ArrayPrep Target Preparation System
Contents
1. A Understanding the Protocol Screen 1 Start the ArrayPrep software by clicking the desktop icon or selecting the program from the Start Menu Program Files SciGene ArrayPrep 2 From the main screen click File Run Protocol and select the sample protocol titled QuickTest Desktop ArrayPrep_ Protocols folder Fig V A 1 See Table 2 for details on fields and descriptions in the Run Protocol screen s2 E Diagnostics DiagnosticRun2 i o x 1 DIAGNOSTIC RUN A Deck Layout 2 Lood Tos Pite 51 Corn Path and Filename Eee 1 3 Aspirate Plate 6 Column 1 Vol200 Gul 0 55mm from wel bottom 100 Singe Sod 0 Gul Ar Gap 50 Qul Overif k 4 Dispense Plate 11 Column 12 Vol200 0uL 1 0mm from wel bottom 100 Syringe Sod tips250ul os50ul 5 Mx Plate 211 Column 12 Vol30uL 3 Cycles Imm from well bottom 100 Syringe Sod 0 Qul Ar Gap f 7 p 6 Rect Tips Plate 216 Column 1 18 19 2 8 Load Tips Plate 1 Cokmn 12 3 pass pass pcr 9 je Plate amp 7 Column 7 Vol250 Qul 0 55mm from well bottom 100 Syange Sod 0 Gul Ar Gap on 10 Dispense Plate 11 Column 1 Vol250 Gul 1 0mm from well bottom 100 Synnge Spd 11 ect Tips Plate 16 Colunn2 12 n 1 13 Load Tips Plate 2 Column 5 6 3 9 0 14 Aspirate Plate 17 Column Vol3 Qul 0 2mm from wel bottom 100 Syringe Sod 1 0uL Ar Gap none 1 none bott agbead 15 Dispense Plate 414 Column 12 Vol3ul_ 0 Jam from well bottom 100 Syring2. 5 501 23 623 Fig III G 1 Motion Pendant screen If any status bars appear yellow or red the robot is not ready Determine the robot s state by reading the text within the bars For example if the robot is still homing one of the status bars will be yellow and display the message Robot Homing See Table 1 for details Table 1 Robot Status Messages Status Bar Color Action Needed Connection red Ensure main instrument power is ON Check connections on right side of instrument Verify robot is properly connected via the Ethernet cable to the laptop Click the Connect Robot button on the Motion Pendant screen Wait one minute to allow robot to finish homing Click the Home Robot button on the Motion Pendant screen Wait one minute to allow robot to power up red Check Emergency Stop switch and power connection to robot If needed click the High Power Enable button on the Motion Pendant screen Nia red If robot does not operate contact SciGene Technical Service at 408 733 7337 or techserv scigene com or your local distributor 5 Test Robot X Y Z and Pipetting Head Motion On the Motion Pendant screen click the buttons one at a time to verify movement e X RIGHT e Z UP e SYRINGES DOWN e X LEFT e Z DN e Y OUT e Y IN e SYRINGES UP Version 1 4 August 2012 11 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL For example clicking on the largest X R
3. Aspirate command For example if previous Aspirate command was from Column 1 a 2 will be placed in the Column of the current menu M Single Tip Mode Displays Row for aspirating with Pipetting Head See Fig V E 1 for details Row Row of plate Single Tip Mode Dispense Deck position of plate for dispensing Column on plate for dispensing Dispense Volume uL Volume in microliters to be dispensed into plate per well Distance from Bottom of Distance from the end of the pipette tips to the bottom of the wells in Well mm millimeters Syringe Speed of Max Speed of Pipetting Head plungers as a percentage of the maximum speed MiNext Column Increments Column one to the right from previous Dispense command For example if previous Dispense command was from Column 1 a 2 will be placed in the Column of current menu M Single Tip Mode Displays Row for dispensing with Pipetting Head See Fig V E 1 for details Row of plate Well mm wells in millimeters during an Empty command Syringe Speed of Max Speed of Pipetting Head plungers as a percentage of the maximum speed MINext Column Increments Column one to the right from previous Empty command For example if previous Empty command was from Column 1 a 2 will be placed in the Column of current menu M Single Tip Mode Adds Row parameter for emptying with Pipetting Head R
4. HIGH the ArrayPrep contains unshielded high voltage VOLTAGE pins components and surfaces Version 1 4 August 2012 3 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL DANGER High Voltage This instrument should be serviced by trained Do NOT attempt personnel only Please contact SciGene or your to service this a gt inetrimnent local Distributor for all service related matters See instrument user guide for further instructions HAZARDOUS Do not use in vicinity of VOLTAGE flammable or combustible Disconnect power materials before servicing Fire or explosion may result This symbol indicates the potential for a Hand Crush Do not place hands or arms under the guard while a protocol is running This symbol indicates the potential presence of a Hot Surface Use care when working in this area to avoid being burned Version 1 4 August 2012 4 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL ll SITE PREPARATION The ArrayPrep System requires a flat level surface of at least 48 inches wide by 23 inches deep 122 x 58 cm with vertical clearance of 32 inches 81 cm Locate the left side of the instrument within 6 feet 2 meters of a single power outlet that delivers 115V 230V with at least 920 Watts of constant power Avoid circuits with multiple pieces of equipment connected partic
