Mondrian™ SP Workstation
Contents
1. Description Section Page s Provide cartridge handling guidelines v2 Eee 2 Correction to dimensions v2 LE 3 Remove Ingress Protection from Specifications v2 LE 4 Add Appendix A a table of updates to this user manual VIA 29 version versus the previous version v2 Corrections to descriptions of LED lights v3 III B 17 BGs 1720 Updated screen shots v3 D 59 Added instructions about how to unpack the instrument LA 9 v3 Added instructions for cleaning the Workstation in the IV A 25 event of a filler fluid spill v3 NuGEN Technologies Inc Headquarters USA Europe 201 Industrial Road Suite 310 P O Box 149 San Carlos CA 94070 USA 6680 AC Bemmel Toll Free Tel 888 654 6544 The Netherlands Toll Free Fax 888 296 6544 Tel 31 13 5780215 custserv nugeninc com Fax 31 13 5780216 techserv nugeninc com europe nugeninc com For our international distributors contact information visit our website www nugeninc com NuGEN imagine more from lesse E 2012 NuGEN Technologies Inc All rights reserved The Ovation and Applause families of products and methods are covered by U S Patent Nos 6 692 918 6 251 639 6 946 251 7 354 717 7 771 946 and 8 071 311 and other issued and pending patents in the U S and other countries NUGEN Ovation SPIA Ribo SPIA WT Ovation Encore Applause Prelude Mondrian and Imagine More From Less are trademarks or registered trad2. After confirming you want to start a protocol the run will begin and the Running Protocol screen will display the run status until the run is completed Figure 29 Running Protocol screen Running cartridge pre check 15 minutes remaining 1 Flags Stop Run Running Protocol Running 4 Complete 2011 10 19 14 24 09 The Running Protocol screen shows the time remaining for a run and allows the user to stop the run at any time The number of error flags if any detected by the software is also reported During the run the user can select Stop Run at any time A screen will appear advis ing the user that run is in the process of canceling The Flags touchkey will display any errors in the protocol detected by the software These error flags will also be recorded in the run log file which can be downloaded at the end of the run 23 Mondrian SP Workstation lll Mondrian SP Workstation User Interface 24 Mondrian SP Workstation D Managing Log Files The Mondrian SP Workstation records the presence of any error flags detected by the system during a run Repeated errors should be referred to NUGEN Technical Support to ensure the system is functioning normally Pressing the Log touchkey on the main menu refer to Figure 20 opens the Log Listing screen Figure 30 Log Listing screen 4 Library Preparation Method 1 Start Time 2011 11 09 07 49 23 Status Completed 3 Library Preparation Method 1 Sta
3. Remove Protocol Cancel and notify the user that the protocol has been removed Figure 19 Notification after deleting a protocol Mondrian SP Protocol removed successfully 17 Mondrian SP Workstation Ill Mondrian SP Workstation User Interface 18 Mondrian SP Workstation Deleting a protocol cannot be undone If it s necessary to reinstall an accidentally deleted protocol the protocol should be downloaded to the NuGEN supplied USB device and added via the Add Protocols function described above Software Update Settings Software and firmware updates bin files can also be loaded onto the NUGEN supplied USB memory device Upon choosing Update Software or Update Firmware the compatible files present on the attached USB memory device will be automatically detected by the Mondrian SP Workstation Choose which bin file to load from the touchscreen menu The update will be installed automatically and when complete the user interface screen will display the main menu Advanced Settings Enter Bridge Mode Bridge Mode is a service mode for the system allowing it to be connected to an external computer and should only be entered by a NUGEN Technologies service representative Entering this mode will render the instrument unusable by the customer until the mode is exited Export Instrument Log The Instrument Log is used for troubleshooting NUGEN Technical Support may request the user expor
