VERSION A. Affymetrix GeneTitan Instrument User's Guide

Transcription

1 VERSION A Affymetrix GeneTitan Instrument User's Guide

2 Affymetrix GeneTitan Instrument User s Guide P/N Rev. A November 2008

3 For research use only. Not for use in diagnostic procedures. Trademarks Affymetrix, GeneChip,, HuSNP, GenFlex, Flying Objective, CustomExpress, CustomSeq, NetAffx, Tools To Take You As Far As Your Vision, The Way Ahead, Powered by Affymetrix, GeneChip-compatible, and Command Console are trademarks of Affymetrix, Inc. All other trademarks are the property of their respective owners. Limited License Limited License. Subject to the Affymetrix terms and conditions that govern your use of Affymetrix products, Affymetrix grants you a non-exclusive, non-transferable, non-sublicensable license to use this Affymetrix product only in accordance with the manual and written instructions provided by Affymetrix. You understand and agree that except as expressly set forth in the Affymetrix terms and conditions, that no right or license to any patent or other intellectual property owned or licensable by Affymetrix is conveyed or implied by this Affymetrix product. In particular, no right or license is conveyed or implied to use this Affymetrix product in combination with a product not provided, licensed or specifically recommended by Affymetrix for such use. Patents Software Software products may be covered by one or more of the following patents: U.S. Patent Nos. 5,733,729; 5,795,716; 5,974,164; 6,066,454; 6,090,555; 6,185,561; 6,188,783; 6,223,127; 6,228,593; 6,229,911; 6,242,180; 6,308,170; 6,361,937; 6,420,108; 6,484,183; 6,505,125; 6510,391; 6,532,462; 6,546,340; 6,687,692; 6,607,887; 7,062,092; 6,090,555; 6,611,767; 6,687,692; 6,829,376; 7,130,458, and other U.S. or foreign patents. Genetitan Instruments Products may be covered by U.S. Patent Nos. 6,114,122; 6,287,850; 6,391,623; 6,422,249; and other U.S. or foreign patents. Scanners Products may be covered by one or more of the following patents: U.S. Patent Nos. 5,578,832; 5,631,734; 5,834,758; 5,936,324; 5,981,956; 6,025,601; 6,141,096; 6,171,793; 6,185,030; 6,201,639; 6,207,960; 6,218,803; 6,225,625; 6,252,236; 6,335,824; 6,403,320; 6,407,858; 6,472,671; 6,490,533; 6,650,411; 6,643,015; 6,813,567;6,597,000; 7,406,391; 6,407,858; 6,403,320; 6,294,327; 6,262,838; 6,141,096, and other U.S. or foreign patents. Autoloaders Products may be covered by one or more of the following patents: U.S. Patent Nos. 6,511,277; 6,604,902; 6,705,754; 7,108,472; and other U.S. or foreign patents. Hybridization Oven Products may be covered by one or more of the following patents: U.S. Patent Nos. 6,050,719; 6,386,749; 6,705,754; and other U.S. or foreign patents. Copyright 2008 Affymetrix Inc. All rights reserved.

4 CONTENTS Chapter 1 The GeneTitan Instrument Overview Introduction User Documentation Safety Safe Operation Hazards Laser Safety Other Warnings and Precautions When to Contact Affymetrix GeneTitan Instrument Specifications Technical Support Contact Information Regulatory and Conformity GeneTitan Instrument Compliance Regulatory Approval China RoHS Restriction of Hazardous Substances Compliance SJ/T 电子信息产品污染控制标识要求 Chapter 2 The GeneTitan Instrument Introduction Components of the Instrument Components and Connections Indicator Lights and Power Buttons Principles of Operation Translation Stage Plate Gripper Input/Output Drawers Bulk Fill / Drain System CDA Interface

