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OpenArray AccuFill System User Guide (PN 4456986A)

1. 10 Prepare the reagents for use in the master mix 10 Sample plate preparation kk kK kK kK KK KK KK KK IK KK KK kk kk kk kk eee eae 11 Prepare sample plate for a TaqMan OpenArray Real Time PCR run 13 Materials and equipment required 13 Sample plate preparation 0 0 0 cece kk KK KK kK KK KK kk kk kK kk kK kk kk kk 13 Prepare sample plate for a TagMan OpenArray Genotyping run 15 Sample plate preparation kk kk kK KK kK KK KK KK KK KK see 15 Prepare the DNA samples 16 Quantity of DNA wi kis x w SE yane mi ale me e uc e erroe Se ee E e ER E WE vies 16 Quantification procedure for human DNA samples 16 Perform multi sample loading 17 CHAPTER 2 Sample Loadi g si ss ss idirin Dil k ha kay oDi 23 Materials and equipment required 24 VORTON E C Sena eden hak N Na AA ant E ARA DAN aah ats iL 24 Important guidelines for handling the plate 25 Initialize the System Le lt salna Godage hee OI CREE kalar dees Cla 25 Preparethe Cases vetitis A Ara tue Aes t ox Ab EU ae b kr or iE use An 29 Prepare for loading 3 e Re dt a RI t Ue eee s 29 Load a
2. 2006 95 EC This instrument has been tested to and complies with standards EN 61010 1 2001 second edition Safety Requirements for Electrical Equipment for C Measurement Control and Laboratory Use Part 1 General Requirements OpenArray AccuFill System User Guide 71 Appendix D Safety Chemical safety Australian EMC Standards EMC This instrument meets European requirements for emission and immunity EMC Directive 2004 108 EC This instrument has been tested to and complies with standard IEC 61326 Group 1 Class A Electrical Equipment for Measurement Control and Laboratory Use EMC Requirements The OpenArray AccuFill instrument has been tested to and complies with standard AS NZS 2064 Limits and Methods Measurement of Electromagnetic Disturbance Characteristics of Industrial Scientific and Medical ISM Radio frequency Equipment Chemical safety General chemical safety Chemical hazard warning Chemical safety guidelines 72 WARNING CHEMICAL HAZARD Before handling any chemicals refer to the Safety Data Sheet SDS provided by the manufacturer and observe all relevant precautions WARNING CHEMICAL HAZARD AII chemicals in the instrument including liquid in the lines are potentially hazardous Always determine what chemicals have been used in the instrument before changing reagents or instrument components Wear appropriate eyewear protective clothing and gloves when worki
3. Physical hazard safety Ultraviolet light WARNING ULTRAVIOLET LIGHT HAZARD Looking directly at a UV light source can cause serious eye damage Never look directly at a UV light source and always prevent others from UV exposure Follow the manufacturer s recommendations for appropriate protective eyewear and clothing Compressed gases A WARNING PHYSICAL HAZARD Nonflammable compressed nitrogen gas Contents are under pressure Receive proper training on the handling of compressed gases before use Exposure to rapidly expanding gas may cause frostbite High concentrations of vapors in the immediate area can displace oxygen and cause asphyxiation Use only in areas with adequate ventilation Read the SDS and follow the handling instructions Wear appropriate protective eyewear clothing and gloves A WARNING EXPLOSION HAZARD Pressurized gas cylinders are potentially explosive and can cause severe injury if not handled properly Always cap the gas cylinder when it is not in use and attach it firmly to the wall or gas cylinder cart with approved brackets or chains Moving parts A WARNING PHYSICAL INJURY HAZARD Moving parts can crush and cut Keep hands clear of moving parts while operating the instrument Disconnect power before servicing the instrument a WARNING PHYSICAL INJURY HAZARD Do not operate the instrument without the arm shield in place Keep hands out of the deck area when the instrument is spotting
4. Safety Alerts acte racer hd OE ve awe o ee bla ee 76 General alerts for all chemicals 76 Specific alerts for instrumentation WW kk kk KK KK KK KK KK KK KK KK KK KK 76 OpenArray AccuFill System User Guide 65 Appendix D Safety Instrumentation safety Instrumentation safety Symbols on instruments Electrical The following table describes the electrical symbols that may be displayed on Applied symbols on Biosystems instruments instruments Symbol Description Indicates the On position of the main power switch Indicates the Off position of the main power switch Indicates a standby switch by which the instrument is switched on to the Standby condition Hazardous voltage may be present if this switch is on standby Indicates the On Off position of a push push main power switch Indicates a terminal that may be connected to the signal ground reference of another instrument This is not a protected ground terminal Indicates a protective grounding terminal that must be connected to earth ground before any other electrical connections are made to the instrument Indicates a terminal that can receive or supply alternating current or voltage Indicates a terminal that can receive or supply alternating or direct current or voltage IDA OGO Safety symbols The following table describes the safety symbols that may be displayed on Applied Biosystems
5. The second sample for the subarray comes from section 8 of the sample plate which holds samples 49 to 96 An example of two samples per subarray is shown on page 20 OpenArray9 AccuFill System User Guide 19 Chapter 1 Sample Preparation Prepare sample plate for a TagMan OpenArray Genotyping run Sample Plate 1 Sample 49 Sample 96 Sample 1 Fd Load 2 Sample 48 Load 1 Sample 1 Sample 49 Subarray A1 Subarray D12 Sample 48 Sample 96 OpenArray Plate OpenArray AccuFill System User Guide 20 Set up the sample plate for three samples OpenArray 1 Sample 1 OpenArray 1 Sample 3 OpenArray 2 Sample 2 Chapter 1 Sample Preparation Prepare sample plate for a TaqMan OpenArray9 Genotyping run These instructions describe how to set up a sample plate with three separate DNA samples 1 Label the three sections of the sample plate so that you can keep track of what is loaded in each section An example is shown in the following illustration OpenArray Sample 2 OpenArray 2 Sample 1 OpenArray 2 Sample 3 IMPORTANT Be sure to track where the samples are in the sample plate For each sample you use Applied Biosystems recommends creating a sample information file in CSV format This CSV file can be used in sample integration See Use Sample Integration on page 39 for more information 2 Use the following loading arrangem
6. case OpenArray 29 sample 10 sample plate 11 13 15 pressurized fluids safety 69 Q quantification procedure 16 R radioactive waste handle 74 reagents 57 prepare 10 Real Time PCR run 11 repetitive motion safety 71 run types 61 Genotyping 15 Real Time PCR 11 SYBR 10 11 TaqMan OpenArray Real Time PCR 13 safety before operating the instrument 68 biological hazards 75 chemical 72 chemical waste 73 compressed gases 69 electrical 70 ergonomic 71 guidelines 72 73 74 instrument operation 68 OpenArray AccuFill System User Guide move and lift computers and monitors 68 move and lift instrument 68 moving parts 69 physical hazard 69 pressurized fluids See also compressed gases safety repetitive motion 71 solvents 69 standards 71 ultraviolet light 69 workstation 71 safety labels oninstruments 8 67 safety standards 71 safety symbols on instruments 66 Sample Integration 39 53 79 sample loading force single 53 more than one 17 sample plate 10 11 13 15 clean 15 files 39 50 samples load three DNA 21 load two DNA 18 preparation 10 16 quantify human DNA 16 SDSs about 8 description 73 obtaining 73 78 seal plates 42 serial numbers 30 53 79 setup and load plates 29 51 SNP file 39 software license agreement 53 OpenArray AccuFill software 50 options 52 versions 53 solvents safety 69 spills clean 64 standards EMC 71 safety 71 storage directories 39 40 support technical 7
7. loading Hold the OpenArray plate by the edges at the end opposite from the barcode Do not touch the through holes e Within one hour after opening the plate packaging load the TaqMan OpenArray plate with sample place the loaded plate in a OpenArray Genotyping Case then seal the case f you drop a loaded OpenArray plate discard it in the appropriate waste container Initialize the system Initialize the system to prepare for the loading operation 1 Make sure that the enclosure door is closed Double click the OpenArray9 AccuFill icon to launch the software The software checks the computer and connections as the system starts M aos Opend rray AccuFill After the application has been launched it displays a message requesting you to clear the deck and empty the waste bin of used tips System Self Test Please clear the deck empty and replace the waste bin and close the door before performing the System Self Test a Open the instrument by grasping the enclosure door handle and gently but firmly pulling the enclosure door up The opened instrument is shown below OpenArray AccuFill System User Guide 25 Chapter 2 Sample Loading Initialize the system Note To safely operate the instrument it is important to keep the deck clear and have enough room in the waste bin to eject the used pipette tips Waste bin Plate Holder a b Empty the waste bin and place it bac
8. Do not attempt to lift or move the computer or the monitor without the assistance of others Depending on the weight of the computer and or the monitor moving them may require two or more people Things to consider before lifting the computer and or the monitor Make sure that you have a secure comfortable grip on the computer or the monitor when lifting Make sure that the path from where the object is to where it is being moved is clear of obstructions Do not lift an object and twist your torso at the same time Keep your spine in a good neutral position while lifting with your legs Participants should coordinate lift and move intentions with each other before lifting and carrying Instead of lifting the object from the packing box carefully tilt the box on its side and hold it stationary while someone slides the contents out of the box Ensure that anyone who operates the instrument has Received instructions in both general safety practices for laboratories and specific safety practices for the instrument Read and understood all applicable Safety Data Sheets SDSs See About SDSs on page 73 OpenArray AccuFill System User Guide Appendix D Safety Instrumentation safety Clean or T CAUTION Before using a cleaning or decontamination method other than decontaminate the those recommended by the manufacturer verify with the manufacturer that the instrument proposed method will not damage the equipment
9. Solvents and WARNING PHYSICAL INJURY HAZARD Always wear eye protection when pressurized fluids working with solvents or any pressurized fluids OpenArray AccuFill System User Guide 69 Appendix D Safety Instrumentation safety Electrical safety Fuses Power Overvoltage rating 70 WARNING PHYSICAL INJURY HAZARD To avoid hazards associated with high pressure fluids in polymeric tubing e Be aware that PEEK tubing is a polymeric material Use caution when working with any polymer tubing that is under pressure Always wear eye protection when near pressurized polymer tubing Extinguish all nearby flames if you use flammable solvents Do not use PEEK tubing that has been severely stressed or kinked Do not use PEEK tubing with tetrahydrofuran or nitric and sulfuric acids Beaware that methylene chloride and dimethyl sulfoxide cause PEEK tubing to swell and greatly reduce the rupture pressure of the tubing Beaware that high solvent flow rates 40 mL min may cause a static charge to build up on the surface of the tubing Electrical sparks may result WARNING ELECTRICAL SHOCK HAZARD Severe electrical shock can result from operating the AccuFill without its instrument panels in place Do not remove instrument panels High voltage contacts are exposed when instrument panels are removed from the instrument WARNING FIRE HAZARD Improper fuses or high voltage supply can damage the instrument wiring system and c