4. cotton or any other material that could leave particles behind e Isopropyl alcohol e Canned air Procedure 1 Turn the instrument off and unplug from the power source Soak the swab in isopropyl alcohol Firmly rub all pins with the swab 2 3 4 Wait 2 minutes 5 Blow the area dry with canned air 6 Plug the instrument back in and turn it on Cleaning the Mondrian SP Workstation in the Event of a Filler Fluid Spill On rare occasions Filler Fluid may leak and or be spilled over the cartridge deck and may leak into the machine itself If this occurs please contact NUGEN Technical sup port for further instructions Do not continue to use the instrument 25 Mondrian SP Workstation IV Maintenance B Decontamination Decontaminating the Instrument The instrument should be decontaminated if there is a spill of potentially biologically hazardous material on the instrument or if the instrument is to be returned to NUGEN Persons performing the decontamination process must be familiar with the basic setup and operation of the instrument NUGEN recommends the use of 70 isopropyl alcohol for the decontamination of infectious agents and blood Always wear protective gloves and safety glasses when handling contaminated instruments or performing the decontamination procedure A face shield is recommended whenever there is a pos sibility of aerosol contamination Materials e 70 Isopropyl alcohol e Deionized or distilled w
5. 60 non condensing e Excessive Ambient Light Bright sunlight or fluorescent light may degrade the quality of DNA or other reagents loaded on the cartridge Operate away from excessive light and never operate with the lid open e Dust Excessive dust and debris on the cartridge surface can contaminate sample or reagent wells A clean work area is necessary to ensure the best performance Il Mondrian SP Workstation Installation and Components 9 Mondrian SP Workstation RJ 45 receptacle for 10 100 1000 Mbps Ethernet Warning Power Rating The instrument s power cord must be connected to a power receptacle that provides voltage and current within the speci fied rating for the system Use of an incompatible power receptacle may produce electrical shock and fire hazards Warning Electrical Grounding Never use a two prong plug adapter to connect primary power to the external power supply Use of a two prong adapter disconnects the utility ground creating a severe shock hazard Always connect the power cord directly to a three prong receptacle with a functional ground Connect the power cord to the back of the instrument Plug the power cord into an appropriate power receptacle Turn on the instrument The Mondrian SP Workstation has a single power switch on its back panel Figure 3 For all operations including cartridge recognition by the instrument during insertion the instrument will need to be ON To turn on the worksta
6. The instrument s power cord must be con nected to a power receptacle that provides voltage and current within the specified rating for the system Use of an incompatible power receptacle may produce electrical shock and fire hazards Warning Electrical Grounding Never use a two prong plug adapter to connect primary power to the external power supply Use of a two prong adapter disconnects the utility ground creating a severe shock hazard Always connect the power cord directly to a three prong recep tacle with a functional ground Warning Internal Voltage Always turn off the power switch and unplug the power supply before cleaning the outer surface of the instrument Failure to do so may produce an electrical shock hazard Warning Liquids Avoid spilling liquids on the instrument fluid seep age into internal components creates a potential shock hazard Wipe up all spills immediately Do not operate instrument if internal components have been exposed to fluid Warning Potential Biohazards Some assays or specimens may pose a biohazard Adequate safety precautions should be taken as outlined in the reagent kit s package insert or your organization s standard operat ing procedures Warning Hot Surface The instrument cartridge deck may be hot at times during the instrument s operation Use caution when touching the deck surface Warning Unspecified Use Failure to operate the instrument according to the guidelines set
7. forth in this document could result in a hazardous condition gt gt peee D Warning Quality Control The operator must follow the manufacturer s assay package insert Failure to do so could result in erroneous test data I Introduction G Safety Safety Symbols Some of the following symbols may appear on the instrument Mondrian SP Workstation Safety Symbols NU Alternating current a Direct current Both direct and alternating current Caution refer to accompanying documents Warning hot surface Warning optical radiation oO wD AN Warning risk of electric shock 6 Mondrian SP Workstation 7 Introduction Mondrian SP Workstation H Components System Contents e Mondrian SP Workstation e Dummy Shipping Cartridge e Power Cable e Package Insert e Allen key e USB drive Additional Equipment Supplies and Labware e Lab wipes e Cleaning Swabs e lsopropanol For other application specific equipment reagents and labware please consult the appropriate Mondrian SP Reagent System User Guide or Third party reagent Application Note http www nugeninc com mondriansupport Il Mondrian SP Workstation Installation and Components 8 Mondrian SP Workstation A Installation 1 Inspect the packaging workstation and other parts and accessories for shipping damage Look for evidence of excessive shock scratches marring and cracked or br