5 ii GeneTitan Instrument User s Guide Scanner Handoff Station Clamp/Unclamp Station Hybridization Oven Trash Station Notification The Scanner The UPS Unit Clean Dry Air Supply Software Interface Barcode Reader Workstation System Workflows Chapter 3 Operating the GeneTitan Instrument Setting Up the Instrument Maintaining Proper Fluid Levels Filling the Reagent Bottles Starting the Instrument Power On/Off Procedure Processing an Array Plate Hyb-Wash-Scan Mode Wash-Scan Mode Hyb-Wash Mode Scan Mode GeneTitan Instrument Recovery procedure Recovering the instrument from a power interruption Resuming the process from a workstation or application freeze Shutting Down

6 contents iii Chapter 4 Care and Troubleshooting GeneTitan Instrument Care Cleaning and Maintenance Monthly Every Six Months Troubleshooting Problems and Solutions Index

7 iv GeneTitan Instrument User s Guide This page intentionally left blank.

8 Chapter1 THE GENETITAN INSTRUMENT OVERVIEW Introduction The Affymetrix designed the GeneTitan Instrument to serve a variety of users that include, but are not limited to, core laboratories and service providers, academic institutes, and high volume and industrial sites (Figure 1.1). This system supports 96- well high throughput array plates (Figure 1.2) and integrates a high throughput fluidics station, the high throughput array plate scanner and a hybridization oven. Figure 1.1 The GeneTitan System Instrument

9 6 GeneTitan Instrument User s Guide Figure 1.2 The GeneTitan scan tray (left) and the GeneTitan 96 HT array plate (right) The software of the GeneTitan Instrument allows you to select different modes of operation to process an array plate. Each mode of operation performs one or more process steps within the instrument. This system allows you to perform the following operations: Hyb-wash-scan. Wash-scan Hyb-wash Scan The manual part of the operation requires that you load array plates, hybridization trays, stain trays and scan trays. The process of wash-scan occurs with no human intervention. The GeneTitan Instrument requires a workstation equipped with the Affymetrix GeneChip Command Console. The AGCC Launcher starts the GeneTitan Instrument user interface, See the Affymetrix GeneChip Command Console User s Guide (P/N ) for more details. All.dat files generated from the scanner are compatible with AGCC and imported automatically into AGCC for analysis using the AGCC image viewer. You can view the status of the array plate process through all instruments steps during operation from the GeneTitan Instrument user interface. This includes the status of hybridization, fluidic wash and stain, and scanning processes. The GeneTitan Instrument updates the AGCC workflow monitor about the status of the array process at the beginning and at the end of a major process step such as hybridization, wash and stain or scan.

10 chapter 1 The GeneTitan Instrument Overview 7 You can view the composite.cel file (all sub-array.cel files of an array) after scanning is completed using AGCC Image Viewer. You can also view individual sub array.dat files in the AGCC image viewer. User Documentation The operation of the GeneTitan Instrument requires familiarity with other user documentation. Those manuals that are relevant for you will depend on your system configuration. For the HT array system configuration, refer to the following documents. Site Preparation Guide Affymetrix GeneTitan Instrument (P/N ) GeneChip Expression Analysis Technical Manual For HT Array Plates Using the GeneChip Array System (P/N ) Affymetrix GeneChip Command Console User s Guide (P/N ) AGCC Installation Instructions (P/N ) Safety This section deals with safety issues and hazards concerning the scanner present during regular operation.to ensure safe operation of the GeneTitan Instrument, read this section completely before operating the instruments. CAUTION The power supply cord is used as the main disconnect device. Ensure that the socket outlet is located and installed near the equipment and is easily accessible. ATTENTION Le cordon d alimentation est utilisé comme interrupteur general. La prise de courant doit être située ou installée a proximité du materiel et être facile d accés. ACHTUNG Zur sicheren Trennung des Gerätes vom Netz ist der Netzstecker zu ziehen. Vergewissern Sie sich, daß die Steckdose leicht zugänglich ist. Safe Operation The GeneTitan Instrument is intended for indoor, laboratory use in a controlled environment. Do not attempt to service the instruments. Any attempt at unauthorized service may result in injury or damage the instrument and/or void the warranty. Failure to properly support the instruments may cause serious damage or injury and may void the warranty.