10. even when the OpenArray plate is formatted for 2 or 3 samples per subarray This method is a convenient way to create technical replicates for analysis Help The Help menu contains information about the OpenArray AccuFill System including a summary of the system serial numbers and versions of software and firmware A link to the Software License Agreement is also provided OpenArray9 AccuFill System User Guide 53 Chapter5 OpenArray AccuFill Software Help 54 OpenArray AccuFill System User Guide APPENDIX A Ordering Information This appendix covers How to order from the Applied Biosystems website 56 Required equipment eere beet ee en teret es 56 Required equipment and materials not included 56 Optional materials idees eee an W eid le ene R Panda se 57 R quired reagents k x ak MINA KARA DA ee eed 57 Required consumables scesi cress eren rk w Ka B n lek eee kik Hl L eens 58 OpenArray AccuFill System User Guide 55 Appendix A Ordering Information How to order from the Applied Biosystems website How to order from the Applied Biosystems website To order Procedure Instrument parts and accessories 1 Go to www appliedbiosystems com 2 Click Products Gene Expression Gene Expression Analysis Instruments gt OpenArray Real Time PCR Platform Reagents Consumables In the OpenArray Re
11. gt applied he by kile technologies OpenArray AccuFill System User Guide For Research Use Only Not intended for any animal or human therapeutic or diagnostic use This user guide is the proprietary material of Applied Biosystems LLC or its affiliates and is protected by laws of copyright The customer of the OpenArray AccuFill is hereby granted limited non exclusive rights to use this user guide solely for the purpose of operating the OpenArray AccuFill System Unauthorized copying renting modifying or creating derivatives of this user guide is prohibited Information in this document is subject to change without notice NOTICE TO PURCHASER Limited Licenses The OpenArray AccuFill system as well as methods and systems involving the same are covered by US Patent No 7 547 556 and corresponding claims in any foreign counterpart patents thereof No right is conveyed expressly by implication or by estoppel under any other patent claim such as claims to apparatus reagents kits or methods such as 5 nuclease methods other than device claims covering the purchased product Further information on purchasing licenses may be obtained from the Director of Licensing Applied Biosystems 850 Lincoln Centre Drive Foster City California 94404 USA WARRANTIES APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS
12. it into the Plate Holder with the barcode face up and to the left You can place one to four plates for one loading run If you are using more than one OpenArray plate repeat step 6 and step 7 as necessary OpenArray AccuFill System User Guide Chapter 2 Sample Loading 2 Prepare for loading 8 By default the AccuFill software identifies the next available section of the sample plate section 1 in the following illustration When you choose a section of the sample plate you will see the corresponding color on the illustration of the OpenArray plates at the right You can choose only the location of the first sample The application automatically chooses the next available section of the sample plate in the order shown For multi sample or multi plate loading you can choose sections in any order by repeating the setup procedures between plates The setup procedure is described in Perform multi sample loading on page 17 M Note A warning appears if you choose a sample section that you have recently used for another loading run 9 Click Next OpenArray9 AccuFill System User Guide 31 Chapter 2 Sample Loading Load an OpenArray plate Load an OpenArray plate Workflow Load a single OpenArray plate Remove the foil from the sample plate l Load the OpenArray plate l Remove the OpenArray plate l Insert the OpenArray plate into a case Load multiple OpenArray plates Remove the foil from a s
13. next plate Spill accidents If liquids or other materials spill inside the AccuFill instrument turn off the instrument by pressing the power switch on the left side of the instrument Unplug the power cord from the electrical outlet Contact Applied Biosystems service personnel For the latest service and support information go to www appliedbiosystems com Power switch Power cord outlet 64 OpenArray AccuFill System User Guide APPENDIX D Safety This appendix covers Instrumentation safety Ke lk E R eee n 66 Symbols on instruments 66 Locations of safety labels on instruments 67 General instrument safety 68 Physical hazard safety Sos estes eus ss dan sa del l sey a e o san k 69 Electrical Safety a k sese dl kd ate kik a d ets 70 Workstation safety nak kl n a E Rb x ed ae ie nie 71 Safety and electromagnetic compatibility EMC standards 71 Chemical Safety s4x 33224an Sed rh wee on a n e wie Lawes sand te Ga okt 72 General chemical safety 72 SDSS2 5 Lage EG Eada eines estimated esse 73 Chemical waste safety 73 Biological hazard safety 0 KK KK KK KK KK KK KK KK KK KK KK KK KK K 75
14. nor does it apply to the OpenArray NT Imager 1 Position the OpenArray plate and case on a laboratory wipe so that the black framed side faces up Make sure the frame is clean without any residual adhesive from previous runs Use scissors to cut two rectangles from the frame adhesive IMPORTANT Use scissors that are clean and also not rusty OpenArray AccuFill System User Guide 45 4 Chapter 4 Prepare the plate for the NT Cycler Frame the case Cut two rectangles each about 3 mm in length from the frame adhesive as shown 4 With forceps remove the backing from one side of the tape of one rectangle exposing a sticky side Stick the tape in the middle of a long side of the frame 5 Repeat step 4 to place adhesive on the other long side of the assembly 46 OpenArray AccuFill System User Guide Chapter 4 Prepare the plate for the NT Cycler YA Frame the case 6 With forceps peel the backing off the pieces of tape Align two corners of the frame with two corners of the case and bring the other corners of the frame down onto the case Flatten the frame against the case for 10 seconds The OpenArray plate is now sealed framed and ready to insert in the OpenArray NT Cycler OpenArray AccuFill System User Guide 47 4 Chapter 4 Prepare the plate for the NT Cycler Frame the case 48 OpenArray AccuFill System User Guide CHAPTER 5 OpenArray AccuFill Software This chapter cove
15. not contain PCR inhibitors e Has an A 69 239 ratio between 1 7 and 1 9 e Has an A goy2go ratio between 1 7 and 1 9 Is intact as visualized by gel electrophoresis Has not been heated above 60 C temperatures above 60 C can cause degradation Applied Biosystems recommends that you quantify the amount of genomic DNA in your samples Note that The TaqMan OpenArray plate requires 250 copies of haploid genome for each individual through hole reaction For optimal cluster plot results it is important to normalize all genomic DNA samples in an experiment so that each through hole receives the same input quantity of sample For an example quantification procedure see the following topic Quantification procedure for human DNA samples Quantification procedure for human DNA samples Quantify human DNA samples 16 The recommended amount of template for each through hole reaction in a TaqMan OpenArray plate is 250 copies of the haploid genome equivalent to 0 84 ng for human DNA samples Quantify human DNA samples using the TaqMan RNase P Detection Reagents Kit and the TaqMan DNA Template Reagents Kit M Note The recommended starting concentration for human DNA samples is 50 ng mL See the DNA Calculator in the Applied Biosystems TaqMan OpenArray Genotyping System User Guide PN4377476 Generate a standard curve using the DNA template standards provided in the TaqMan DNA Template Reagents Kit and the RNase P gene
16. primers and probe provided in the TaqMan RNase P Detection Reagents Kit Note Refer to the appropriate instrument user guide for detailed instructions on performing and analyzing runs gt Note For chemical hazards alerts see Appendix D Safety OpenArray AccuFill System User Guide Chapter 1 Sample Preparation 1 Prepare sample plate for a TagMan OpenArray Genotyping run To quantify human genomic DNA 1 Create and set up a sequence detector plate document 2 Prepare the reaction plate using the following components 2X TaqMan Universal PCR Master Mix No AmpErase UNG s 20X Primer and TaqMan Probe FAM dye mix DNA template standard or genomic DNA sample e DNase free sterile filtered water Use at least three replicates of each standard or sample and use all five DNA standards to ensure an accurate standard curve is generated The range of known copy number should bracket anticipated copy numbers of the unknown samples on the same reaction plate 3 Run the reaction plate on an Applied Biosystems Real Time PCR System using the following thermal cycling conditions avaa er av B PCR HOLD CYCLE 40 cycles Denature Anneal extend Time 10 min 15 sec 1 min Temp 95 C 92 C 60 C 4 Generate a standard curve to quantify the amount of DNA in each sample The recommended starting concentration for human DNA samples is 50 nanograms per milliliter See the DNA Cal
17. to cure then turn the switch to OFF C Open the door turn the cases over so the other side faces the light Cure the glue again Remove the OpenArray cases Instrument Product Curing time OpenArray NT Imager TaqMan OpenArray Genotyping case 2 minutes OpenArray NT Cycler OpenArray Real Time PCR case 3 minutes each side 44 OpenArray AccuFill System User Guide Frame the case Chapter 4 Prepare the plate for the NT Cycler 4 Frame the case The cases with OpenArray plates in the Case Sealing Station are shown Note The Case Sealing Station emits UV light as indicated on the label not shown above Keep at least 25 cm 10 in away from the light when operating the Case Sealing Station If there is glue on the side of the case carefully remove it with a razor blade Clean the case with a laboratory wipe that has been thoroughly sprayed with ethanol To dry the case wipe the case downward with a clean laboratory wipe Gently handle the case be sure to not apply pressure on the OpenArray plate within the case Note Dust glue or excess sample on the case may interfere with thermal uniformity and can fluoresce Make sure you thoroughly clean each case To ensure that the case achieves tight contact with the OpenArray NT Cycler thermal block you must adhere a frame with an adhesive pad to the OpenArray case Note Framing the case does not apply to TaqMan OpenArray Genotyping Analysis kits