5. III E 7 Version 1 4 August 2012 8 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL Assembling the Safety Guard Fig IIl E 3 Place washers on Fig IIl E 4 Remove screws from the top the outside of the Side Guard right and bottom left of the robot s left side Fig IIl E 5 Attach the Side Guard Fig IIl E 6 Attach a Corner to the left side of the robot Bracket to each Side Guard Fig IIl E 7 Attach the Front Guard to each Corner Bracket Version 1 4 August 2012 9 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL F Computer and Power Connections 1 Connect the Ethernet cable and Emergency Stop Switch to the instrument as shown in Fig IIl F 1 Ensure the power connection from the instrument base to the robot is secure Be certain that the Emergency Stop Switch is easily accessible and that all personnel using the instrument are aware of its location and function d a X Ethernet Cable Emergency Stop Switch Cable j L Robot Power Cord Fig IIl F 1 Connect cables to robot Fig IIl F 2 Connect cables to laptop 2 Connect the other end of the Ethernet cable and the power supply to the laptop Fig III F 2 and then connect the power supply to a wall outlet 3 Connect the base unit power cord to the left side of instrument Fig III F 3 and to a wall socket with app
6. right side of the Create Protocol screen for accuracy If the worktable is incorrect click the Edit button to make changes If correct continue to step 4 4 On the Create Protocol screen select commands for the robot to perform from the buttons at top right Refer to Table 4 for descriptions of command functions and to Table 5 for selectable parameters of the command functions For each command parameter created a line of script is generated and appears on the left side of the screen 5 To save the file click the Save button at any time A dialog box will open for creating or selecting a filename 6 To edit steps within a protocol use the Editing buttons on the far right of the Create Protocol screen See Table 6 for details of the editing commands and options available 7 Toinsert a step into an existing protocol first add the step at the end of the protocol and then move it to the correct position within the script Steps may be edited for changes to parameters but commands may not be changed To change a command delete the step and insert a new step 8 When finished click Save Table 4 Robot Commands Command Function Raises syringe plungers for aspirating liquid from plate into pipette tips Dispense Lowers syringe plungers for dispensing liquid from pipette tips into plate or tubes Eject Tips Ejects tips from Pipetting Head nozzles Pipetting Head lowers pipette tips into plate then aspirates amp dispenses E
7. would other types of Windows files The protocol and worktable files must have the same filename but with a pro extension for the protocol file and a wtb extension for the worktable file Both files must reside in the same directory for editing or running from the ArrayPrep software H Using the Emergency Stop Switch To immediately stop the instrument press the red Emergency Stop Switch connected by a cable to the instrument Fig V H 1 When pressed movement of the robot will stop however the three temperature controlled blocks will continue to receive power To restore power to the robot release the EMO button by rotating it a quarter turn clockwise The protocol will not resume upon releasing the EMO switch and must be restarted from the beginning Fig V H 1 Emergency Stop Switch Fig V H 2 Z Release Button I Using the Z Release Button The Z Release is a small red button on the back of the casing atop the Y axis that is not utilized during normal operation Fig V H 2 When the instrument is plugged in and powered on this button may be used by a Service Representative to manually move the Pipetting Head up or down to verify correct alignment Before pressing the Z Release button hold the Pipetting Head securely to prevent it from falling Never allow the head to fall onto the deck as damage will result This symbol indicates the potential for a Hand Crush Do not place hands or arms under the Safety Gua
8. 1 4 August 2012 24 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL Vil SPECIFICATIONS Table 9 ArrayPrep System Specifications Electrical Power supply 115V AC 50 60 Hz 920W 8 Amps cat 2000 00 1 230V AC 50 60 Hz 920W 4 Amps cat 2000 00 2 Processing Control Software controlled by external laptop Pipetting Range 1 to 250 uL Pipetting Precision 3 CV Temperature Control Range 4 to 99 C 41 to 194 F Blocks 17 18 19 Regulation 0 2 C from set point Environmental Ambient temperature Operation 15 to 32 C 58 to 90 F Storage 20 to 60 C 4 to 140 F Relative humidity Operation 20 to 80 RH non condensing Storage 10 to 90 RH non condensing Overvoltage category Il Physical Dimensions Instrument 35 x 48 x 26 5 inches 89 x 122 x 67 cm HxWxD Crate 36 x 53 x 33 inches 91 x 135 x 84cm Weight Net 77 kg 170 Ibs Gross 136 kg 300 Ibs in crate Dimensional 325 lbs 148 kg domestic 172 kg international Vill ORDERING INFORMATION Table 10 SciGene Ordering Information for ArrayPrep Reagents and Labware SciGene Cat Product Description 2000 80 0 Tip 250 ul 96 tips rack neal 2000 80 1 Tip 50 ul 96 tips rack 50 Case 2000 81 0 Incubation Plate 96 well 50 Case ze Version 1 4 August 2012 25 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL IX TROUBLESH
9. 5mm from well bottom 46 Gect Tips Plate 216 Cokenn4 il Reset Gripper Button En z Exit Protocol Script Button 50 0uL 0 55m trom well botom 100 Sytinge Sod 0 0ul Ar Gap 00 Syringe Sod Fig V A 1 Run Protocol screen Table 2 Fields in the Run Protocol Screen Field Description Pause Button After current protocol step completed moves Pipetting Head up and stops Button text changes to RESUME and color changes to green Clicking RESUME will start robot moving again at next step in protocol Ext Button Closes Run Protocol screen and displays Home screen after aborting or abnormally stopping protocol Version 1 4 August 2012 14 408 733 7337 techserv scigene com SC G e Nn e ArrayPrep Thermal Profiling System USER MANUAL B Running a Test Protocol 1 From the Run Protocol screen for the QuickTest protocol see section V A Understanding the Protocol Screen view the three status bars and verify that all are green If the bars are not green see Table 1 for instructions 2 Place labware on the deck as indicated by the Deck Layout on the Run Protocol screen 3 Pipette 5ml of water into column 1 of the VGroove Reservoir in position 9 4 Place the plastic tip bucket provided with the instrument on the bench adjacent to position 10 Used pipette tips will be ejected off the deck into the tip bucket AN Do not use Heated Lids while the robot is moving It may interfere with the movement of t