8. Mondrian SP Workstation PART NO 8000 Developed and Manufactured for NUGEN by Advanced Liquid Logic a21 NUGEN imagine more trom lesse Patents Licensing and Trademarks 2012 NuGEN Technologies Inc All rights reserved NUGEN Ovation SPIA Ribo SPIA WT Ovation Applause Encore Prelude Mondrian and Imagine More From Less are trademarks or registered trademarks of NUGEN Technologies Inc Other marks appearing in these materials are marks of their respective owners The Mondrian SP Workstation is covered by certain patents and trade secrets of Advanced Liquid Logic Inc licensed to NUGEN Inc Sale of the Mondrian SP Workstation to NUGEN Inc customers comes with a limited research use only sublicense to use the Mondrian SP Workstation for preparing a nucleic acid sample for analysis on a separate system by sequencing microarray or real time PCR The sublicense specifically excludes the right to use the Mondrian SP Workstation for biothreat detection forensic testing production animal health testing and food safety testing except for genomics research in these fields and for human and veterinary diagnostics The purchase of this product conveys to the buyer the limited non exclusive non transferable right without the right to modify reverse engineer resell repackage or further sublicense under these patent applications and any patents issuing from these patent applications to use this product and methods ac
9. P Workstation Specifications Size Weight Dimensions Lid Closed 216 Dx80 W157 Weight Power Supply 25 b Input voltage 115 230 VAC 8 4 A 60 50 Hz Workstation Features Cartridge Deck Cartridge deck designed to accommodate Mondrian SP digital microfluidic cartridges for library preparation Magnetic Actuator 8 focused field locations Touch Screen Display 7 diagonal WVGA 800 x 480 pixels with LED backlight Internal Computer 1 66 GHz Intel Atom N450 with 2 GB RAM 4 GB solid state compact flash drive Thermal Control Heated Zones Heater Temperature Range in Cartridge Ambient to 95 C Chiller Zones Chiller Temperature Range in Cartridge Ambient to 10 C External Connectors USB 2 0 Host Front bezel 1 and rear panel 2 type A receptacles USB 2 0 Client Rear panel 1 type B receptacle 10 100 1000 MBit Ethernet Rear panel AC Mains IEC 60320 C14 Input Rear panel 4 Introduction Mondrian SP Workstation Mondrian SP Workstation Specifications continued Environmental Operating Temperature 422 C 23 C Operating Humidity 40 60 relative humidity non condensing Operating Altitude 0 7500 above mean sea level Storage Temperature OFC to t50 Storage Humidity 20 80 relative humidity non condensing F Mondrian SP Works
10. ater e Safety glasses e Gloves e Lab coat e Paper towels or lint free cotton cloths Procedure 1 Turn off the instrument and unplug from power supply and computer Warning Never immerse the instrument in liquid 2 Moisten a paper towel or cloth with 70 isopropyl alcohol Do not soak the towel or cloth 3 Wipe all exposed surfaces of the instrument including the handle 4 Open the lid see Figure 4 and wipe the aluminum deck and all interior surfaces of the lid with 70 isopropyl alcohol 5 Wait 20 minutes Allow the isopropyl alcohol to dry slowly Do not wipe dry 6 Moisten a paper towel or cloth with deionized or distilled water and wipe all sur faces that have been cleaned with isopropyl alcohol 7 Use a dry paper towel or cloth and dry all wet surfaces 8 Discard paper towels or cloths and gloves in an approved biohazard container 26 Mondrian SP Workstation V Technical Support For Technical Support please contact NUGEN at U S only 888 654 6544 Toll Free Phone or 888 296 6544 Toll Free Fax or email techserv nugeninc com In Europe contact NUGEN at 31 0 135780215 Phone or 31 0 135780216 Fax or email at europe nugeninc com In all other locations contact your NUGEN distributors Technical Support team 27 Mondrian SP Workstation VI Appendix A Update History This document the Mondrian SP Workstation user manual M01264 v3 is an update to address the following topics