18. with the safety symbols described in the preceding section Hazard symbol English Francais CAUTION Hazardous chemicals Read the Safety Data Sheets SDSs before handling ATTENTION Produits chimiques dangereux Lire fiche technique associ e au produit avant toute manipulation CAUTION Hazardous waste Refer SDS s and local regulations for handling and disposal ATTENTION D chets dangereux Lire fiche technique associ e et prendre connaissance de la r gulation locale associ es la manipulation et l limination des d chets DANGER High voltage DANGER Haute tension WARNING To reduce the chance of electrical shock do not remove covers that require tool access No user serviceable parts are inside Refer servicing to Applied Biosystems qualified service personnel AVERTISSEMENT Pour viter les risques d lectrocution ne pas retirer les capots dont l ouverture n cessite l utilisation d outils L instrument ne contient aucune pi ce r parable par l utilisateur Toute intervention doit tre effectu e par le personnel de service qualifi venant de chez Applied Biosystems OpenArray9 AccuFill System User Guide CHAPTER 1 Sample Preparation This chapter covers Prepare sample plate for a SYBR OpenArray Real Time PCR run 10 Prepare sample plate for a TagMan OpenArray Real Time PCR run 13 Prepare sample plate for a TagMan OpenArr
19. 3 chemical waste safety 74 TaqMan OpenArray plate handle 25 H hazard icons See safety symbols on instruments hazard symbols See safety symbols on instruments hazards See safety Help menu 53 human DNA samples quantify 16 IMPORTANT description 7 initialize the system 25 installation category 70 instrument log 52 Instrument menu 51 instrument operation safety 68 integration sample 39 81 Index L load multiple OpenArray plates 36 multi sample 17 OpenArray plates 29 33 loader tips clean 15 loading arrangement 18 21 force single sample 53 history 38 history show 51 prepare for 29 three samples 21 two samples 18 log show instrument 51 M menus software 50 moving and lifting safety computers and monitors 68 instrument 68 moving parts safety 69 multiple plates load 36 multiple samples load 17 N NT Cycler plate preparation 42 0 OpenArray AccuFill System description 60 initialize 25 summary 53 turn on off 64 OpenArray case immersion fluid 42 seal 29 sealing station 45 79 OpenArray plate files 40 load multiple plates 36 loading 29 seal 42 serial number 30 setup and load 51 82 OpenArray plates load 33 operate the instrument 68 ordering information 55 overvoltage category rating 70 P physical hazard safety 69 plate files 39 40 50 Plate Holder 26 79 clean 15 64 plate loading 51 plate sample 10 11 13 15 power switch and outlet 64 preparation
20. 7 SYBR OpenArray Real Time PCR 10 11 61 symbols safety 66 OpenArray AccuFill System User Guide Index System Self Test 25 28 51 52 T TaqMan OpenArray Genotyping 61 Genotyping run 15 Real Time PCR 61 Real Time PCR run 13 run 15 TaqMan OpenArray plate guidelines for handling 25 technical support 77 training information on 78 transcript file 39 80 U ultraviolet light safety 69 W WARNING description 7 waste bin 26 64 waste disposal guidelines 74 waste profiles description 74 workflow load an OpenArray plate 32 plate preparation 42 sample loading 24 workstation safety 71 83 Part Number 4456986 Rev A 06 2010 445698618 gt applied A biosystems by Lefe technologies Headquarters 5791 Van Allen Way Carlsbad CA 92008 USA Phone 760 603 7200 www lifetechnologies com Technical Resources and Support For the latest technical resources and support information for all locations please refer to our Web site at www appliedbiosystems com
21. FOR A PARTICULAR PURPOSE TO THE FULLEST EXTENT ALLOWED BY LAW IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE WHETHER IN CONTRACT TORT WARRANTY OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL INCIDENTAL INDIRECT PUNITIVE MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING BUT NOT LIMITED TO THE USE THEREOF WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES TRADEMARKS The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners Excel and Windows are trademarks of Microsoft Corporation Pluronic is a trademark of BASF Corporation LightCycler is a trademark of Roche Diagnostics TaqMan is a registered trademark of Roche Molecular Systems Inc Copyright 2010 Life Technologies Corporation All rights reserved Part Number 4456986 Rev A 06 2010 Contents About This Guide eet kk kk kk kk kk kk kk kk kk kak kk kk 7 PURPOSE 5 Em 7 Safety information e a HRH a T a a HHHH e 7 Safetyalert Words eines a ha 2 ttle tee al a War breed 7 SDSS Be DA ee ac Re tux toe dee els E 8 Safety labels on instruments 2 8 CHAPTER 1 Sample Preparation 9 Prepare sample plate for a SYBR OpenArray Real Time PCR run 10 Materials and equipment required
22. G BIOHAZARD Biological samples such as tissues body fluids infectious agents and blood of humans and other animals have the potential to transmit infectious diseases Follow all applicable local state provincial and or national regulations Wear appropriate protective equipment which includes but is not limited to protective eyewear face shield clothing lab coat and gloves All work should be conducted in properly equipped facilities using the appropriate safety equipment for example physical containment devices Individuals should be trained according to applicable regulatory and company institution requirements before working with potentially infectious materials Read and follow the applicable guidelines and or regulatory requirements in the following U S Department of Health and Human Services guidelines published in Biosafety in Microbiological and Biomedical Laboratories www cdc gov od ohs biosfty bmbl5 bmbl5toc Occupational Safety and Health Standards Bloodborne Pathogens 29 CFR 1910 1030 www access gpo gov nara cfr waisidx_01 29cfr1910a_01 html Your company s institution s Biosafety Program protocols for working with handling potentially infectious materials Additional information about biohazard guidelines is available at www cdc gov OpenArray AccuFill System User Guide 75 Appendix D Safety Safety alerts Safety alerts For the definitions of the alert words IMPORTANT CAUTION WARNI
23. NG and DANGER see Safety alert words on page 7 General alerts for all chemicals Avoid contact with skin eyes and or clothing Read the Safety Data Sheets SDSs and follow the handling instructions Wear appropriate protective eyewear clothing and gloves Specific alerts for instrumentation 76 WARNING PHYSICAL INJURY HAZARD Moving parts can crush and cut Keep hands clear of moving parts while operating the instrument ZN WARNING ULTRAVIOLET LIGHT HAZARD Looking directly at a UV light source can cause serious eye damage Never look directly at a UV light source Follow the manufacturer s recommendations for the appropriate eyewear and clothing CAUTION PHYSICAL INJURY HAZARD Do not attempt to lift or move the ZN OpenArray AccuFill instrument without the assistance of others the use of appropriate moving equipment and proper lifting techniques Improper lifting can cause painful and permanent back injury Depending on the weight moving or lifting an instrument may require two or more persons CAUTION Do not tip the OpenArray AccuFill instrument on end Tipping damages the instrument hardware and electronics and is an unsafe practice OpenArray AccuFill System User Guide Documentation and Support Related documentation The following related documents are shipped with the system Document Pari Description number OpenArray AccuFill 4457095 Provides info
24. OpenArray plate stored in the Open Array Plate Input Folder After loading the sample the OpenArray AccuFill System generates an output file for each OpenArray plate in TPF format The unique alphanumeric plate identification number that is coded for each OpenArray plate This number is visible opposite the barcode the plate and is tagged to the information contained within the plate file A single nucleotide polymorphisms SNP plate file that is the output of Sample Integration It is used to process an OpenArray plate in the OpenArray NT Cycler SYBR Green I Dye a fluorescent dye that binds preferentially to double stranded DNA The optics in the OpenArray NT Cycler can detect the intensity of fluorescence emitted from bound SYBR Green I Based on fluorescence monitoring from SYBR Green I the OpenArray NT Cycler calculates the number of copies of target DNA OpenArray9 AccuFill System User Guide 79 Glossary subarray TagMan target DNA through hole file 80 The OpenArray plate is divided into 48 subarrays each subarray consists of 64 through holes in an 8x8 square configuration A dual labeled probe that is commonly used in laboratories for qPCR studies The TaqMan OpenArray Real Time PCR Plates qPCR platform is ideally suited for TaqMan assays The particular sequence of DNA in the sample in which your research is focused Bottomless reaction wells in the OpenArray plate There are 3072 throu
25. al Time PCR Platform page click Related Products Required equipment The OpenArray AccuFill System PN 4457243 includes the following components supplied by Applied Biosystems Item Part Number OpenArray AccuFill Instrument 4457244 OpenArray AccuFill Software 4457245 Computer 4398961 Monitor 4404414 Required equipment and materials not included 56 The following items are not supplied Item Source TaqMan OpenArray Real Time PCR Platform Applied Biosystems PN 4408510 OpenArray NT Cycler System Applied Biosystems PN 4453106 OpenArray NT Imager Applied Biosystems PN 4412491 OpenArray Case Sealing Station Applied Biosystems PN 4409361 Uninterruptible Power Supply UPS Franek PN 5135 003 recommended Electrical power strips Bleach 10 DNA ExitusPlus AppliChem PN A7089 Ethanol Compressed nitrogen gas OpenArray9 AccuFill System User Guide Optional materials Item Appendix A Ordering Information Optional materials Source Barcode reader Fine point silver marker Required reagents Reagents required for an OpenArray Real Time PCR plate run Item Source Hi Di Formamide Applied Biosystems PN 4311320 Pluronic F 68 10 stock Invitrogen PN 24040 032 LightCycler FastStart DNA Master SYBR Green kit Roche Applied Science PN 12239264001 Alb
26. ample plate l Repeat loading removing and encasing steps for each OpenArray plate 32 OpenArray AccuFill System User Guide Chapter 2 Sample Loading 2 Load an OpenArray plate Load an OpenArray plate To load an OpenArray plate 1 Visually verify that the Tip Status window in the software matches the state of the tips on the deck Make sure that Gray areas in the Tip Status window indicate that no tips are present White areas indicate that tips are present If the software and the tips on the deck do not match click the appropriate section in the Tip Status window Select the state of the tip boxes by clicking on the sections Tip Box 1 Note Use tips within one week after opening the box Discard any unused tips after one week OpenArray AccuFill System User Guide 33 2 Chapter 2 Sample Loading Load an OpenArray plate 2 Verify each of the following conditions and when verified select its check box Tips are configured as shown in step 1 Waste bin is empty e OpenArray plate is in the Plate Holder Setup Deck E E Select the state of the tip boxes by clicking on the sections Tip Box 1 Tip Box 2 Verify The tips are configured as shown above The Waste Bin is empty The OpenaArray Plate is in the Plate Holder F Remove foil from the highlighted section of the Sample Plate Close the Instrument Door lt Back Load Cancel Note The software wi