10. 7 REMOVING the Shipping Bracket cessioni a a E a i 8 Assembling the Safety Guard ssesnsssseensssererssssrrrrsssrrresssrrresssrerosserresssereesssrreeesssreresssreesreressererssseeeee 8 Computer and Power CONNECTIONS cccccccssseececseeessecccceeseccesaeueeceeseuussececssuaeeceessuaseceesauaseeeeeeeeeessages 10 Performing a System Check cissccscdensncoodessaicceacsuusaipedcvaseuaioadeasaaneacasadaleeddvausabetanesasaedondassiseaddeussedavsaabanaseeas 10 USING THE TEMPERATURE CONTROLLED BLOCKS sssssosssseossessossossossosesssosssssosseseossossossossossoseossoo 13 Setune BIOCk Temper IUOS ee ene ee ee er mee ee ee eee ee eee 13 eine Te QU GL IGG cas digth peer E E 13 OPERATION cicirine E ERa E 14 Understanding the Protocol SereEMssessrcsernidinrerniisodrodineni na inaa ERREA n E RR 14 Running a Test PrOTOCO scsi faiccicesegotsnecnctaseqedmnsaesurcaneefonsdiesaiseaevanetieedseietaboes ES ATES EEE iE 15 Running a Pre Installed Protocol ccccccsssssecsssssssecsssssssecuccssesssencesssscencosssssencesssssencesssssceesssensesssssens 16 creatine and Editing ProtOCOlS ceccoanurcosinainn ne E 16 eine Smee TIO MOUE sireni a E E A E ssgeurcoeesneucees 20 Using the Move Plate Command cccccssssseccccceseccecceeseccecceasecceeauaeececeeseaueceeesaueceessuaaeceessuaeesseeeeeeas 20 imporing a PLOTOCO sarunen aa EEE AAE SEEE A 21 Using the Emergency Stop SWItCH cccccsssscccccesseccccceseceececeeseccessaeeccesseu
11. IGHT button will move the robot 10 mm to the right 6 Test Plate Gripper On the Motion Pendant screen Fig III G 1 click the Activate Gripper button The Pipetting Head motor will activate and lower Gripper Fingers slightly a Click Gripper Down button a few times to verify Gripper Fingers are descending from inside the Pipetting Head b When finished click the De Activate Gripper button same as Activate Gripper button Version 1 4 August 2012 12 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL IV USING THE TEMPERATURE CONTROLLED BLOCKS This symbol indicates the potential presence of a Hot Surface Use care when working in this area to avoid being burned Deck positions 17 18 and 19 on the ArrayPrep System provide heating and cooling of 0 2 ml PCR plates and tubes Each block is individually controlled to provide a range of temperatures from 4 to 99 C 0 2 C The temperature controllers are calibrated at the factory to provide accurate plate temperatures Re calibration is required only if e When using a calibrated digital thermometer the block temperature differs by more than one degree 1 C from the actual temperature shown on the controller display See section VI D Calibration of the Temperature Controlled Blocks for details A Setting Block Temperatures Each block has a temperature controller with a dual LED display and four push buttons Th
12. OOTING Table 11 Troubleshooting the ArrayPrep System Indication Probable Cause Corrective Action Robot not responding A Ethernet cable is disconnected Check Ethernet cable connections B Power is turned off or power Check the main ON OFF switch power switches to cord is unplugged temperature controllers on deck position 17 19 and power cord from outlet to robot C Network settings in laptop On the laptop in Network Connections Local Area Connection Properties Internet Protocol TCP IP Properties enter Address 192 168 0 2 and Subnet Mask 255 255 255 0 disabled enabled up position power on and wait for robot to re home Manually move robot to middle position of X Y Z axes stop Click Home Robot on Run Protocol screen Robot stuck in down Robot is jammed in down position Activate emergency stop switch push down Hold up Z position and will not move causing power supply to cycle on off Axis amp Pipetting Head while simultaneously pushing Brake a protective feature Release button on back of Z Axis Caution Z Axis may drop suddenly when Brake Release button is pushed if not properly supported Tips Not Ejecting Calibration needs to be reset Contact SciGene Technical Service techserv scigene or Completely your local distributor for assistance loading tips your local distributor for assistance tips leak into tips calibration problem your local distributor for assistance Gripper stuck in down P
13. SC G e n e www scigene com ArrayPrep Target Preparation System USER MANUAL CAT 2000 00 1 115V 2000 00 2 230V FOR RESEARCH USE ONLY Not for Use in Diagnostic Procedures 470 Lakeside Dr Ste F Sunnyvale CA 94085 USA e Tel 408 733 7337 Fax 408 733 7336 techserv scigene com SC G e Nn e ArrayPrep Thermal Profiling System USER MANUAL Serial Number The following serial number identifies the specific instrument you have purchased and must be referenced when requesting service A copy is affixed to the instrument Technical Service 408 733 7337 techserv scigene com Warranty SciGene warrants that the ArrayPrep Target Preparation System described in this manual shall be free of defects in materials and workmanship for a period of 12 months from date of delivery This warranty does not cover removable parts or accessories In the event of a defect during the warranty period SciGene s limit of liability will be to provide repair service at its factory at no charge or at its sole discretion replace the product The foregoing warranty is void in the event the unit was abused or modified or used in a manner inconsistent with its intended purpose SciGene makes no other warranty expressed or implied including warranties of merchantability and fitness for a particular purpose In no event shall SciGene be liable for any direct indirect special incidental or consequential damages or for any damages resultin