11. companying this package insert for research and development purposes solely in accordance with the intended use described and the written instructions provided in this user guide No license to make or sell products by use of this product is granted to the buyer whether expressly by implication by estoppels or otherwise In particular the purchase of this product does not include or carry any right or license to use develop or otherwise exploit this product commercially and no rights are conveyed to the buyer to use the product or components of the product for purposes including commercial services or clinical diagnostics Warranty NuGEN warrants that this product meets the performance standards described in the Company s product and technical literature for a period of twelve months from the date of purchase provided that the product is handled and stored according to published instructions and that the product is not altered or misused If the product fails to meet these performance standards NuGEN will replace the product free of charge or issue a credit for the purchase price NuGEN s liability under this warranty shall not exceed the purchase price of the product NUGEN shall assume no liability for direct indirect consequential or incidental damages arising from the use results of use or inability to use its products NUGEN reserves the right to change alter or modify any product to enhance its performance and design NuGEN s pro
12. d that the deck lever is in the down position Figure 26 Refer to the appropriate SP Cartridge User Guide SP Reagent System User Guide or 3rd Party Reagent Application Note for detailed loading instructions Ill Mondrian SP Workstation User Interface Figure 26 The cartridge deck is raised and the deck lever is down therefore the cartridge is engaged with the workstation electronics and ready to run an assay il Note that the tips of the machined arrows at the front of the cartridge deck area are flush with the front edge of the cartridge and the cartridge electrodes at the back edge of the cartridge should not be visible when the cartridge is properly inserted into the deck Figure 27 If the front of the cartridge is not aligned with the tips of the machined arrows and or the cartridge electrodes at the back of the cartridge are vis ible Figure 28 the cartridge is not properly inserted into the deck Figure 27 A properly inserted cartridge The front edge of the cartridge is flush with the tips of the machined arrows A and the cartridge electrodes are not vis ible B OO6OO 22 Mondrian SP Workstation lll Mondrian SP Workstation User Interface Figure 28 An incompletely inserted cartridge The front edge of the cartridge is not flush with the tips of the machined arrows A and the cartridge electrodes are still visible B EERTE EESSI E4 E5 E7 DSa DO D7 i 4h hh hh Ah Ah An Filler Fluid
13. ducts are developed designed and sold FOR RESEARCH USE ONLY This product is not to be used for diagnostic or therapeutic purposes nor is it to be administered to humans or animals Except as expressly set forth herein no right to modify reverse engineer distribute offer to sell or sell NUGEN s product is conveyed or implied by buyer s purchase of this NUGEN prod uct The buyer agrees to use NUGEN products accompanying the product insert in accordance with the intended use and the written instructions provided Table of Contents Contents L roduc ToN eenn sn caensesoransseceansnchensnecanenenonsnoatenenosennacttanspecoetoseacnans 1 A Background and Intended Use Statement ceccceccseccsecceeeeeeeeeeeeeeeeeeeeeeeeeeeees 1 B Digital MCL OTM CS ssemrerm rarr eroriren i EN E TEE ETEO 1 e C E E A A E Z PE ae 2 E nee nr eee ee re cee eer A T ee ee oe ee eer 2 E Mondrian SP Workstation Specifications ss cics cceaisncnsescoorecstsersnsdensasesteshctensicecs 3 F Mondrian SP Workstation Notes and WarningS ccccccssccccccececeeeeeeeeeeeeeeeeeeens 4 Gh a aaetean E T E E 6 Pe CORPO E a E R E E EAEE O E ee 7 Il Mondrian SP Workstation Installation and Components ssceccsssseeeesseees 8 As Matala i essa cicada sews wo cl era tenn ds wien nsec aaa Wrage Sa elena eee co wees 8 Be SOMOS eS accep unseprors ee aett T E E 10 Ill Mondrian SP Workstation User Interface csccccssssseccecesssecccessseccceeeseee
14. emarks of NUGEN Technologies Inc Other marks appearing in these materials are marks of their respective owners For research use only M01264 v3
15. icated protocols for a range of sample preparation applications The Mondrian SP Workstation has very few moving parts making it highly reliable and requiring minimal maintenance Operation via a menu driven user friendly touch screen interface offers true walk away capability Single instruments accommodate lower throughput requirements effectively while multiple units can be used in tandem with HTP robotics to further streamline larger workflow processes The use of Peltier cooling and individual heating zones allow for temperature gradients of 10 C to 95 C Purification steps are enabled within the cartridge through the use of magnetic beads and a controllable magnetic device B Digital Microfluidics At the core of the Mondrian SP System operation is a technology termed digital micro fluidics Cartridges for the instrument consist of an oil layer Filler Fluid sandwiched between a PCB substrate onto which insulated electrodes are patterned and a top plate By manipulating the relative voltages of the patterned electrodes aqueous droplets containing reagents and substrates can be manipulated to perform complex assays Droplets can be dispensed from loading ports transported to various locations on the cartridge mixed incubated and collected using only software control Figure 1 shows a cutaway side view schematic of a cartridge Figure 1 Cartridge cutaway side view S lt Droplet Filler fluid oil I E Insulating poly