27. ard safety 75 S VET Tp TTT 76 General alerts for all chemicals 76 Specific alerts for instrumentation 76 Documentation and Support 77 Related documentation 52224 s n oag ag meet au e ERR lk eae Road 77 Obtaining Support scis reet ceed edge aan Rae de Ped Pe HHH 78 GIOSSA TX kanuna n en E ea ceo etra a x malla ede i de a aei Matt a avan 79 pi a Sa SS eeu see r pp 81 OpenArray AccuFill System User Guide 5 Contents 6 OpenArray AccuFill System User Guide Purpose Safety information Safety alert words OpenArray AccuFill System User Guide About This Guide The OpenArray AccuFill System User Guide provides reference information for the OpenArray AccuFill system and describes how to prepare maintain and troubleshoot the system Note For general safety information see this section and Appendix D Safety on page 65 When a hazard symbol and hazard type appear by a chemical name or instrument hazard see the Safety Appendix for the complete alert on the chemical or instrument Four safety alert words appear in Applied Biosystems user documentation at points in the document where you need to be aware of relevant hazards Each alert word IMPORTANT CAUTION WARNING DANGER implies a particular level of Observation or action as defi
28. ate adjust the total volume OpenArray AccuFill System User Guide 11 12 Chapter 1 Sample Preparation Prepare sample plate for a SYBR OpenArray Real Time PCR run OpenArray 1 Sample 1 OpenArray 3 Sample 1 OpenArray 5 Sample 1 OpenArray 7 Sample lue 1 4 Plan which sections of the sample plate you will load with samples Each 4 x 12 well rectangular area corresponds to one OpenArray plate You may find it helpful to mark these areas with a fine point silver marker as shown in the following illustration OpenArray 2 Sample 1 OpenArray 4 Sample 1 OpenArray 6 Sample 1 OpenArray 8 Sample 1 5 Pipette 3 5 uL OpenArray PCR Master Mix into each well of the 48 well section of the 384 well sample plate designated OpenArray 1 6 Pipette 1 5 uL of the template into each well 7 Pipette gently up and down to mix Do not use a vortex mixer 8 Cover the sample plate with sealing tape Centrifuge the plate for 1 minute at 1000 rpm 9 Place the plate on ice to keep the samples cold OpenArray AccuFill System User Guide Chapter 1 Sample Preparation Prepare sample plate for a TagMan OpenArray9 Real Time PCR run Prepare sample plate for a TaqMan OpenArray Real Time PCR run This section provides instructions on preparing a sample plate for a TaqMan OpenArray Real Time PCR run Materials and equipment required See Ordering Information on page 55 for a list of equipment kits and con
29. ause a fire Before turning on the instrument verify that the fuses are properly installed and that the instrument voltage matches the power supply in your laboratory WARNING FIRE HAZARD For continued protection against the risk of fire A replace fuses only with fuses of the type and rating specified for the instrument WARNING ELECTRICAL HAZARD Grounding circuit continuity is required for the safe operation of equipment Never operate equipment with the grounding conductor disconnected WARNING ELECTRICAL HAZARD Use properly configured and approved line cords for the voltage supply in your facility WARNING ELECTRICAL HAZARD Plug the system into a properly grounded receptacle with adequate current capacity The AccuFill system has an installation overvoltage category of II and is classified as portable equipment OpenArray9 AccuFill System User Guide Appendix D Safety Instrumentation safety Workstation safety Correct ergonomic configuration of your workstation can reduce or prevent effects such as fatigue pain and strain Minimize or eliminate these effects by configuring your workstation to promote neutral or relaxed working positions AN CAUTION MUSCULOSKELETAL AND REPETITIVE MOTION HAZARD These hazards are caused by potential risk factors that include but are not limited to repetitive motion awkward posture forceful exertion holding static unhealthy positions contact pressure and o
30. ay Genotyping run 15 OpenArray AccuFill System User Guide 9 1 Chapter 1 Sample Preparation Prepare sample plate for a SYBR OpenArray Real Time PCR run Prepare sample plate for a SYBR OpenArray Real Time PCR run This section provides instructions on preparing samples for a SYBR OpenArray Real Time PCR run Materials and equipment required See Ordering Information on page 55 for a list of equipment kits and consumables necessary for this procedure Prepare the reagents for use in the master mix To prepare the reagents for use in the master mix 1 Dilute the concentrated stock of SYBR Green I dye to 240X shown Reagent Volume in pL SYBR Green dye 5 Water 495 Total volume 500 2 Check the stock concentration a Dilute a 10 uL aliquot of diluted SYBR Green I dye into 90 uL water b Measure the optical density at 494 nm c Adjust the OD to 0 5 to 0 6 units by adding SYBR Green I dye or water to the 240X dilution d Store at 20 C in 20 uL aliquots 3 Prepare 10 mg mL BSA working solution as shown Store at 20 C in 500 uL aliquots Reagent Combine BSA 100 mg Water 10 mL Total volume 10 mL at 10 mg mL 4 Prepare 15 glycerol working solution as shown Store at room temperature Reagent Combine Glycerol 75 mL Water 42 5 mL Total volume 50 0 mL at 1596 10 OpenArray AccuFill System User Guide Chapter 1 Sam
31. ay plate You may find it helpful to mark these with a fine point silver marker as shown in the following illustration OpenArray 1 OpenArray 2 Sample 1 Sample 1 OpenArray 3 OpenArray 4 Sample 1 Sample 1 OpenArray 5 OpenArray 6 Sample 1 Sample 1 OpenArray 7 OpenArray 8 Sample 1 Sample 1 4 Pipette 3 8 uL of Master Mix into each well of the 48 well section of the 384 well sample plate designated OpenArray plate 1 5 Pipette 1 2 uL of the sample into each well 6 Cover the sample plate with sealing tape Centrifuge the plate for 1 minute at 1 000 rpm Place the plate on ice to keep the samples cold 14 OpenArray AccuFill System User Guide Chapter 1 Sample Preparation 1 Prepare sample plate for a TagMan OpenArray Genotyping run Prepare sample plate for a TaqMan OpenArray Genotyping run This section provides instructions on preparing a sample plate for a TaqMan OpenArray Genotyping run Sample plate preparation A single OpenArray plate can accept one to three loads from a sample plate depending on how many samples per subarray are required To prepare a sample plate for a TaqMan Genotyping run do the following steps Note For chemical hazard alerts see Appendix D Safety pp y 1 Be sure that the OpenArray 384 well sample plate OpenArray AccuFill Loader Tips and Plate Holder are completely clean and dry Soak the plate guide loader tips and Plate Holder in 10 bleach for at least 10 minute
32. cal requirements for container storage Minimize contact with chemicals Wear appropriate personal protective equipment when handling chemicals for example safety glasses gloves or protective clothing For additional safety guidelines consult the SDS Minimize the inhalation of chemicals Do not leave chemical containers open Use only with adequate ventilation for example fume hood For additional safety guidelines consult the SDS Handle chemical wastes in a fume hood After emptying a waste container seal it with the cap provided Dispose of the contents of the waste tray and waste bottle in accordance with good laboratory practices and local state provincial or national environmental and health regulations Waste disposal If potentially hazardous waste is generated when you operate the instrument you must 74 Characterize by analysis if necessary the waste generated by the particular applications reagents and substrates used in your laboratory Ensure the health and safety of all personnel in your laboratory Ensure that the instrument waste is stored transferred transported and disposed of according to all local state provincial and or national regulations D IMPORTANT Radioactive or biohazardous materials may require special handling and disposal limitations may apply OpenArray9 AccuFill System User Guide Appendix D Safety Chemical safety Biological hazard safety General biohazard A WARNIN
33. case and have approximately 1 cm 0 39 in of space at the top 4 If necessary adjust the fluid level so it is at the top of the OpenArray plate Remove any excess immersion fluid with a transfer pipette Seal the OpenArray plate Seal the OpenArray plate in the case with ultraviolet UV glue Note If your tube of glue has been open longer than two weeks discard it and use a new tube Store glue in a dark place for example a drawer because ambient light can cure the glue in the tip 1 Place a drop of UV glue on one edge of the case opening fill until it reaches the top of the OpenArray plate Angle the pipette tip so that the glue reaches the inside rail as shown 2 Place a similar amount of glue on the other side of the case opening as shown OpenArray AccuFill System User Guide 43 4 Chapter 4 Prepare the plate for the NT Cycler Seal the OpenArray plate 3 Add glue on each side of the case until the glue runs together in the middle Fill the case to the top Make sure both the left and right sides are covered with glue as shown 4 If there are air bubbles in the glue carefully remove them by inserting a small transfer pipette 5 With a laboratory wipe wipe any excess glue from the surface of the glass To cure the glue place the OpenArray case into the Case Sealing Station a Open the door Place up to two cases into the device and close the door b Turn the switch to ON Allow the glue
34. caution label shown below is located on the OpenArray AccuFill instrument in two places Near the power switch on the left side of the instrument Near the power inlet OpenArray AccuFill System User Guide 67 Appendix D Safety Instrumentation safety General instrument safety Move and lift the instrument Move and lift stand alone computers and monitors Operate the instrument 68 T WARNING PHYSICAL INJURY HAZARD Using the instrument in a manner not specified by Applied Biosystems may result in personal injury or damage to the instrument WARNING PHYSICAL INJURY HAZARD For safety information related to the centrifuge and thermal cycler refer to the manufacturer s documentation WARNING PHYSICAL INJURY HAZARD Using the centrifuge or thermal cycler in a manner not specified by the manufacturer may result in personal injury or damage to the instrument T CAUTION PHYSICAL INJURY HAZARD The instrument is to be moved and positioned only by the personnel or vendor specified in the applicable site preparation guide If you decide to lift or move the instrument after it has been installed do not attempt to lift or move the instrument without the assistance of others the use of appropriate moving equipment and proper lifting techniques Improper lifting can cause painful and permanent back injury Depending on the weight moving or lifting an instrument may require two or more persons T WARNING
35. ck OK Open the instrument Remove OpendArray Plate carefully remove the loaded OpenArray plate Please remove OpenArray Plate 1 from the Plate Holder and insert it into an immersion fluid filled case and immediately insert it into a prepared case See Insert the loaded OpenArray plate into a Plate Holder Position 1 case on page 42 Skip steps 7b through 7g and Remove proceed to Loading history on page 38 j Plate Holder Position 2 b If you are loading more than one OpenArray plate you will see the Remove OpenArray Plate window on page 37 when the load Plate Holder Position 3 sequence is done Open the instrument carefully remove the loaded OpenArray plate and insert it into a prepared Plate Holder Position 4 case immediately See Insert the loaded OpenArray plate into a case on page 42 c Remove the foil from the next sample plate section as indicated by the illustration in the window and close the enclosure door d Select the Remove foil check box and click OK e Close the instrument door f The instrument loads the next OpenArray plate 36 OpenArray AccuFill System User Guide Chapter 2 Sample Loading 2 Load an OpenArray plate g Continue from step b until the last OpenArray plate has been loaded Remove OpenArray Plate Please remove OpenArray Plate 1 from the Plate Holder and insert it into an immersion fluid filled case Plate Holder Position 1 Remove fo