14. SciGene Technical Services techserv scigene com or your local distributor for assistance DANGER 3 The motor power supply for the robot portion of HIGH the ArrayPrep System contains unshielded high VOLTAGE voltage pins components and surfaces DANGER High Voltage Do NOT attempt This instrument should be serviced by trained to service this personnel or only instrument See instrument user guide for further instructions A Lockout Procedure If a malfunction or need for service occurs comply with the following lockout procedure for restricting use of the instrument All users upon observing that the instrument is locked out for servicing or maintenance shall not attempt to start energize or use the equipment 1 Notify all affected users that servicing or maintenance is required and that the instrument must be shut down and locked out to perform the servicing or maintenance 2 Ifthe machine is operating shut it down by the normal stopping procedure turn off blocks and main power or press the EMO switch turn off laptop 3 Disconnect the power cords from the wall socket s and from the instrument and laptop so that all equipment is isolated from energy sources 4 Twist and remove the fuse Place in a locked safe Contact SciGene Technical Services techserv scigene com or your local distributor to arrange for service B Fuse Replacement The fuse may be replaced by turning off and unpluggin
15. another deck position e Pipetting Head raises up then moves to left side amp remains there for length of time specified Single Tip Mode Utilizes Pipetting Head Channel A for single tip operation Limited to certain deck positions See Fig V E 1 Lowers syringe plungers to bottom of syringes for dispensing all liquid inside tips Version 1 4 August 2012 17 408 733 7337 techserv scigene com SC e n e ArrayPrep Thermal Profiling System USER MANUAL Table 5 Protocol Commands Command Parameters Description Aspirate Plate Deck position of plate for aspirating Column on plate for aspirating Aspirate Volume uL Volume in microliters to be aspirated into tips per channel Distance from Bottom of Distance from the bottom of the pipette tips to the bottom of the wells in Well mm millimeters during an aspiration Syringe Speed of Max Speed of Pipetting Head plungers as a of the maximum speed Air Gap uL Air volume in microliters to be aspirated before placing the pipette tips into the wells of a plate for aspirating liquid Ensures all liquid dispenses from tips during an Empty command Overfill then Dispense back Additional liquid in microliters to be aspirated then immediately uL dispensed back into well Minimizes mechanical backlash of Pipetting Head system when transferring very small volumes MNext Column Increments Column one to the right from previous
16. ct Amount of Time for Time in minutes or USER PAUSE Selecting USER PAUSE will Pause minutes cause robot to pause until user clicks OK Table 6 Editing Commands Command Parameter Description Action Edit Step Step Number Number of step to be The drop down box will show the step numbers in edited the protocol To edit a step select the step number and click OK Make the necessary changes in the command dialog box that appears and click OK Move Step Move This Step Protocol step to be moved Select the step number to be moved in the Move This Step box and the destination step number in the To This Step box Click the OK button to re To This Step Destination step number in number the protocol protocol Delete Step Delete Step Number of the step to be Select the step number to be deleted Click the OK deleted button to re number the protocol Comment Comment Type in any text or a space Insert comments into a protocol or add a blank line for a blank line to divide sections of a protocol Version 1 4 August 2012 19 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL E Using Single Tip Mode Single Tip Mode uses the innermost channel Channel A of the 8 channel Pipetting Head for all liquid handling operations Fig V E 1 Single Tip mode is limited to deck positions 1 10 and 17 19 deck positions 11 16 are not compatible with Singl
17. e LED display shows the block temperature in red on the left and the set temperature in green on the right CALIBRATE To activate the controller Fig IV A 1 Set temperature 1 To use a temperature controlled block turn ON the power switch to the left of the controller 2 Set the desired block temperature by using the up and down arrows to change the SET temperature display Allow sufficient time for the block temperature to Stabilize before use 3 Turn the power switch OFF when not in use B Using Heated Lids These symbols on the Heated Lid alert the user that the lid must be removed prior to operating the robot and that the inner metal surface of the lid can get hot Always use the black handle to position or remove the Heated Lid To use the Heated Lid insert the gray plug into the receptacle marked Heated Lid on the Control Panel The arrow indicator lt gt on the plug should be facing up as it is inserted Use the black handle to position the Heated Lid over the Temperature Controlled Block To disconnect remove the plug by pulling straight back and use the black handle to lift the lid Fig IV B 1 Heated Lid connection Version 1 4 August 2012 13 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL V OPERATION Before performing any of the steps below ensure that your instrument has been calibrated by an authorized installation technician