16. mer PCB substrate Electrode Hydrophobic coating 2 Introduction Mondrian SP Workstation C Cartridges Cartridges are unpacked inserted into the workstation loaded with filler fluid samples and reagents and a run is initiated through the touch screen user interface Cartridges are one time use only Cartridge re use is not supported even if a run is canceled prior to completion To ensure proper assay performance cartridge loading procedure must be strictly followed Consult the Mondrian SP Universal Cartridge User Guide and appropriate Application Note or Application User Guide for proper cartridge loading and setup procedure to achieve optimum results Do not handle the cartridge by the contacts and ensure the cartridge contacts are clean prior to loading onto the instrument Open the packaging with scissors only taking care not to flex or distort the cartridge Figure 2 shows a diagram of an SP Cartridge Figure 2 SP Cartridge diagram D SP Reagents NuGEN offers a range of Ovation and Encore reagent systems and protocols to provide complete NGS workflow solutions Selected protocols will also be provided for use with third party reagents on SP Universal Cartridges to supplement the expanding menu of NUGEN optimized protocols for major NGS platforms Documentation and ordering information are available at http www nugeninc com mondriansupport 3 Introduction Mondrian SP Workstation E Mondrian S
17. mes Figure 4 Mondrian SP Workstation lid in closed and open position Cartridge Deck and Lever The cartridge deck is where the cartridge resides during the assay run The deck lever engages the cartridge with the Workstation s control electronics When the deck lever is up the cartridge deck is down and the cartridge is disengaged Figure 5A When the deck lever is down the cartridge deck is up and the cartridge is engaged Figure 5B 10 Mondrian SP Workstation Il Mondrian SP Workstation Installation and Components 11 Mondrian SP Workstation Figure 5 Locking the cartridge deck In Figure 5A the deck lever is up and the cartridge deck is down meaning the cartridge is not engaged with the control electronics In Figure 5B the deck lever has been pulled down raising the car tridge deck and engaging the cartridge with the control electronics To lock cartridge in place pull lever forward and or down The cartridge deck features a Peltier cooling device silver metal area to the right in Figure 6 three metal heating bars to maintain elevated temperatures during incuba tions black metal bars in the center and a set of motorized magnets for magnetic bead based separations silver metal circles to the left of the heater bars Figure 6 Cartridge deck features Peltier cooling device Motorized magnets Heating bars The control electronics are located at the back of the cartridge deck area as show
18. n in Figure 7 Il Mondrian SP Workstation Installation and Components Figure 7 Control electronics Control electronics Peltier cooling device Workstation Status LEDs Two LEDs on the front of the Mondrian SP Workstation indicate its current status Figure 8 The LED on the left is the Power LED which indicates the power state of the instrument During power up the system performs a self test and the LED lights up in a multicolor mode This LED should always be green while the instrument is on If the instrument is on and the Power LED is off turn the instrument off immediately and call for service The LED on the right is the Status LED which indicates the current working state of the instrument e Solid or blinking green workstation is running an assay e Solid yellow or red workstation is in standby mode waiting for the next run e Blinking red call NUGEN Technical Service Figure 8 Photo of the Mondrian SP Workstation touchscreen interface showing the Power and Status LEDs to the lower right of the touchscreen The Power LED left is solid green indicating the workstation is on The Status LED right is solid yellow indicating the workstation is in standby mode waiting for the next run SETTINGS 12 Mondrian SP Workstation lll Mondrian SP Workstation User Interface A Main Menu The software used to control the Mondrian SP Workstation employs a touch screen user interface Upon connecting the