36. culator in the Applied Biosystems TagMan OpenArray Genotyping System User Guide PN4377476 Perform multi sample loading The OpenArray AccuFill system enables you to load more than one sample per subarray Before performing multi sample loading set up the sample plates to accommodate the number of samples you will use per subarray for Genotyping applications The following table shows sample plate volumes in microliters for two sample and three sample loads Sample PlateVolumes pL Two samples Three samples 4 3 Note Multi sample loading is available only for Genotyping applications OpenArray9 AccuFill System User Guide 17 1 Chapter 1 Sample Preparation Prepare sample plate for a TagMan OpenArray Genotyping run Set up the sample These instructions describe how to set up a sample plate with two separate DNA plate for two samples samples 1 Label the two sections of the sample plate so that you can keep track of what is loaded in each section An example is shown in the following illustration OpenArray 1 Sample 2 OpenArray 2 OpenArray 2 Sample 1 Sample 2 OpenArray 3 Sample 2 OpenArray 4 OpenArray 4 Sample 1 Sample 2 D IMPORTANT Be sure to track where the samples are in the sample plate For each sample you use Applied Biosystems recommends creating a sample information file in comma separated values CSV format This CSV file can be used in sample integration See Use Sample Int
37. egration on page 39 for more information OpenArray 1 Sample 1 OpenArray 3 Sample 1 2 Use the following loading arrangement Refer to the example on page 20 for the locations of the sample plate sections e OpenArray 1 OpenArray plate for the first run is in Plate Holder position 1 The first sample for the subarray comes from section 1 of the sample plate which holds samples 1 to 48 The second sample for the subarray comes from section 2 of the sample plate which holds samples 49 to 96 e OpenArray 2 OpenArray plate for the second run is in Plate Holder position 2 The first sample for the subarray comes from section 3 of the sample plate which holds samples 1 to 48 The second sample for the subarray comes from section 4 of the sample plate which holds samples 49 to 96 18 OpenArray AccuFill System User Guide Chapter 1 Sample Preparation 1 Prepare sample plate for a TagMan OpenArray Genotyping run OpenArray 3 OpenArray plate for the third run is in Plate Holder position 3 The first sample for the subarray comes from section 5 of the sample plate which holds samples 1 to 48 The second sample for the subarray comes from section 6 of the sample plate which holds samples 49 to 96 e OpenArray 4 OpenArray plate for the fourth run is in Plate Holder position 4 The first sample for the subarray comes from section 7 of the sample plate which holds samples 1 to 48
38. ent OpenArray 1 OpenArray plate for the first run is in Plate Holder position 1 First sample for the subarray comes from section 1 of the sample plate which holds samples 1 to 48 Second sample for the subarray comes from section 2 of the sample plate which holds samples 49 to 96 Third sample for the subarray comes from section 3 of the sample plate which holds samples 97 to 144 e OpenArray 2 OpenArray plate for the second run is in Plate Holder position 2 First sample for the subarray comes from section 3 of the sample plate which holds samples 1 to 48 Second sample for the subarray comes from section 4 of the sample plate which holds samples 49 to 96 Third sample for the subarray comes from section 6 of the sample plate which holds samples 97 to 144 An example of three samples per subarray is shown on page 22 OpenArray AccuFill System User Guide 21 Subarray Al 22 Chapter 1 Sample Preparation Prepare sample plate for a TagMan OpenArray Genotyping run Sample 1 Sample 48 N N Sample Plate Sample 97 Sample 49 Load 1 Load 3 Sample 1 00000000 00000000 Sample 97 OpenArray Plate e z7 pek Sample 96 zU 7 gi N N N Sample 144 Load 2 Sample 48 00000000 00000000 Subarray D12 OpenArray AccuFill System User Guide CHAPTER 2 Sample Loading This chapter covers Materials and
39. equipment required 24 Work l OW Al ssi xi ette ee xer deb E K igh GA de r M a de 24 Important guidelines for handling the plate 25 Initialize the system 25 Prepare the G S S2 Xin wid e REN dp en EVE Epp 29 Prepare for loading ose tree ek k Weda Sala Qis lk Re dei et 29 Load an OpenArray plate 32 OpenArray AccuFill System User Guide 23 2 Chapter 2 Sample Loading Materials and equipment required Materials and equipment required See Ordering Information on page 55 for a list of equipment kits and consumables necessary for this procedure Workflow The workflow for preparing the OpenArray AccuFill instrument and OpenArray cases summarizes the simplest loading scenario which involves one sample and one OpenArray Workflow Initialize the system page 25 l Prepare the cases page 29 l Prepare for loading page 29 l Load an OpenArray plate page 32 24 OpenArray AccuFill System User Guide Chapter 2 Sample Loading 2 Important guidelines for handling the plate Important guidelines for handling the plate Wear gloves that are one size smaller than the size you typically wear to help prevent excess glove material from contacting the OpenArray plate while
40. er the unique serial number of the OpenArray plate that is loaded in the first position of the Plate Holder The procedure to enter the serial number varies depending on whether you use Sample Integration If you are not using Sample Integration enter the plate serial number by either Typing the serial number or Using a barcode reader to scan the serial number from the plate itself If you are using Sample Integration enter the plate serial number using any one of the following three methods e Type the serial number There must be a file by the same name in the default directory Use a barcode reader to scan the serial number from the OpenArray plate itself There must be a file by the same name in the default directory Click the Browse button and locate the file for the OpenArray plate As you enter the serial number it is reflected in the representation of the OpenArray plates in the lower section of the window Note If you enter the name of an OpenArray plate that you have already used the software warns you that the name has already been used but will not prevent you from continuing Place the OpenArray plate into the Plate Holder When handling OpenArray plates Always hold OpenArray plates by the edges If you inadvertently drop a loaded OpenArray plate discard it in the sharps waste container Besure to load OpenArray plates within an hour after you open them Hold the OpenArray plate by the edges and place
41. gh holes in each OpenArray plate Each through hole contains a single assay A self metering loading system ensures a consistent 33 nL reaction volume within each through hole Proprietary plate coatings hold reagents within the through holes A transcript plate file that is the output of Sample Integration It is used to process an OpenArray plate in the OpenArray NT Cycler OpenArray9 AccuFill System User Guide A Applied Biosystems website 56 biohazardous waste handle 75 case sealing station 45 79 cases OpenArray 29 CAUTION description 7 chemical safety 72 chemical waste safety 73 74 chemistries available 61 cleaning instructions 15 64 comma separated values CSV file 18 21 38 39 79 compressed gases safety See also pressurized fluids safety 69 consumables required 58 D DANGER description 7 directories storage 39 40 50 dispose waste 26 DNA samples prepare 16 documentation 77 E edit system preferences 52 electrical safety 70 electromagnetic compatibility standards See EMC standards EMC standards 71 empty waste 26 equipment and materials 56 ergonomics safety 71 OpenArray AccuFill System User Guide Index F files spf 39 tpf 39 comma separated values CSV 18 21 38 39 79 plate 39 sample plate OpenArray plate 50 SNP 39 storage 50 transcript 80 force single sample loading 53 G glossary 79 guidelines chemical safety 72 chemical waste disposal 7
42. il from these Sample Plate sections Plate Holder Position 2 Plate Holder Position 3 Plate Holder Position 4 M Note After you have finished your experiment clean the OpenArray AccuFill instrument OpenArray AccuFill System User Guide 37 2 Chapter 2 Sample Loading Load an OpenArray plate Loading history The software displays the loading history which logs the following information for the completed load e OpenArray Plate Barcode Sample Plate Barcode e Sample Plate Selected Area Sample Number Plate Holder Position Sample Load Time e Load Status Save the loading You can save the load information by either history Clicking the Copy All button to capture the contents of the table You can then paste the data into an existing spreadsheet or word processing document The contents are copied in a tab delimited format Clicking the Save As button to save the contents of the table This method saves the data to a CSV file with a name and location of your choosing To not save any information click Close 38 OpenArray9 AccuFill System User Guide Use Sample Integration CHAPTER 3 Sample Integration Sample Integration combines the information about your samples stored in a comma separated values CSV file with the information about the pre loaded assays in the OpenArray plate The output of Sample Integration is the assignment of all samples to their respective as
43. ile Use Sample Integration Force Single Sample Loading Sample Plate TestSamplePlate Plate Holder Position 1 Plate Holder Position 2 Plate Holder Position 3 Plate Holder Position 4 Select Samples to Load Click the section on the sample plate from which the first sample will be extracted The image on the right shows how the sample will be applied to the OpenArray Plates Plate Holder Position 1 15101 late Holder Position 2 TST02 Plate Holder Position 3 late Holder Position 4 l ll OpenArray AccuFill System User Guide 29 30 Chapter 2 Sample Loading Prepare for loading Ifthe enclosure door on the AccuFill instrument is not open open it by grasping the door handle and lifting the door up Type the name of the sample plate in the Sample Plate field The sample plate name can also be scanned with a barcode reader which is not supplied with the AccuFill system Insert the 384 well sample plate with the foil cover still in place Press on the plate until you hear it snap into place Note Do not remove the foil from the 384 well sample plate at this stage If you are using sample integration see Use Sample Integration on page 39 If you are performing multi sample loading see Perform multi sample loading on page 17 Select 1 from the Samples Per Subarray drop down list In the Plate Holder Position 1 text field ent