18. e Sod om3 96 16 Gect Tips Plate 16 Coluenn3 7 1 4 15 1 18 Load Tips Plate 12 Column 12 19 Aspirate Plate 17 Column 12 Vol3 Gul 0 2nm from wel botom 100 Syringe Sod 1 Gul Ar Gap 1 20 Empty Plate 14 Column 0 3m from well bottom a eee pass a e250 21 Rect Tips Plate 216 Column 10 A 23 Load Tips Plate 12 Column 24 e Piste 18 Column VolS0 Qul 0 49 from well bottom 100 Singe Sod 0 Qul Ar Gap 25 Dispense Plate 19 Column 12 VolS0 QuL 0 3mm from well bottom 100 Syringe Sod 26 Gect Tips Plate 16 Column 11 27 28 Load Tips Plate 12 Column 12 23 Aspirate Plate 18 Column7 VolSO Qul 0 4mm from well bottom 100 Synge Spd 0 0ul Ar Gap Robot Status 309 0 Piate 19 Column 1 Vol50 0uL 0 3mm from wel bottom 100 Syringe Sod 31 Gect Tips Plate 216 Cohen 12 Robot Connected 32 33 Move Plate from 9 to 210 Gap Offset 0 Onm Orop Offset 1 mm Move Plate from 10 to 29 Gap Offset 0 Onm Orop Offset 0 Onm 38 Load Tips Plate 12 Coksmn2 39 Aspirate Plate 7 Cohumn3 VolS0 40 Dispense Plate 11 Column3 VolS0 Oul Jmm from well bottom 100 41 Gect Tins Plate 12 Coluenn2 42 Move Plate from 11 to 210 Gap Offset 0 Onm Drop Offset 1 Sim 43 Load Tos Plate 212 Coemn2 Robot Status Bars Roset Gripper e Pi 44 Aspirate Plate 10 Column3 Vol7QulL 5 2mm from wel bottom 100 Syringe Sod Sul Ar Gap 45 Emoty Plate 2715 Commn 1 1
19. e Tip Mode When operated in Single Tip Mode the operator can select both row and column for tip pick up and liquid handling Channel H 4 i Ry Channel a AL my Single Tip Mode Channels A and H of 8 channel Pipetting Head BO oa Single Tip Accessible Deck Locations i i m j Accessible Pipette Tip Accessing Wellplate S Not Accessible in Single Tip Mode Fig V E 1 Single Tip Mode Operation F Using the Move Plate Command The Move Plate command moves labware from one deck position to another using the integrated plate gripper as defined in the Worktable The pickup position is preset approximately 6 35 mm from the top edge of the defined labware The plate gripper releases the plate at a distance from the deck as specified in the Dropoff Offset From Deck parameter The default offset is 0 however there are conditions for which the user must define a specific offset for UBottom plates Table 7 Table 7 Worktable Offsets for UBottom Plates FROM Position TO Position Offset atop Temperature Controlled Bio ondeck eo if block was previously empty none in worktable Version 1 4 August 2012 20 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL G Importing a Protocol To import a protocol simply drag amp drop the protocol file _ pro and the worktable file _ wtb to the desired Windows directory as you
20. e com or your local distributor D Creating and Editing Protocols 1 Onthe ArrayPrep software menu bar click File New Protocol The Create Protocol screen will appear with a Worktable dialog box in the center showing all deck positions 1 19 Fig V D 1 Fig V D 1 Worktable dialog box in the Create Protocol screen 2 Choose specific labware for each deck position from the dropdown selections Deck positions without labware can be left blank or select none When finished click OK in the Worktable to close the dialog box and return to the Create Protocol screen Table 3 Labware Options for Creating Custom Protocols Labware Description Vendor Part deepwell_v_12 ArrayPrep Open Reagent Reservoir Deep well 2000 82 2 emptytiprack Empty 50uL or 250uL tip rack green or blue Pee Se magbead96 96 well Magnetic Ring Stand ABI AM10050 Includes height of ubottom96 plate on top MaiTai_4x44K Mai Tai base plate 1075 10 0 per96 o ArrayPrep PCR Incubation Plate 96 well 2000 81 0 Tall_PCR_96 96 Deep Well Plate conical bottom 500 ul E amp K Scientific 205096 tips250uL ArrayPrep Tip 250 ul blue rack 2000 80 0 tipsSOuL ArrayPrep Tip 50 ul green rack 2000 80 1 polystyrene U bottom ArrayPrep 12 Channel Reagent Reservoir V Groove Version 1 4 August 2012 16 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL 3 Review the deck layout shown on the
21. g from loss arising out of or in connection with the sale use or performance of the product Copyright Copyright 2010 2012 SciGene Corporation All rights reserved SciGene and ArrayPrep are trademarks of SciGene Corporation Sunnyvale California USA All other trademarks used in this manual are the property of their respective owners Intended Use The intended use of this instrument is for pipetting heating and cooling small volumes of liquid containing biological samples This instrument should only be used according to instructions provided in this User Manual and other SciGene technical documents If the equipment is used in a manner not specified by the manufacturer the protection provided by the equipment may be impaired Version 1 4 August 2012 1 408 733 7337 techserv scigene com A Aanmo9O w gt ey IT O nmu NWE VI xI SC G e Nn e ArrayPrep Thermal Profiling System USER MANUAL Table of Contents SAFETY NOTICES gaits seis nner oss occas sameeren mune cere naan E 3 FAS EY CN SS sererenao an ennn N EEEREN ENA EE ENARRARE AS 3 COSTES AIG Lane oe E EE A OT E ENA 3 SITE PREPARATION arrana a E E E E E E E E cecunecoseaneneraetaes 5 UNPACKING AND SETUP siisisin ea S 6 Uncratune and verifying Temenici pa e E E AEN 6 Identifying System Components ccccccccssssecccccesseccecceeseccecceeeccecseaaseeceeseaeeceeseaaeceessuaseeeesaaeeeseaeseeeeas 7 MOVING the INSUE aoran aE EE E E EEE EAEE TEA
22. g the unit then gently twisting and removing the old fuse Replace with a new fuse slow blow with the same electrical rating 250V 15A for 115V or 250V 8A for 230V Version 1 4 August 2012 27 408 733 7337 techserv scigene com SciGene XI DECLARATION OF CONFORMITY ArrayPrep Thermal Profiling System USER MANUAL ArrayPrep Target Preparation System SciGene 470F Lakeside Drive Sunnyvale CA 94085 USA Declares that the above referenced product s meets the essential requirements of the following European Union Directives by using the relevant standards shown below to indicate compliance EMC Directive 2004 108 EC EN 61326 1 EN 61000 4 2 EN 61000 4 3 EN 61000 4 4 EN 61000 4 6 LVD Directive 2006 95 EC EN 60204 1 2006 EN 61010 1 2004 2 Edition Terry Gill Name of Authorized Representative 2006 1995 2006 2004 2007 Electrical equipment for measurement control and laboratory use to include A1 1998 A2 2001 Electrical equipment of machines Safety requirements for measurement control and laboratory use Part 1 General requirements Sunnyvale California USA Place of Issue Director of Product Manufacturing June 17 2010 Title of Authorized Representative 1 PLM 4s Date of Issue Signature of Authorized Representative Version 1 4 August 2012 28 408 733 7337 techserv scigene com