19. oken components and enclosures If you suspect that the instrument has been mishandled in shipping notify NUGEN Technical Support Keep the workstation and all packing materials undisturbed for the carrier s inspection 2 Remove the cords USB drive and documentation from the top foam block 3 Remove the top foam block and set aside making sure to retain the block as directed above 4 Carefully remove the plastic wrapped instrument from the box being careful to support the system from the bottom and place on a level surface 5 Carefully remove the plastic wrap from the instrument Pull the deck lever towards you downwards to unlock the deck Remove the dummy shipping cartridge marked with a label that reads Remove from Mondrian SP Workstation prior to instrument use from the cartridge deck and set aside 6 Place all packing material back into shipping box for repacking if the workstation needs to be shipped at a later date Note Install the Mondrian SP Workstation on a level stable surface where ambient temperatures of 22 C 3 C can be maintained and with unobstructed access to an appropriate power receptacle The workstation is sensitive to environmental conditions Avoid the following e Excessive Humidity Condensation directly on the electronics can cause the instrument to fail internal quality control measures and may present a shock or fire hazard The specified relative humidity range of the workstation is 40
20. om the main menu shown in Figure 9 contains controls for changing the basic settings of the Workstation adding or removing protocols software and firmware updates and advanced features General Settings Figure 12 The General Settings menu About Screen Brightness Sereen Calibration l Volume Clock Power Off About Displays system and software version information Screen Brightness Brings up a slider bar to adjust the screen brightness level Screen Calibration Runs a wizard to adjust the touchscreen calibration Volume Brings up a slider bar to adjust system alert sound volumes Clock Allows date time settings for the workstation to be adjusted Power Off Turns the workstation off This can also be done by holding down the power button below the touchscreen lll Mondrian SP Workstation User Interface Protocol Settings Figure 13 The Protocol Settings menu Add Protocols The Mondrian SP Workstation requires periodic updates to implement software updates and protocols which will be distributed on NUGEN s website at www nugeninc com mondriansupport New software and protocols should be downloaded from the website to the USB memory device provided with the Mondrian SP Workstation Use of unauthorized USB devices is discouraged as compatibility problems may damage the software and firmware of the instrument Once new protocol tiles have been downloaded to the NUuGEN supplied USB memory device cho
21. ose Add Protocol from the Protocol Settings menu The available and com patible protocol tiles present on the attached USB memory device will be displayed Figure 14 Figure 14 Listing available protocols for import Mondrian SP The user selects the protocol to be uploaded to the Mondrian SP Workstation then the system will request confirmation from the user as shown in Figure 15 15 Mondrian SP Workstation lll Mondrian SP Workstation User Interface Figure 15 Confirming protocol installation Install protocol archive F protocols par Install Protocol Cancel The software will notify the user when the upload is complete Figure 16 Notification after installing a protocol Protocol archive installed successfully Remove Protocols Protocols can be removed from the Mondrian SP Workstation by choosing Remove Protocols from the Protocol Settings menu The system will prompt the user to select a protocol 16 Mondrian SP Workstation lll Mondrian SP Workstation User Interface Figure 17 Listing available protocols to delete Ovation SP Ultralow DNA Library System Version 1 Cactndge n a Samples 0 Duration 0 00 Library Preparation Method 1 Version 1 Carindge 8010 Samples S Duration 3 17 00 confirm the choice prior to deleting Figure 18 Confirming a protocol is to be deleted Mondrian SP Remove protocol Library Preparation Method 1 This action cannot be undone