11 8 GeneTitan Instrument User s Guide The instruments must be surrounded by adequate airspace. Slots and openings in the instruments and the electronics compartment covers are for ventilation. Do not block or cover them. Never push an object into the instrument ventilation slots; equipment damage or injury may result. Do not set liquids on top of the instrument. The instrument has an AC receptacle with a safety ground appropriate for the country of destination. The plug is designed to connect only to a 3-prong ground receptacle. This safety feature should not be compromised in any way. If the instrument AC plug does not mate with the available power source receptacle, consult a licensed electrician to install one that does. Do not open the instrument electrical cabinets. These contains electrical hazards. WARNING: Do not open the instrument mechanical cabinet or stick fingers into the instrument. Moving the unit's axes can cause a risk of pinch or crush hazards! Be aware of the placement of all assemblies before starting a run. Make sure the instrument s enclosure is secure before beginning a run; if it is not, make sure no one is working inside the system. Do not wear loose clothing or hanging jewelry while working with the instrument. Tie back long hair. Read, understand, and follow the safety information contained in this manual prior to operating or using this equipment. Pay close attention to all safety labels. Hazards The following sections and Table 1.1 describe possible hazards present in this scanner. General Hazards IMPORTANT: If you use the GeneTitan Instrument instruments in a manner not specified in this user s guide, you may impair the protection provided by the equipment.

12 chapter 1 The GeneTitan Instrument Overview 9 Table 1.1 Hazards Hazard Present? Description Chemical No Control No Control software Electrical Yes V power Ergonomic Yes User interface Gas Mechanical Laser Noise Pneumatic Radiation Temperature Ultrasonic Vibration No Yes, instrument weight (heavy instrument) Yes (if you remove the system enclosure) and external barcode reader No Clean Dry Air (CDA) for operating the fluidics in the system No Yes, Integrated Hybridization oven and fluidics station No No Heat No Total power generated is less than 100 watts. E-Fields H-Fields No No Mechanical Hazards Do not open the instrument mechanical cabinet or stick fingers into the instruments. Moving the unit's axes can cause a risk of pinch or crush hazards! Be aware of the placement of all assemblies before starting a run. Make sure the instrument s enclosure is secure before beginning a run; if it is not, make sure no one is working inside the system. Do not wear loose clothing while working with the instruments. Tie back long hair. Remove any jewelry that hangs down. IMPORTANT: Heavy object. Two people are required to lift the GeneTitan Instrument.

13 10 GeneTitan Instrument User s Guide Electrical Hazards Do not use the instruments if you see damaged or frayed electrical cords. Tag and report them as unsafe. Do not place any liquids or containers holding liquids on or near electrical systems. Ergonomic Hazards The workstation has a user interface that may pose ergonomic issues. To avoid fatigue or muscle pain, follow basic precautions including the following: Read, understand, and follow your workplace ergonomic recommendations. Move user interface so that you can use it comfortably. Take short, regular breaks away from the instruments. Make sure the area is well-lit and you are able to see the information on the screen clearly. Laser Safety The scanner is equipped with an internal laser barcode reader. The laser complies with US 21CFR and except for deviations pursuant to Laser Notice No. 50 dated July 26, 2002 and IEC :+A1:1997+A2:2001. WARNING: The GeneTitan Instrument scanner is a Class 1 laser product. The scanner contains an internal Class 2 laser barcode reader. Class 2 laser radiation exposure if the scanner cover is opened. Do not stare into barcode laser reader beam. Always take note of laser safety labels; they indicate areas where exposure to laser beams may be hazardous. When used according to the instructions in this manual and when all covers are in place, the GeneChip HT Array Plate Scanner is classified as a Class 1 Laser Device per 21 CFR 1040 and IEC/EN Other Warnings and Precautions The GeneTitan Instrument instrument system is for research use only. It is not for use in diagnostic procedures. All biological specimens and materials with which the operator may come into contact should be handled as if capable of transmitting infection and disposed of with proper precautions in accordance with federal, state, and local regulations including