23. he Pipetting Head AN Press the Emergency Stop Switch immediately to stop the instrument if a problem occurs 5 Click the Start button to begin the protocol The robot will move plungers up and down to reset the Plate Gripper 6 Verify that the instrument is performing all steps as indicated by the highlighted line in the Protocol Script area as expected e tips are loading and ejecting e the volume of liquid aspirated and dispensed is uniform between the tips e plates are being picked up and moved correctly 7 The protocol may be paused by clicking the Pause button or aborted by clicking the Abort button or Emergency Stop Switch If the Abort button or Emergency Stop Switch are used the protocol will not resume and must be restarted from the beginning 8 When the protocol is finished the robot will move up to the left and then stop The Run Protocol screen will display a Protocol Finished message box Click OK Version 1 4 August 2012 15 408 733 7337 techserv scigene com SC G e Nn e ArrayPrep Thermal Profiling System USER MANUAL C Running a Pre Installed Protocol The instrument comes configured with validated protocols for specific applications Refer to the ArrayPrep Method document for specific details on how to set up the instrument for a specific application Method sheets can be found online www scigene com support protocols html or can be requested from SciGene Customer Service custserv scigen
24. itch Underneath View a a Cooling Fan Air Intake Vent Pipetting Head Guard Rear Forced a Air Vents i Rear View Power Switch Power Cord Heated Lid es Deck Ethernet Cable Front View Emergency Stop Switch Cable F ual i Temperature Controller Power Switch Temperature Controller Front Forced Air Vents Heated Robot Power Cord Lid Jack Emergency Laptop Computer Stop Switch Temperature Calibration Jack Temperature Controlled Block Fig III B 1 Identification of System Components C Moving the Instrument The ArrayPrep System weighs approximately 170 Ibs 77 kg Never attempt to lift or move the instrument alone Use caution when lifting the unit to protect yourself and others from personal injury Do not lift the unit by the blue robot Always grip the instrument from underneath the black base when lifting With the assistance of another person place your hands under the bottom of the instrument NOT THE ROBOT and carefully lift the instrument out of the crate and onto a gurney or other moveable platform Transport to the laboratory site and place on benchtop Version 1 4 August 2012 7 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL D Removing the Shipping Bracket 1 Unscrew all 14 attachment screws securing the red Shipping Bracket covering the Pipetting Head using either a 9 64 Allen wre
25. nch or Phillips screwdriver Carefully retain all screws for immediate reuse Remove the metal bracket and place back in crate for storage Replace the screws into their original locations on the instrument as shown in Fig Ill D 1 ITEM NO 6 32 X 3 8 Black 8 32 X 1 2 Black Flat 8 32 X 3 4 Black M4 X 25MM Socket DESCRIPTION Phillios Head Screw Head Screw Socket Cap Screw Cap Screw QUANTITY Fig IIl D 1 Locations and types of screws in Shipping Bracket E Assembling the Safety Guard 1 Zi Remove the protective paper covering the Safety Guard components Using the 4x 8 32 x screws and washers removed from the shipping bracket attach the Side Mount Bracket to the black base as shown in Fig III E 1 Attach the clear Side Guard to the Side Mount Bracket using 2x 6 32 x 3 4 screws 2x M4 flat washers and 2x 6 32 nuts with star washers Fig III E 2 The M4 flat washers should be on the outside against the Side Guard Fig IIl E 3 Remove the screws at bottom left and top right on the left side of the robot Fig IIl E 4 Place screws inside a bag in the crate Attach Side Guard to the left side of robot using 2x M4 x 50mm screws and 2x M4 flat washers Fig IIl E 5 Attach a Corner Bracket to each Side Guard using 4x 6 32 nuts with star washers Right side shown in Fig III E 6 Attach Front Guard to Corner Brackets Requires 4x 6 32 nuts with star washers Fig
26. ow of plate Version 1 4 August 2012 18 408 733 7337 techserv scigene com SC e n e ArrayPrep Thermal Profiling System USER MANUAL Load Tips Deck position of tip rack for tip loading Load Column Column on tip rack for tip loading MNext Column Increments Column one to the right from previous Load Tips command For example if previous Load Tips command was from Column 1 a 2 will be placed in the Column of current menu Adds Row parameter for tip loading with Pipetting Head Distance from Bottom of Distance from the end of the pipette tips to the bottom of the wells in Well mm millimeters Syringe Speed of Max Speed of Pipetting Head plungers as a of the maximum speed MINext Column Increments Column one to the right from previous Mix command For example if previous Mix command was from Column 1 a 2 will be placed in the Column of current menu M Single Tip Mode Adds Row parameter for tip loading with Pipetting Head Row Row of plate Move Plate Move Plate From Deck position for picking up plate see section V Move Plate To Destination deck position D Dropoff Offset from deck Distance from bottom of plate to deck when gripper releases plate in mm millimeters Reverse previous move Reverses the Move Plate From and Move Plate To values from last Move Plate command Does not update Dropoff Offset Sele