22. power cord and switching on the Mondrian SP Workstation an Advanced Liquid Logic logo should briefly appear followed by the NuGEN Technologies Inc logo The main menu should then appear with three touchkeys Run Log and Settings Figure 9 Figure 9 Mondrian SP Workstation main menu In the black strip running across the bottom of the user interface the title of the current screen is shown on the bottom left of the window the software version is shown in the bottom middle and the date and time are shown in the bottom right Figure 9 While the Mondrian SP Workstation functions as a stand alone system file importing and exporting is necessary for adding new application protocols retrieving log files and updating system software A USB memory device is supplied with the system for these tasks Only approved USB devices should be used for file transfers as compat ibility problems may cause malfunction of the Mondrian SP internal software The USB port for this purpose is on the right side of the touchscreen at the front of the Mondrian SP Workstation Figure 10 Figure 10 USB port for file transfers USB port for file transfers 13 Mondrian SP Workstation lll Mondrian SP Workstation User Interface 14 Mondrian SP Workstation B Settings Menu Figure 11 The Settings menu Protocols Software Update Advanced The Settings menu accessed by selecting the Settings touchkey fr
23. rt Time 2011 11 09 07 48 53 Status Completed 2 Library Preparation Method 1 Start Time 2011 11 09 07 44 11 Status Completed 1 Protocol Deleted Start Time 2011 10 25 10 31 42 Status Failed The Log Listing screen shows the available log files for each run Pressing the Export touchkey causes all log files to be downloaded to the NUGEN supplied USB drive the user will be notified if the USB drive is not attached Individual log files can be downloaded to the USB drive by choosing individual log files in the Log Listing screen The individual Log File screen will appear which also includes an Export function The user will be notified when the log files have been successfully downloaded to the USB memory device To clear the logs please refer to the Advanced Settings gt Reset Database command above IV Maintenance A Routine Maintenance Cleaning The surface of the cartridge deck on the instrument may be cleaned using isopropanol and lab wipes The control electronics can be cleaned using isopropanol and a lint free wipe or swab For safety ensure the power is turned off and the instrument unplugged during the cleaning process Cleaning the Instrument Contact Pins The pins on the instrument cartridge interface may become dirty and cause perfor mance issues If this happens the interface pins will need to be cleaned Materials e Foam or cloth swab such as Contec Constix Sealed Foam Swabs do not use
24. s 13 Pe AVIA WSU seo scacontncdoincsanatadnceeabendieciiaensabphnicenebaphiaanaed EEE 13 BE a e E en ce cerca cern one A ted ue nates aac E encores 14 Ce RUINS Sr FIC1O CON a E E R 18 Wa GIN Log Files acrayernsavaneeusswantsicanpinunetiicesaiuuinsedavaw snes anlacaaledaaiensibleincisentedievaents 24 PVs VVC TAIN CC suriri T E S E ENEE E 25 A Routines Mamtenante ssrssseofensraiiresih rina rinin O ENEE ASE RER E sE rN Z5 BD SCOT a Ia HOM rne r EEEE R 26 vM Techical SUD DOM rnoes EEE EEEE 27 VE APOENA ocra EE E E 28 1 Introduction Mondrian SP Workstation A Background and Intended Use Statement The Mondrian SP System is an innovative new approach to automated genomic sam ple preparation based on the use of digital microfluidics for liquid handling The system software includes a range of sample preparation methods that use pre configured and quality controlled NUGEN brand reagents as well as reagents from other providers The software is dynamically configurable to allow users to add new protocols as they become available from NuGEN Sample preparation is performed in nanoliter volumes within disposable cartridges The system provides plug and play automation with a simple user interface and load and go cartridge operation to significantly reduce the hands on time for genomic sample preparation The Mondrian SP System consists of a benchtop workstation microfluidic cartridges optimized reagents and system software that includes ded
25. station User Interface Figure 22 Protocol Information screen Encore SP Rapid Version 1 0 Cartridge 8010 Duration 3 59 00 Automated amplification free library preparation for Illumina SBS using NUGEN s Encore SP Rapid Library Systems In the Run Information screen Figure 23 the user will be asked to provide specific information about the run including the operator name cartridge number run number notes sample identifiers and other data Figure 23 Run Information screen Mondrian SP The information is entered via a touchscreen keyboard that appears when each data field is touched Figure 24 20 Mondrian SP Workstation lll Mondrian SP Workstation User Interface 21 Mondrian SP Workstation Figure 24 Touchscreen keypad and completed Run Information screen Operator Name Piet M Cartridge Number A235 7 Run Number 1928 Motes Exome capture lib prep pmm SS pEoponpoponan EA mA On m me pre pa men me en pem m a nna Ce EEL TDL ELLIE After entering all relevant run information no fields are strictly required the user touches the Next touchkey The software will ask the user to confirm the selected pro tocol to be run Figure 25 Confirming to run a protocol Start Protocol Encore SP Rapid Start Run l The user must ensure that an appropriate cartridge correctly loaded with Filler Fluid and reagents has been inserted into the workstation an