14 chapter 1 The GeneTitan Instrument Overview 11 adherence to the OSHA Blood Borne Pathogens Standard (29 CFR ) for blood-derived and other samples governed by this act. Never pipette by mouth. Avoid specimen contact with skin and mucous membranes. Wear gloves when using the GeneTitan Instrument. Exercise standard precautions when obtaining, handling, and disposing of potentially carcinogenic reagents. Do not send your instrument elsewhere for service or attempt to service it yourself. To protect your warranty and ensure safe operation, the instrument should be serviced only by Affymetrix or its representatives. If the instrument is not working correctly, please contact your Affymetrix Technical Support representative. Do not use the GeneTitan Instrument instruments in ways not specified by Affymetrix. Doing so may impair the protections provided by the GeneTitan Instrument. The GeneTitan Instrument instrument system requires two people to lift and handle it safely. Each person should firmly grasp the base of the instrument at the end opposite the other to lift. Use OSHA standards for lifting techniques. The GeneTitan Instrument instrument system is intended for indoor, laboratory use in a controlled environment. When to Contact Affymetrix Under any of the following conditions, unplug the instrument from the power source and contact technical Support: When the power cord is damaged or frayed. If any liquid, such as scan buffer, has been spilled into the instrument. If the instrument has been penetrated by water. If, after service or calibration, the instrument does not perform in accordance with the capabilities stated in the specifications. If the instrument has been dropped or otherwise damaged. If the instrument must be returned for repair, call Affymetrix Technical Support.

15 12 GeneTitan Instrument User s Guide GeneTitan Instrument Specifications Table 1.2 lists the important instrument specifications. Table 1.2 The Specifications of the GeneTitan Instrument Item Parameter Value Weight Crated for Shipping GeneTitan Hyb and Fluidics GeneTitan Scanner Free-standing (uncrated) GeneTitan Hyb and Fluidics GeneTitan Scanner GeneTitan Instrument Total Weight GeneTitan is packed in two crates: approx 328 lb (149 Kg) approx 214 lb (97 Kg) approx 182 lb (82.6 Kg) approx 127 lb (57.6 Kg) approx 309 lb (140 Kg) Dimensions Width 55 (139.7 cm) Power Working Environment (indoor use only) Depth Height Voltage Current Line Frequency. Temperature Humidity Clearance Pollution Degree Installation Category 33 (83.82 cm) 26 (66 cm) V (± 10%) A Hz 41 F-104 F (5 C to 40 C) Maximum relative humidity 80% for temperatures up to 31 C decreasing linearly to 50% relative humidity at 40 C. 6 (15.24 cm) in rear 12 (30.48 cm) on left side 25 (63.5 cm) on right side 2 environment II Altitude <2000m Electrical Supply Main Supply Voltage Fluctuations Provide voltage, frequency or power rating per unit label. Circuit breaker. Mains supply voltage fluctuations up ±10% of the nominal supply voltage (Transient overvoltages typically present on the mains supply)

16 chapter 1 The GeneTitan Instrument Overview 13 Technical Support Contact Information When to Contact Technical Support Under any of the following conditions, unplug the instrument from the power source and contact Affymetrix Technical Support: when the power cord is damaged or frayed; if any liquid has penetrated the instrument; if, after service or calibration, the instrument does not perform to the specifications stated in Table 1.2. If the instrument must be returned for repair, call Affymetrix Technical Support. IMPORTANT: Make sure you have the model and serial number. Affymetrix provides technical support to all licensed users via phone or . Contact information is listed below. Affymetrix, Inc Central Expressway Santa Clara, CA USA support@affymetrix.com Tel: (1-888-DNA-CHIP) Fax: Affymetrix UK Ltd., Voyager, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe HP10 0HH United Kingdom saleseurope@affymetrix.com supporteurope@affymetrix.com UK and Others Tel: +44 (0) France Tel: Germany Tel: Fax: +44 (0) Affymetrix Japan, K. K. Mita NN Bldg. 16 Floor, Shiba, Minato-ku, Tokyo Japan Tel: (03) Fax: (03)