27. pensing into Wet and Dry Plates a Turn on the ArrayPrep instrument and temperature controllers for deck positions 17 and 18 Set both controllers to 4 C and wait 15 minutes for temperature to stabilize b Place a 50 ul tip rack in deck position 1 Place clean PCR Plates in deck positions 17 and 18 Fig VI E 1 Put a plastic container for used tips on the bench adjacent to position 10 Fig VI E 2 17 18 19 4 C Fig VI E 1 Deck layout for testing small volumes Fig VI E 2 Tips container c Manually pipette 50 ul of water into each well of column 1 in the PCR plate in position 17 d Manually pipette Sul of water into each well of columns 4 6 and 10 12 in the PCR plate in position 18 e Launch the ArrayPrep software go to the Run menu and select the Desktop ArrayPrep_Protocols Diagnostics folder Choose Small Volume Dispensing and press Start The instrument transfers 1 2 and 3 ul of water from column 1 of position 17 into the PCR plate in position 18 f After completion of the protocol use a calibrated handheld pipettor 10 ul with graduated disposable tips to check well volumes to ensure they match expected volumes Table 8 Table 8 Expected Well Volumes in Position 18 Dry Dispensing Wet Dispensing Accuracy should be within 0 5 ul If the instrument does not meet this specification contact SciGene Technical Services at techserv scigene com or your local distributor Version
28. rature Fig VI D 2 Use thermometer 2 Using the cable provided with the digital thermometer SciGene cat 1051 52 0 plug one end into the blue receptacle found next to the temperature controller and the other into the digital thermometer Fig VI D 2 3 Turn onthe thermometer using the ON OFF button on the keypad The temperature of the block will be displayed 4 On the temperature controller press the green loop button G 5 four times until Cal appears 5 Calculate the difference in the temperature shown on the controller and the digital thermometer 6 Use the up and down arrows to enter the offset value calculated in Step 5 For example if the temperature controller is 37 C and the digital thermometer is 36 8 C use the down arrow button to correct offset by 0 2 7 Press the Infinity Key cc on the controller to return to the original display The controller is now calibrated for the set temperature you selected Repeat the calibration process for the remaining two controllers if necessary Version 1 4 August 2012 23 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL E Checking Dispensing Performance To determine the precision and accuracy of aspirating and dispensing small volumes of water perform the following test At completion the amount transferred is checked with a calibrated handheld pipettor 10 ul with graduated disposable tips 1 Dis
29. rd while a protocol is running Version 1 4 August 2012 21 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL VI SYSTEM MAINTENANCE AN Observe all national regional and local regulations for waste disposal and management Biological hazards can be associated with the materials used on this instrument Potentially infectious waste must be treated in accordance with good laboratory practice guidelines This symbol indicates the potential presence of a Hot Surface Use care when cleaning a spill in this area to avoid being burned A Deck Spills 1 Turn off the main power switch located on the left side of the ArrayPrep instrument Wipe the spill using absorbent material pulling the liquid to the front of the instrument away from the control panel Clean the deck with a cloth or paper towel and an appropriate disinfectant solution e g 70 ethanol for the type of contamination that may be present Dispose of the spill in a manner that is in accordance with good laboratory practices Wipe the deck dry B Tips Labware and Reagent Disposal Some chemicals used on this instrument can be hazardous Please adhere to good laboratory practices when disposing of the tips labware and reagents used on this instrument C Cleaning The following procedures are recommended after every use wipe down the deck Remove any condensation which may have collec
30. ropriate voltage and power requirements See section VII Specifications Do not block access to the main power switch Fig IIl F 3 Connect power cord to left side of instrument G Performing a System Check This symbol indicates the potential for a Hand Crush Do NOT place hands or arms under the Safety Guard while the robot is in motion protocol is running 1 Turn ON the power switch located on the left side of the instrument The instrument will perform a power up routine then move the robot to its home position homing 2 Turn on the laptop and allow it to boot up 3 Onthe laptop screen start the ArrayPrep software by clicking the ArrayPrep User icon or by selecting the program from the Start A i Menu Program Files SciGene ArrayPrep The laptop is provided without password protection Version 1 4 August 2012 10 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL 4 Select Controls Motion Pendant from the ArrayPrep software menu bar A dialog box will open Locate the Robot Status section All three status bars should be green Fig III G 1 a Motion Pendant josh x Pap Z UP SYRINGES UP GRIPPER UP X LEFT X RIGHT lt lt lt lt lt lt gt gt gt gt gt gt Activate Gripper i v Y v Button1 v v v Vv Ki Zs M Y OUT Z DOWN SYRINGES DOWN GRIPPER DOWN Robot Position Robot Status x Z SYRINGES 192 777
31. rotocol interrupted during plate Click Reset Gripper button in the Run Protocol screen If position movement problem persists contact SciGene Technical Service techserv scigene or your local distributor for assistance at correct height plate position Move Plate step in protocol not Edit Gripper Dropoff Offset parameter in Move Plate at correct height defined correctly line of protocol Gripper fingers open too wide Open file Calibrations txt in C Program before it starts slowly closing Files ArrayPrep Data and reduce value for GRIPPER_CLOSED 50 to 49 for example Gripper taking too long to grab plate or fingers not descending Labware not found in Worktable specifying labware is not Compare worktable labware names against labware worktable file in the labware definitions file definitions in the Edit Labware menu or C Program Files ArrayPrep Data labware txt Loose connection on Peltier driver Connections on Peltier driver board may be loose or need board replacement Contact SciGene Technical Service for assistance Paper or other object blocking Check underneath ArrayPrep base for objects blocking the heatsink fans heatsink fans Temperature is not stable or not reaching set temperature Version 1 4 August 2012 26 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL X SERVICE Instrument servicing is NOT to be completed by the customer Contact