44. instrument Its columns include Number sequential numbering of the events Date the date and time the event took place Message a description of this event To close the instrument log select Hide Instrument Log from the Instrument menu Run System Self Test This command displays a message telling you to clear the deck empty the waste bin and close the door before moving forward with the System Self Test After you have completed all those tasks clicking Proceed starts the system self test The test runs and displays its progress in a System Self Test window When the test is done the window closes and you can proceed with normal operation Edit Preferences This command opens the Preference window that enables you to establish settings for several software options Preferences 52 OpenArray AccuFill System User Guide Chapter5 OpenArray AccuFill Software Help The software options are Require Sample Integration When you select this option Sample Integration is automatically selected in the Setup Load Information window and you cannot change that selection Force Single Sample Loading When you select Force Single Sample Loading Single Sample Integration is automatically selected in the Setup Load Information window and you cannot change that selection With Single Sample Loading the same sample is loaded into each of the 64 through holes that make up a subarray of the OpenArray plate
45. instruments Each symbol may appear by itself or with text that explains the relevant hazard see Safety labels on instruments on page 8 These safety symbols may also appear next to DANGERS WARNINGS and CAUTIONS that occur in the text of this and other product support documents Symbol Description Indicates that you should consult the manual for further information and to proceed with appropriate caution gt Indicates the presence of an electrical shock hazard and to proceed with appropriate caution Indicates the presence of a hot surface or other high temperature hazard and to proceed with appropriate caution gt 66 OpenArray AccuFill System User Guide Appendix D Safety Instrumentation safety Environmental The following symbol applies to all Applied Biosystems electrical and electronic symbols on products placed on the European market after August 13 2005 instruments Symbol Description Do not dispose of this product as unsorted municipal waste Follow local municipal waste ordinances for proper disposal provisions to reduce the environmental impact of waste electrical and electronic equipment WEEE European Union customers Call your local Applied Biosystems Customer Service office for equipment pick up and recycling See www appliedbiosystems com for a list of customer service offices in the European Union V Ld Locations of safety labels on instruments The
46. k on the deck 2 If there is a Plate Holder on the deck check if there are any OpenArray plates on it If necessary remove them 3 If there is not a Plate Holder on the deck place one on the deck Orient the Plate Holder so that the text etched on it is readable with the barcode on the left 26 OpenArray AccuFill System User Guide Chapter 2 Sample Loading 2 Initialize the system D IMPORTANT The locating bars and Plate Holder must be clean and free of any foreign material which can cause a shift in location To insert the Plate Holder into its place on the deck align the top and left edges with the metal guide bars on the deck and firmly press down You will hear it snap into place Metal guide bars 4 If necessary replace the tip boxes M Note Tip boxes contain 384 tips divided into 8 sections When you click Load the AccuFill instrument loads as though a new full box of tips is on the deck System software prompts you to verify that tips are in the locations shown in the Setup Deck screen Clicking a section in the Setup Deck window confirms that tips are in that section of the tip box We recommend using a full tip box a Place tip boxes into the assigned locations OpenArray AccuFill System User Guide 27 Chapter 2 Sample Loading Initialize the system b Place tip boxes on the deck in the two side by side recessed rectangular platforms See the illustration for the location of the
47. late File Folder 50 The Instrument menu 224 E a A AEA E 51 Setup and Load OpenArray Plates 51 Cancel Current Operation kk kk kk kk kk KK kK KK KK KK KK es 51 Show Deck mer HE ioe nee bee w oe 51 Show Loading History 52x m kay da dala ca ede td 51 Show Instrument Log kk kk kk kk kk kk kk kK kK kK kK KK kk kk kk rn 52 Ramn Systemi Self Tests l Aslan kal Der REEL RUM dead Cr pu p PER 52 EditiPReterencesr c a Ak l Ab da unb tt est Lett Lots M MA 52 Help LM 53 Ordering Information bb How to order from the Applied Biosystems website 56 Required equipment 222543224248 no ere 3 wis kk kk kk kk kk be kk kk 56 Required equipment and materials not included 56 Optional materials ee kk n 57 Required reagents see wep kk kk ta eve be dew kk kk kk kk kk kk kk kk k 57 Required consumables eee donee dak KL hina Sees cod eo See eee yess terne 58 System Overview 2ic ub dr RR nets kk kk kk kk kk kk ak 59 OpenArrayS AccuFill Systemi oct annm baled ee ee OIN ied 60 Availablesrun types ise Mend ges RH Eu LEER 61 OpenArra
48. ll not continue until you select all the check boxes 3 With forceps peel off the foil covering the area of the sample plate containing the samples to be loaded on the OpenArray plate 4 Select the check box Remove foil from the highlighted section of the Sample Plate 5 Close the instrument door 34 OpenArray AccuFill System User Guide Chapter 2 Sample Loading 2 Load an OpenArray plate 6 Click Load Note If the number of OpenArray plates in the instrument differs from the number that is entered in the Setup Load Information window an error message instructs you to remove any extra OpenArray plates Correct the error and continue You can follow the progress of the OpenArray plate loading on the screen The samples in each tip are loaded in the OpenArray plate Each tip fills the 64 through holes in one subarray travelling in the pattern shown the following illustration shows the load path for only one sample stop Sections of the sample plate are loaded in a three sample subarray order first section 2 then section 1 and then section 3 OpenArray AccuFill System User Guide 35 Chapter 2 Sample Loading Load an OpenArray plate 7 Ifyou are loading only one OpenArray plate follow step a If you are loading more than one OpenArray plate follow step b through step g a If you are loading only one OpenArray plate you will see the Remove OpenArray Plate window when the load sequence is done Cli
49. m draws the master mix and sample across the surface of an OpenArray plate The solution does not need to be dispensed in specific volumes because the holes are self metering Nor does the solution need to be forced into the holes The same coating process that holds liquid in the through holes allows the liquid to be drawn in by capillary action Because there are no closed wells air bubbles are not trapped during the dispensing process The OpenArray AccuFill instrument and its component parts are shown Enclosure door Tip box System stop button Waste bin Sample plate Plate Holder 60 OpenArray AccuFill User Guide Appendix B System Overview Available run types Available run types The loading procedure is optimized for the downstream Real Time PCR application on the OpenArray platform You may choose to perform qPCR using one of the following available chemistries SYBR OpenArray Real Time PCR TaqMan OpenArray Real Time PCR or TaqMan OpenArray Genotyping Use only the chemistry that your application requires For SYBR OpenArray Real Time PCR runs with OpenArray SYBR Real Time PCR Plates see Prepare sample plate for a SYBR OpenArray real time PCR run on page 10 For TaqMan OpenArray Real Time PCR runs with TaqMan OpenArray Real Time PCR Plates see Prepare sample plate for a TaqMan OpenArray real time PCR run on page 13 For TaqMan OpenArray Genotyping runs with TaqMan O
50. n OpenArray plate cse eU yak KK KK KK kk pees be PASE A MS Ru 32 WorkflOWE utr ka y kan ka en ba dn ku dak ede ee nite RME Yek tug 32 Load an OpenArray plate n tete TRIS e RERI te RN e eng 33 loadingehiStoby ss coe karn oL eS ME ELM In m M TU A E a ve DE 38 OpenArray AccuFill System User Guide 3 Contents CHAPTER 3 CHAPTER 4 CHAPTER 5 APPENDIX A APPENDIX B Sample Integrallohi a a s kes se olana a dal aa ak cadens 39 Use Sample Integration 0 000 kk kK kK kK KK KK kK KK KK kk kk kk kk kk kK kK kk kk kK kk kk 39 Prepare the plate for the NT Cycler 41 Workflow s a ean nin Awal tak eee ERE KWE k a ba aban Re ean Coat ke Qur 42 Insert the loaded OpenArray plate into a case 42 Seal the OpenArray plate 43 Frame the case siiis x xalka MR kak AN ad MM d KA 45 OpenArray AccuFill Software 49 OVERVIEW c ney acct ac enm hrs CREE eel E E W eee W dated andy ee 50 THe File3menuse ze Se wa n e TO bn ea sores ares eaten 50 Create Template Sample Plate File Folder 50 Explore OpenArray Plate File Folder cc KK KK KK KE KK KK 50 Explore Sample Plate File Folder 50 Explore Loaded OpenArray P
51. ned below IMPORTANT Indicates information that is necessary for proper instrument operation accurate chemistry kit use or safe use of a chemical ZN AN ZN CAUTION Indicates a potentially hazardous situation that if not avoided may result in minor or moderate injury It may also be used to alert against unsafe practices WARNING Indicates a potentially hazardous situation that if not avoided could result in death or serious injury DANGER Indicates an imminently hazardous situation that if not avoided will result in death or serious injury This signal word is to be limited to the most extreme situations Except for IMPORTANTS each safety alert word in an Applied Biosystems document appears with an open triangle figure that contains a hazard symbol These hazard symbols are identical to the hazard symbols that are affixed to Applied Biosystems instruments see Safety symbols on page 66 About This Guide Safety information SDSs The Safety Data Sheets SDSs for any chemicals supplied by Applied Biosystems or Ambion are available to you free 24 hours a day For instructions on obtaining SDSs see SDSs on page 73 IMPORTANT For the SDSs of chemicals not distributed by Applied Biosystems or Ambion contact the chemical manufacturer Safety labels on instruments The following CAUTION WARNING and DANGER statements may be displayed on Applied Biosystems instruments in combination
52. ng on the instrument AN WARNING CHEMICAL HAZARD Four liter reagent and waste bottles can crack and leak Each 4 liter bottle should be secured in a low density polyethylene safety container with the cover fastened and the handles locked in the upright position Wear appropriate eyewear clothing and gloves when handling reagent and waste bottles A WARNING CHEMICAL STORAGE HAZARD Never collect or store waste in a glass container because of the risk of breaking or shattering Reagent and waste bottles can crack and leak Each waste bottle should be secured in a low density polyethylene safety container with the cover fastened and the handles locked in the upright position Wear appropriate eyewear clothing and gloves when handling reagent and waste bottles To minimize the hazards of chemicals Read and understand the Safety Data Sheets SDSs provided by the chemical manufacturer before you store handle or work with any chemicals or hazardous materials See About SDSs on page 73 Minimize contact with chemicals Wear appropriate personal protective equipment when handling chemicals for example safety glasses gloves or protective clothing For additional safety guidelines consult the SDS OpenArray AccuFill System User Guide Appendix D Safety Chemical safety Minimize the inhalation of chemicals Do not leave chemical containers open Use only with adequate ventilation for example fume hood Fo