17 14 GeneTitan Instrument User s Guide Regulatory and Conformity GeneTitan Instrument Compliance We Affymetrix, Inc Central Expressway Santa Clara, California, USA declare under sole responsibility that the Affymetrix GeneTitan Instrument and associated Workstation with software, is manufactured in the United States of America, with U.S. and Non-U.S. components. This device complies with Part 15 of FCC Rules. Operation is subject to the following two conditions: (1) This device may not cause harmful interference, and (2) This device must accept any interference received, including interference that may cause undesired operation. This Class A digital apparatus meets all requirements of the Canadian Interference- Causing Equipment Regulation. Cet appareil numérique de la classe A respecte toutes les exigences du Règlement sur le matériel broullier du Canada.

18 chapter 1 The GeneTitan Instrument Overview 15 Regulatory Approval This device has been approved by the following regulatory agencies (Table 1.3). Table 1.3 Regulatory Approval Regulatory Agency Certification EU EMC Directive 2008/108/EC EU Low Voltage Directive 73/23/EEC IEC CSA C :1992 (Canada) UL 61010A-1:2002 (USA) EN :2001 (EU) Mechanical Safety: EN 1050:1996 Laser Safety: EN A2:2001 and 21 CFR 1010 and 1040 Compliant with directive 2002/96/EC (WEEE) (WEEE German Registration) WEEE Registration France Complies with requirements of Radiocommunications (Electromagnetic Compatibility) Standard 2008 CE Mark Declaration of Conformity The Affymetrix GeneTitan Instrument conforms with the relevant provisions of the following standard(s) and/or other normative document(s): EMC Directive 2004/108/EC ICES-003:2004 Class A EN :2006 Class A FCC (g) CISPR 22: 1997):2007 ICES-003:2004 Class A Radiated emissions - Radio disturbance characteristics Radiated emissions - Radio disturbance and immunity CISPR :2006 Radiated emissions - ANSI C63.4:2003 Conducted emissions - Radio disturbance characteristics CISPR 22:2005 +A1:2005 and A2:2006

19 16 GeneTitan Instrument User s Guide EN :2006 Class A FCC :2007 Class A EN :2006 EN :2006 EN :2001 EN :2006 +A1:2007 EN :2004 EN :2005 EN :2006 EN :2001 EN :2004 EU Low Voltage Directive 73/23/EEC EN A2:2001 EN/IEC :2001 Conducted emissions - Radio disturbance and immunity CISPR :2005 Conducted emissions - ANSI C63.4:2003 Electrical equipment for measurement, control, and laboratory use - EMC requirements Voltage changes, voltage fluctuations and flicker in public low-voltage supply systems, for equipment with rated current 16 A per phase and not subject to conditional connection Electrostatic discharge immunity Radiated, radio frequency, electromagnetic field immunity Electrical fast transient/burst immunity Surge immunity Immunity to conducted disturbances, induced by radio frequency fields Power frequency magnetic field immunity test Voltage dips, short interruptions and voltage variations immunity Safety of Laser products - Part 1: Equipment classification, requirements, and user's guide. EN/IEC and 21 CFR 1010 and 1040 Safety of laser products EN/IEC :2006 Safety requirements for electrical equipment for measurement, control, and laboratory use Electrical equipment for measurement, control, and laboratory use - EMC requirements

