x Generic 16 x Generic 200yl 8 x Axygen 2ml Free Standing 8 x Generic 1 16 x Generic 200p1 8 x Generic 2ml Free Standing 8 x Generic 1 16 x Generic 200yul 8 x Various Custom 2ml Free Standing 8 x Ge 16 x GIAGEN 200yl 4 x GIAGEN 2ml Free Standing 4 x QIAGEN 16 x QIAGEN 200ul 8 x QIAGEN 2ml Free Standing 8 x QIAGEN 16 x QIAGEN 200ul 8 x QIAGEN 2ml Free Standing 8 x GIAGER 16 x QIAGE

User Manual - The University of Sydney

Contents

Download Pdf Manuals

Related Search

Related Contents