26. t logs to be sent to NUGEN for examination After selecting this option user will be prompted to insert NUGEN supplied USB device to receive the exported log file This file can then be sent electronically to NUGEN Clear Autocomplete Dictionary Clears saved user sample and cartridge information Reset Database Clears all logs C Running a Protocol Pressing the Run touchkey on the main menu Figure 20 displays the Protocol Selection screen The available protocols are displayed in a list which can be navigated by the page up and page down touchkeys lll Mondrian SP Workstation User Interface Figure 20 Mondrian SP Workstation main menu SETTINGS Available protocols are displayed in the Protocol Selection screen Figure 21 Protocol Selection screen Encore SP Rapid Version 1 0 Cartridge 8010 Samples 8 Duration 3 59 00 Library Preparation Method 1 Version 1 1 Cartndge 8010 Samples 8 Duration 3 17 00 Ovation SP Ultralow Version 1 0 Cartndge 8010 Samples 8 Duration 3 02 00 After selecting a protocol the Protocol Information screen appears Figure 22 This screen allows users to confirm they have selected the correct protocol as well as pro viding info about the protocol version and duration After confirming that the correct protocol has been chosen users should touch the Next touchkey to advance to the Run Information screen 19 Mondrian SP Workstation lll Mondrian SP Work
27. tation Notes and Warnings For Research Use Only Not for use in diagnostic procedures Use only the power cord provided with the instrument Use of the instrument outside of the specified environmental conditions may degrade the safety features of this instrument Biological samples of all types from any source should be treated as biohazard ous according to your organization s approved procedure If the instrument is used in a manner not specified by NUGEN Technologies Inc the protection provided by the equipment may be impaired Operate the instrument on a flat surface away from excessive humidity and moisture Performance can be adversely affected by extraneous contaminants such as dust dirt adhesive etc on the cartridge Make sure cartridges are clean and free of debris before use When operated in a safe environment according to the instructions in this docu ment there are no known hazards associated with the use of this instrument However the operator should be aware of certain conditions that could result in injury See Hazards and Precautions for more information The Mondrian SP Workstation should be used only with cartridges reagents and protocols approved or supplied by NuGEN Technologies Inc Use of any other cartridge protocol or reagents is not supported and may cause damage to the System 5 Introduction Mondrian SP Workstation Hazards Mondrian SP Workstation Hazards Warning Power Rating
28. tion flip the power switch on the back to the ON position Then press the power button on the front of the workstation below the touchscreen During power up the system performs a self test and the LED lights up in a multicolor mode The LED will then turn to green If it does not turn off and unplug the workstation and call for service On power up the instrument will initialize its internal software and display several start up screens featuring the Advanced Liquid Logic and NUuGEN Technologies logos Once the workstation is initialized the main menu screen will be displayed If this does not occur within 30 seconds of powering on the instru ment turn the power off and contact NUGEN Technical Support Figure 3 Back of Mondrian SP Workstation USB B receptacle 2x USB A receptacles Power switch Power cord attachment Il Mondrian SP Workstation Installation and Components B Components Lid The lid protects the cartridge from tampering during the application run This is impor tant to limit contamination of sample and reagent wells from aerosol contamination and to prevent possible UV mediated degradation of reagents and or samples The Mondrian SP Workstation lid should always be closed during operation Figure 4 The system will operate with the lid open but sample and reagents are more susceptible to aerosol contamination and degradation We recommend storing the workstation with the lid in the closed position at all ti
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