20 chapter 1 The GeneTitan Instrument Overview 17 China RoHS Restriction of Hazardous Substances Compliance Manufacturers of Electronic Information products (EIPs) that are sold to the People's Republic of China, are required to provide information about lead, cadmium, mercury, hexavalent chromium, polybrominated biphenyls and polybrominated diphenyl ethers contained within. In accordance with the Chinese RoHS (Restriction of Hazardous Substances), Table 1.4 contains information identifying the specific hazardous material(s) and the components/ parts in which they are found. Table 1.4 Table Containing Names and Contents of Toxic or Hazardous Materials * Instrument: GeneTitan Instrument Component/Part Categories Lead (Pb) Mercury (Hg) Cadmium (Cd) Hexavalent Chromium (Cr 6) Polybrominated Biphenyls (PBBs) Polybrominated Diphenyl Ethers (PBDEs) Printed Circuit Boards Rubber & Plastic Parts Electrical Components X O X O O O O O O O O O O O O O O O Internal Metal Parts X O X O O O External Metal Parts O O O O O O Labels O O O O O O Packaging/Shipping Materials Internal Lasers, Optics & Sensors O O O O O O X O X O O O Adhesives O O O O O O Internal Power Supplies O O O O O O Motors and Pumps O O O O O O * X = Indicates that the toxic or hazardous substance contained is above the limit of 1000 ppm for lead and above 100 ppm for cadmium O = Indicates that the toxic or hazardous substance contained is below the limit of 1000 ppm for lead, mercury, hexavalent chromium, polybrominated biphenyls and polybrominated diphenyl ethers; and below 100 ppm for cadmium.

21 18 GeneTitan Instrument User s Guide SJ/T 电子信息产品污染控制标识要求 目前许多电子信息产品由于功能 性能或生产技术的需要, 仍含有大量如铅 (Pb) 汞 (Hg) 镉 (Cd) 六价铬 [Cr (Ⅵ)] 多溴联苯 (PBB) 和多溴二苯醚 (PBDE) 等有毒有害物质或元素 这些含有毒有害物质或元素的电子信息产品在废弃之后, 如处置不当, 不仅会对环境造成污染, 也会造成资源的浪费 因此, 为了达到节约资源 保护环境的目的, 以有毒有害物质或元素的减量化 替代为主要任务的电子信息产品污染控制工作已经提到政府主管部门的议事日程 为此, 信息产业部等七部委以 从源头抓起, 立法先行 的思路和原则, 制定了 电子信息产品污染控制管理办法 ( 信息产业部 39 号部长令, 简称 管理办法 ), 以立法的形式, 推动电子信息产品污染控制工作, 旨在从电子信息产品的研发 设计 生产 销售 进口等环节限制或禁止使用上述六种有毒有害物质或元素 为了进一步落实 管理办法 并达到限制有毒有害物质或元素在电子信息产品中使用的目标, 必须有配套使用的统一的标识方法标准 因此, 为了配合中华人民共和国 管理办法 的实施, 同时也为中华人民共和国信息产业界对六种有毒有害物质或元素铅 (Pb) 汞 (Hg) 镉 (Cd) 六价铬 [Cr (Ⅵ)] 多溴联苯 (PBB) 和多溴二苯醚 (PBDE) 的测试提供一个统一的标识方法, 特制定本标准 ( 表 Table 1.5). Table 1.5 有毒有害物质或元素名称及含量 * 仪器 : GeneTitan Instrument 部件名称 铅 (Pb) 汞 (Hg) 镉 (Cd) 六价铬 [Cr (Ⅵ)] 多溴联苯 (PBB) 多溴二苯醚 (PBDE) 印制电路板 X O X O O O 橡胶和塑料元件 O O O O O O 电子元件 O O O O O O 内部金属零件 X O X O O O 外部金属零件 O O O O O O 标签 O O O O O O 组装 / 装货资料 O O O O O O 内部激光, 光学器件和传感器 X O X O O O 胶粘剂 O O O O O O 内部电源 O O O O O O 马达和唧筒 O O O O O O * : 表示该有毒有害物质至少在该部件的某一均质材料中的含量超出 1000 ppm 铅 (Pb) 100 ppm 镉 (Cd) 的标准规定的限量要求 : 表示该有毒有害物质在该部件所有均质材料中的含量均在 1000 ppm 铅 (Pb) 汞 (Hg), 六价铬 [Cr (Ⅵ) ], 多溴联苯 (PBB), 多溴二苯醚 (PBDE), 100 ppm 镉 (Cd) 的标准规定的限量要求以下 电子信息产品污染控制标识要求 (Marking for Control of Pollution Caused by Electronic Information Products) SJ/T