32. seceessaeseceessuuaneeessaaeesaaneeeees 21 Usine the Z Release BUTTON sarcosacsssecincscpetnccvocusanexdoneutetue S SO 21 SYSTEM MAINTENANCE ose oscc casts resets ae a 22 DECK PI aenn A E E E EA E E E E 22 Tips Labware and Reagent DISPOSAL cisccsdscosantetiarasnccedsantaccuiranstneeetusareneededadsaecdeines aheesssdiedeoonveaantasasoceaousac 22 EAE a T E E E I E EE EEE 22 Calibration of the Temperature Controlled BIOCKS ccccccccssssecceceesseceecaeeesceeseeesseceeseeaseceessaeeeseees 23 Checking Dispensing Performance sssserisrssiirrrsosivirssseririrsurrdssrrerosananit niata Ua sana ss tK ana nsaan nodi iain sarsana nias 24 SPECIFICATIONS esini E 25 ORDERING INFORMATION sxciacesscesiswecdstctensrcadiwestsxestencedens cetewcutsintevenssdewcebinctensedeuscacawcstaiwiacaavocswesteetacc 25 TROUBLESHOOTING orcarina tarnen N 26 SERVICE o ep savesucnte senanessecadewensesanass osuesseecesceecuucancaseeeaceudncesnseceusetenccccastccerceceusuneueste 27 LOCKOUT Procedur srusen E catia E EA 27 F sse RE Ce Mi aoaaa REE A AAEE EEEE 27 DECLARATION OF CONFORMITY socsisicis a a I 28 Version 1 4 August 2012 2 408 733 7337 techserv scigene com SC G e Nn e ArrayPrep Thermal Profiling System USER MANUAL I SAFETY NOTICES A Instrument Safety Before operating the instrument read the information in this section concerning hazards and potential hazards Ensure that everyone involved with the instrument s operation is instruc
33. ted around the Temperature Controlled Blocks Deck use a damp lint free paper towel or cloth to qj N Syringe Nozzles use a lint free paper towel or Cooling Fan cloth with 70 ethanol to wipe down the syringe Air Intake Vent nozzles Fig VI C 1 Air Intake Vent Air Intake Vent with the instrument turned off remove any debris e g paper underneath the instrument that may be blocking the air intake cooling fans Version 1 4 August 2012 22 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL D Calibration of the Temperature Controlled Blocks The frequency of calibration of the Temperature Controlled Blocks should be in accordance with calibration schedules used for other laboratory equipment The three temperature controllers in positions 17 18 and 19 on the ArrayPrep System are calibrated at the factory to provide accurate plate temperatures Re calibration is required only if e When using a calibrated digital thermometer the block temperature differs by more than one degree 1 C from the actual temperature shown on the controller display Follow these steps to adjust the controller s to achieve accurate temperatures using a NIST certified digital thermometer SciGene cat 1051 52 0 1 Turn on the controller s and set the temperature to 37 C Fig VI D 1 Allow 15 minutes for the temperature to stabilize CALIBRATE Fig VI D 1 Set tempe
34. ted in both general safety practices for laboratories and specific safety practices for the instrument B Conventions and Labels The following is a glossary of the safety conventions and symbols that are used on the ArrayPrep Target Preparation System Whenever such symbols appear on instruments please observe appropriate safety measures 1 Conventions DANGER This indicates an imminently hazardous situation which if not avoided will result in serious injury or death Consult the User Guide for further information WARNING This indicates a potentially hazardous situation which if not avoided could result in serious injury or major damage to the equipment Consult the User Guide for further information gt CAUTION This indicates a situation which if not avoided could result in a minor injury or damage to the equipment Consult the User Guide for further information 2 Warning Labels Failure to comply with the following warnings that are affixed to the product can lead to possible personal injury or death This symbol alerts you to consult this User Guide for further information and to proceed with caution This symbol on top of the Heated Lid is to alert the user that the lid must be removed prior to operating the robot This symbol alerts you to a potential Biohazard Precautions must be taken with potentially infectious material DANGER 3 The motor power supply for the robot portion of
35. ularly those drawing large amounts of power Version 1 4 August 2012 5 408 733 7337 techserv scigene com Sc G e n e ArrayPrep Thermal Profiling System USER MANUAL IlI UNPACKING AND SETUP A Uncrating and Verifying Items 1 Open the shipping container by unlatching and removing the lid The lid will be heavy due to the bracing underneath Fig III A 1 2 Remove all items from the small storage compartment behind the instrument Fig IIl A 2 3 Remove the laptop box and dust bag Fig III A 3 Unlatch and remove the sides of the crate Fig IIl A 4 Fig Fig III A 3 Remove box and bag Fig III A 4 Remove all crate sides 5 Verify that the following items are provided Fig III A 5 If there are any discrepancies contact SciGene Technical Service at techserv scigene com or your local distributor Power Cord Emergency Stop Switch amp cable Ethernet Cable Laptop Computer Laptop Power Supply 3x Heated Lids Plastic Tip Bucket Safety Guard 1x Front Guard 1x Side Mount Bracket 2x Side Guards 2x Corner Brackets 2x Screws 6 32 x 4x Flat Washers M4 2x Screws M4 x 50mm 10x Nuts 6 32 star washers Fig III A 5 Items provided with the instrument Version 1 4 August 2012 6 408 733 7337 techserv scigene com SC G e n e ArrayPrep Thermal Profiling System USER MANUAL B Identifying System Components Z Brake Release Robot Status Light Sw
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