53. penArray Genotyping Plates see Prepare sample plate for a TaqMan OpenArray genotyping run on page 15 OpenArray9 AccuFill User Guide 61 62 Appendix B System Overview Available run types OpenArray AccuFill User Guide APPENDIX C Cleaning the OpenArray AccuFill Instrument This appendix covers Cleanirig instr ctionS R cd ba Sa ba eae WENA kk K k 64 Spill accidents DD gh E AD epee oa tee T Be 64 OpenArray AccuFill System User Guide 63 Appendix C Cleaning the OpenArray AccuFill instrument Cleaning instructions Cleaning instructions After you have finished your experiment clean the OpenArray AccuFill instrument Clean the outside of the instrument Clean the outside of the OpenArray AccuFill instrument by wiping it with a clean dry cloth Do not use solvents Clean the inside of the instrument Note For chemical hazard alerts see Appendix D Safety Inside the AccuFill instrument the waste bin and Plate Holder are removable parts that you can clean To clean the parts 1 Remove the waste bin and Plate Holder from the deck of the AccuFill instrument 2 Spray the parts with DNA ExitusPlus and wait 10 minutes 3 Rinse the parts with tap water to wash away the solution 4 Rinse the parts with ethanol 5 Allow the parts to dry for 5 minutes before using them again Make sure the parts are completely dry before loading the
54. penArray plate file folder in a Windows Explorer window The default location of the plate file folder is C openArray Loaded OpenArray Plates 50 OpenArray AccuFill System User Guide Chapter5 OpenArray AccuFill Software 5 The Instrument menu The Instrument menu Setup and Load OpenArray Plates Show Deck Show Loading History Show Instrument Log Run System Self Test Edit Preferences Setup and Load OpenArray Plates This command launches the Setup and Load function Select this menu item when you want to start a run It is similar to the Setup and Load button Cancel Current Operation This command stops the current loading operation The menu item is active only when you have started a run Show Deck This command returns the view to the instrument deck after you have selected another view such as the Diagnostics screen Show Loading History This command opens the Loading History window From the Loading History you can View the record of past loading runs Click the Copy All button to copy the information to an external spreadsheet program Click Save As to save the information to a CSV file OpenArray AccuFill System User Guide 51 5 Chapter 5 OpenArray AccuFill Software The Instrument menu Show Instrument Log This command displays the instrument log on the right side of the screen The log contains a detailed list of each event that happens on the
55. ple Preparation 1 Prepare sample plate for a SYBR OpenArray Real Time PCR run Sample plate preparation To prepare a sample plate for a SYBR OpenArray Real Time PCR run 1 Take the vacuum sealed OpenArray plates out of the freezer and allow them to thaw for approximately 15 minutes before opening the packages Prepare Master Mix using the contents of the LightCycler FastStart DNA Master kit The LightCycler kit comes with four vials labeled 1a 1b 2 and 3 a Pipette 10 uL of LightCycler FastStart Enzyme from vial 1a to vial 1b b Mix thoroughly by pipetting up and down Do not use a vortex mixer c Re label vial 1b with the label vial 1 Master Mix provided in the kit or peel off the label to identify the mix containing the enzyme Protect the vial from light Prepare the OpenArray PCR Master Mix as described in the following table Reagani Volume Stock Final Conc g Conc Conc Units LightCycler DNA Master SYBR 26 4 10 1 0 X Green prepared in step 2 above SYBR Green 1 1 240 1 0 7 Glycerol 8 8 15 0 5 Pluronic F 68 5 3 10 0 2 7 BSA 26 4 10 1 0 mg mL MgCl2 Use a 25 mM solution i e 26 4 25 2 5 mM vial 2 with a blue cap in the LightCycler Kit Formamide 21 1 100 8 0 X Water 70 9 Final volume without sample 186 4 Note The volumes in this procedure are for one OpenArray plate If you are loading more than one OpenArray pl
56. r 4 Prepare the plate for the NT Cycler Workflow Workflow Workflow Insert the loaded OpenArray plate into a case page 42 l Seal the OpenArray plate page 43 l Frame the case page 45 Insert the loaded OpenArray plate into a case D IMPORTANT Immersion fluid in OpenArray cases must not exposed to air for more than 60 minutes Make sure that the immersion fluid is degassed Bubbles in a case negatively affect data quality OpenArray cases are included with the OpenArray Case Sealing Station The front of cases is framed in black the back of the cases is gray To insert the loaded OpenArray plate into the case 1 Gently lift the OpenArray plate from the Plate Holder with the thumb and index finger of your left hand placing your fingers on each side near the end with the barcode Keep the side with the barcode facing you Switch hands and now hold the OpenArray plate by the sides using your index and thumb of your right hand 2 Hold the case at the top with the thumb and index finger of your left hand so that the black framed side is facing you Slide the OpenArray plate into the case so that it sits in the rails along both inside edges of the case 42 OpenArray9 AccuFill System User Guide Chapter 4 Prepare the plate for the NT Cycler 4 Seal the OpenArray plate 3 Slide the OpenArray plate all the way down into the case The bottom of the OpenArray should touch the bottom of the
57. r additional safety guidelines consult the SDS Check regularly for chemical leaks or spills If a leak or spill occurs follow the manufacturer s cleanup procedures as recommended in the SDS Comply with all local state provincial or national laws and regulations related to chemical storage handling and disposal SDSs About SDSs Chemical manufacturers supply current Safety Data Sheets SDSs with shipments of hazardous chemicals to new customers They also provide SDSs with the first shipment of a hazardous chemical to a customer after an SDS has been updated SDSs provide the safety information you need to store handle transport and dispose of the chemicals safely Each time you receive a new SDS packaged with a hazardous chemical be sure to replace the appropriate SDS in your files Obtain The SDS for any chemical supplied by Applied Biosystems is available to you free 24 SDSs hours a day To obtain SDSs 1 Goto www appliedbiosystems com click Support then select SDS 2 In the Keyword Search field enter the chemical name product name SDS part number or other information that appears in the SDS of interest Select the language of your choice then click Search 3 Find the document of interest right click the document title then select any of the following Open To view the document Print Target To print the document Save Target As To download a PDF version of the document to a destination
58. rmation for setting up the OpenArray Site Preparation Guide AccuFill System OpenArray AccuFill Quick 4457450 Provides brief step by step procedures to help you Reference Card quickly learn to use the OpenArray AccuFill System The following document provides supplementary instructions Document Patt Description number TagMan OpenArray 4377476 Provides information about the TaqMan OpenArray Genotyping System User Guide Genotyping System including step by step procedures to e Prepare a TaqMan OpenArray Genotyping Plate using the OpenArray Autoloader and OpenArray Case Sealing Station e Runa TaqMan OpenArray plate on the OpenArray NT Imager then analyze the data with the OpenArray SNP Genotyping Analysis Software Maintain the TaqMan OpenArray Genotyping Instrument Platform OpenArray AccuFill System User Guide 77 Documentation and Support Obtaining support Obtaining support To obtain additional documentation and the latest services and support information for all locations go to www appliedbiosystems com At the Applied Biosystems web site you can e Access worldwide telephone and fax numbers to contact Applied Biosystems Technical Support and Sales facilities Search through frequently asked questions FAQs Submit a question directly to Technical Support Order Applied Biosystems user documents SDSs certificates of analysis and other related documents Do
59. rs OVET VIEW RE idu eer A Kerr b x esr eur Eh 50 The Pile tien 22 ient ec ee serere he e e Rr RMMDWDWEMZEZ 9 50 The Instrument ment s ducie niied eer 4246 Date EM RR X UR deri E ned 51 Help uoti tu hee ru peu Penes tet eese mer ee dee te 53 OpenArray AccuFill System User Guide 49 5 Chapter5 OpenArray AccuFill Software Overview Overview This chapter describes the menus available in the OpenArray AccuFill software and the commands available on them The File menu Create Template Sample Plate File Explore OpenArray Plate File Folder Explore Sample Plate File Folder Explore Loaded OpenArray Plate File Folder Exit Create Template Sample Plate File Folder This command creates a sample plate file in CSV format that you can open in a spreadsheet program such as Microsoft Excel software After you select the command type the file name in the Save As window then click OK Explore OpenArray Plate File Folder This command opens the current OpenArray plate file folder in a Windows Explorer window The default location of the plate file folder is C openArray OpenArray Plates Explore Sample Plate File Folder This command opens the current sample plate file folder in a Windows Explorer window The default location of the plate file folder is C OpenArray Sample Plates Explore Loaded OpenArray Plate File Folder This command opens the current O
60. s a b Rinse with water then rinse with ethanol Let the parts completely air dry If they are immediately needed wipe dry with paper towels and spray with compressed nitrogen gas D IMPORTANT Residual water prevents correct loading of the samples into the TaqMan OpenArray plates 2 Fill the appropriate number of TaqMan OpenArray Genotyping Cases with TaqMan OpenArray Immersion Fluid a Using scissors open a container of immersion fluid b Place the case in the case rack and fill the case approximately two thirds with immersion fluid D IMPORTANT Within one hour after opening the container of immersion fluid fill the case with immersion fluid insert a loaded TaqMan OpenArray plate into the case then seal the case 3 Remove the TaqMan OpenArray plates from the freezer but do not open the packaging Allow the TaqMan OpenArray plates to thaw at room temperature approximately 5 minutes D Note Unopened TaqMan OpenArray plates can remain at room temperature for up to 24 hours D IMPORTANT Thaw only the TaqMan OpenArray plates you will need for the current loading session OpenArray9 AccuFill System User Guide 15 1 Chapter 1 Sample Preparation Prepare sample plate for a TagMan OpenArray Genotyping run Prepare the DNA samples Quality of DNA Quantity of DNA Be sure that the DNA you use for Genotyping experiments Is extracted from the raw material you are testing with an optimized protocol Does
61. says in one new updated plate file The following table shows the file extension used for the resulting Sample Integration file depending on the type of chemistry used in your analysis run Type of chemistry kit File type File extension SYBR OpenArray Real Time kits transcript pf TaqMan OpenArray Real Time kits TaqMan OpenArray Genotyping Analysis kits SNP Spf To use Sample Integration 1 In the Setup Load Information window check the Use Sample Integration check box A Browse button appears next to the Sample Plate field Use Sample Integration Sample Plate Browse Select Use Sample Integration to combine sample information with assay information This method creates a complete plate file that allows you to further process your samples 2 Type the name of a file in the Sample Plate field or click Browse to locate the plate file for the sample in CSV format By default sample plate files are stored in the directory C OpenArray Sample Plates OpenArray AccuFill System User Guide 39 40 Chapter 3 Sample Integration Use Sample Integration 3 Optionally select the Force Single Sample Loading check box to have the same sample loaded in each subarray Note When you select Force Single Sample Loading the same sample is loaded into each of the 64 through holes of a subarray on the OpenArray plate even when the plate is formatted for two or three samples per subarray Set
62. sumables necessary for this procedure Sample plate preparation To prepare a sample plate for a TagMan OpenArray Real Time PCR run follow these steps 1 Take the vacuum sealed OpenArray plates out of the freezer and allow them to thaw for approximately 15 minutes before opening the packages 2 Prepare the OpenArray PCR Master Mix as described in the tables below D IMPORTANT Master Mix components will vary depending on the source of the template you are using Use only one of the tables below depending on whether your experiment uses cDNA or other DNA Reagent for cDNA samples yu inl oe mala GeneAmp Fast PCR Master Mix 32 0 2 5X REmix supplied with the TaqMan 528 5 OpenArray kit Water 158 Final volume without sample 200 6 Reagents for gDNA samples RA An Ma GeneAmp Fast PCR Master Mix 132 0 2 1 0 5X REmix supplied with the TaqMan 52 8 5 1 0 OpenArray kit BSA 1 3 10 0 05 mg mL Water 145 Final volume without sample 200 6 Note The volumes in this procedure are for one OpenArray plate If you are loading more than one OpenArray plate adjust the total volume OpenArray9 AccuFill System User Guide 13 1 Chapter 1 Sample Preparation Prepare sample plate for a TagMan9 OpenArray Real Time PCR run 3 Plan which sections of the 384 well sample plate you will load with samples Each 4 x 12 well rectangular area corresponds to one OpenArr
63. that you choose v Note For the SDSs of chemicals not distributed by Applied Biosystems contact the chemical manufacturer Chemical waste safety Chemical waste CAUTION HAZARDOUS WASTE Refer to Safety Data Sheets and local hazards regulations for handling and disposal WARNING CHEMICAL WASTE HAZARD Wastes produced by Applied Biosystems instruments are potentially hazardous and can cause injury illness or death OpenArray9 AccuFill System User Guide 73 Appendix D Safety Chemical safety WARNING CHEMICAL STORAGE HAZARD Never collect or store waste in a glass container because of the risk of breaking or shattering Reagent and waste bottles can crack and leak Each waste bottle should be secured in a low density polyethylene safety container with the cover fastened and the handles locked in the upright position Wear appropriate eyewear clothing and gloves when handling reagent and waste bottles Chemical waste To minimize the hazards of chemical waste safety guidelines Read and understand the Safety Data Sheets SDSs provided by the manufacturers of the chemicals in the waste container before you store handle or dispose of chemical waste Provide primary and secondary waste containers A primary waste container holds the immediate waste A secondary container contains spills or leaks from the primary container Both containers must be compatible with the waste material and meet federal state and lo
64. ther workstation environmental factors To minimize musculoskeletal and repetitive motion risks Use equipment that comfortably supports you in neutral working positions and allows adequate accessibility to the keyboard monitor and mouse Position the keyboard mouse and monitor to promote relaxed body and head postures Safety and electromagnetic compatibility EMC standards This section provides information on e U S and Canadian safety standards e Canadian EMC standard European safety and EMC standards Australian EMC Standards The OpenArray AccuFill instrument has been tested to and complies with the standards listed below U S and Canadian UL 61010 1 2004 2nd Edition CSA C22 2 No 61010 1 Safety Requirements for safety Electrical Equipment for Measurement Control and Laboratory Use Part 1 General standards Requirements m ANSI UL 61010 1 Safety Requirements for Electrical Equipment for Measurement lb Control and Laboratory Use Part 1 General Requirements CAN CSA C22 2 61010 1 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements Canadian EMC The OpenArray AccuFill instrument has been tested to and complies with ICES 001 standard Issue 3 Industrial Scientific and Medical Radio Frequency Generators European safety and Safety EMC The OpenArray AccuFill instrument meets European requirements for safety standards
65. tip boxes purple and white c Remove the cover before using the tips for loading 5 Close the door on the instrument 6 Begin the System Self Test M Note System Self Test runs only at start up The test does not run again unless the system is restarted or a self test is intentionally run The System Self Test utility is in the Instrument drop down menu in the OpenArray AccuFill application Click Proceed The application performs a number of self tests and is then ready for you to continue 28 OpenArray AccuFill System User Guide Chapter 2 Sample Loading Prepare the cases Prepare the cases Cases for OpenArray plates are included with the OpenArray Case Sealing Station Fill the cases one OpenArray plate per case with immersion fluid 1 Use scissors that are clean and not rusty to open a container of immersion fluid 2 Place a case in the case rack and fill it approximately 3 4 of the way with immersion fluid D IMPORTANT Immersion fluid must not be exposed to air for more than 60 minutes Make sure that the immersion fluid is degassed Bubbles in a case negatively affect data quality Prepare for loading To set up the software 1 Click Setup amp Load The Setup Load Information window opens Setup Load Information Loading information Specify the type of load you want to perform Enter Plate and OpenArray Plate barcodes by scanning them typing them or selecting the associated f
66. umin bovine BSA Sigma PN A7906 SYBR Green Sigma PN 59430 Glycerol 99 Sigma PN G5150 Reagents required for a TaqMan OpenArray plate run Item Source 5X TaqMan OpenArray REMix Solution Applied Biosystems PN 4453927 GeneAmp Fast PCR Master Mix Applied Biosystems PN 4362070 Albumin bovine BSA OpenArray AccuFill System User Guide Sigma PN A7906 Appendix A Ordering Information Required consumables Required consumables 58 Item Source OpenArray 384 Well Sample Plates Applied Biosystems PN 4453929 OpenArray AccuFill Loader Tips Applied Biosystems PN 4457246 TaqMan OpenArray Genotyping Accessories Kit OpenArray Real Time PCR Accessories Kit Applied Biosystems PN 4404572 Applied Biosystems PN 4453975 Pipettes MLS Forceps MLS Scissors MLS Sealing tape MLS OpenArray9 AccuFill System User Guide APPENDIX B System Overview This appendix covers OpenArray AccuFill RIO scents bak NE dee ech e aha hatter ty 60 Available Fun types ses ree eere E bass beac enm 61 OpenArray9 AccuFill User Guide 59 Appendix B System Overview OpenArray AccuFill System OpenArray AccuFill System The OpenArray AccuFill System PN 4457243 is an automated system for loading samples from 384 well plates to OpenArray plates The OpenArray AccuFill syste
67. up Load Information Loading information Specify the type of load you want to perform Enter Plate and OpenArray Plate barcodes by scanning them typing them or selecting the associated file Use Sample Integration Force Single Sample Loading Sample Plate TestSamplePlate Plate Holder Position 1 Plate Holder Position 2 TSTO2 Plate Holder Position 3 L Plate Holder Position 4 4 Select the OpenArray plate file provided by Applied Biosystems by typing the name of the file in the Plate Holder Position field or click Browse to locate the plate file for the OpenArray plate OpenArray plate files are located in C OpenArray OpenArray Plates When the run is done the integrated data is saved with the prefix Loaded by default in C OpenArray Loaded OpenArray Plates The newly created plate file must now be used to process the OpenArray plates in the OpenArray NT Cycler Transfer the newly created plate file by using your local network or some form of portable media such as a CD or a USB drive OpenArray AccuFill System User Guide CHAPTER 4 4 Prepare the plate for the NT Cycler This chapter covers WW GEK ELlO WE gat pE E HN oe o A a ETERA 42 Insert the loaded OpenArray plate into a case 42 Seal the OpenAtray plate ae Loe coe baer eo ehh et KK KK ke 43 Frame the CASE PAN nn nem 45 OpenArray AccuFill System User Guide 41 4 Chapte
68. wnload PDF documents Obtain information about customer training Download software updates and patches 78 OpenArray AccuFill System User Guide case sealing station CSV file frames multi sample loading OpenArray NT Real Time PCR instrument Plate Holder sample DNA sample integration serial number spf file SYBR Glossary Uses UV light to cross link the UV curable glue and seal the OpenArray plates inside cases filled with Immersion Fluid Comma separated values file that contains sample data Black metal curved supports that you affix to the OpenArray cases to ensure good contact with the thermal block on the OpenArray NT Cycler Refers to the process of loading two or three samples each from different sections of the sample plate into one subarray broken into two or three distinct sections Performs simultaneous thermal cycling and imaging of the OpenArray plates Accurately positions the OpenArray plate for sample loading in the OpenArray AccuFill System Additional Plate Holders can be ordered from Applied Biosystems The DNA from any source of interest e g tissue whole organism cDNA library Sample Integration connects the unique identifiers for each sample to their specific locations on an OpenArray plate It does this using two files aCSV file that describes the 384 well Sample Plate stored in the Sample Plate File Folder e a TPF SPF or EPF file that describes the
69. y AccuFill System User Guide Contents APPENDIX C Cleaning the OpenArray AccuFill instrument 63 Clearingitistr ctlolis 2 thai noie Ret inst LAM LE ER 64 Clean the outside of the instrument KK KK KK KK KK KK KK KK KK KIR 64 Clean the inside of the instrument 64 Spill accidents ay rari Ra wey vend te de AU E nent vb mm ade 64 APPENDIX D Safety 242 cea daa UBL Codd then cadet edet EE creme ts 65 Instrumentation safety 2 66 Symbols on instFumeln t5s a goats Alb Kina VE ERI er ER RE KAW 66 Locations of safety labels on instruments 67 General instrument safety 68 Physical hazard aate a a hek W salla ku ogee da Reed ele ends kelek dk ek 69 Ye RE LR LOS RL Ls 70 Workstation safety 2 datas bebe ete ie Di sine 71 Safety and electromagnetic compatibility EMC standards 71 Chemical safety 5 Rane kiss estes TT 72 General chemical safety kK kK KK KK KK KK KK KK KK KK kK KK KK KK KK kK 72 SI DS REM NM T A a E A omen Dh a Cee 73 Chemical waste safety 73 Biological haz

OpenArray AccuFill System User Guide (PN 4456986A)

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