22 Chapter2 THE GENETITAN INSTRUMENT Introduction This section describes the units that make up the GeneTitan Instrument and its auxiliary instrument components. The GeneTitan Instrument by itself primarily consists of a high throughput fluidics station, the hybridization oven and a high throughput scanner. Components of the Instrument The GeneTitan Instrument is one of several components for processing high throughput array plates. Affymetrix will provide the following system components as part of the high throughput system for array processing and scanning. This provides a complete system high throughput processing (Table 2.1). Table 2.1 GeneTitan Instrument and Auxiliary Components Component 1 GeneTitan Instrument 3 External barcode reader 4 Workstation (The particular workstation model is subject to change.) 4 Affymetrix GeneChip Command Console Software 5 APC Smart UPS for 110V or 220V As shown in the schematic in Figure 2.1, the instrument layout consists of the electronic components, the hybridization oven, a buffer and liquid supply and drain system (Wash A, B, de-ionized water supply and a waste drain), a clamp/unclamp unit, a 96 array plate with cover (peg/cover input) and a trash station. The system also includes six input/output drawers.

23 20 GeneTitan Instrument User s Guide Electronics Hybridization Oven Wash B Station Wash A Station Accessories Used Hyb Tray 1 Scan Tray SAPE 1-1 AB 1 SAPE 2-1 Peg/Cover Input Clamp/Unclamp Used Hyb Tray 2 Input/Output Drawer #1 Scan Tray Input/Output Drawer #2 SAPE 1-2 Input/Output Drawer #3 AB 2 Input/Output Drawer #4 Scanner Handoff SAPE 2-2 Input/Output Drawer #5 Hyb Tray Input Input/Output Drawer #6 Trash Station Figure 2.1 The GeneTitan Instrument layout (the scanner is omitted for clarity) Components and Connections The GeneTitan Instrument front components consist of the following items (Figure 2.2): 1) Input/Output drawer #1: hybridization tray output 1 2) Input/Output drawer #2: scantray 1 and scantray 2 3) Input/Output drawer #3: SAPE 1-1 and SAPE 1-2 4) Input/Output drawer #4: AB 1 and AB 2 5) Input/Output drawer #5: scanner handoff 6) Input/Output drawer #6: peg/cover input and hybridization input 7) Confirmation button for opening and closing drawers 8) Waste bottle for drained buffers and residual reagents 9) Wash A buffer bottle 10) Wash B buffer bottle 11) Rinse bottle containing de-ionized (DI) water 12) The fluidics station and the hybridization oven 13) Waste chute for used materials 14) High throughput scanner

24 chapter 2 The GeneTitan Instrument Input/Output Drawer #1: used hybridization tray output 1 and 2 2. Input/Output Drawer #2: scan tray 1 and scan tray 2 3. Input/Output Drawer #3: SAPE 1-1 and SAPE Input/Output Drawer #4: AB 1 and AB 2 5. Input/Output Drawer #5: SAPE 2-1 and SAPE Input/Output Drawer #6: peg/cover input and hybridization input 7. GeneTitan Plate Confirmation Button (to open/close drawers) 14. High Throughput Array Scanner Waste Bottle 9. Wash A Bottle 13. Waste Chute 12. High Throughput Fluidics Station 10. Wash B Bottle 11. Rinse Bottle (DI Water) Figure 2.2 The GeneTitan Instrument components Figure 2.3 shows the rear connections. 1. The scanner circuit breaker button 2. The scanner firewire cable for CCD camera communication 3. The scanner USB cable for data communications 4. The scanner power cable 5. The fluidics station air exhaust 6. The fluidics station clean dry air supply 7. The fluidics station USB cable for data communications 8. The fluidics station power cable

25 22 GeneTitan Instrument User s Guide 1. Scanner Circuit Breaker Button 2. Scanner Firewire Cable for CCD Camera Communications 3. Scanner USB Cable for Data Communications 4. Scanner Power Cable 6. Fluidics Station Air Exhaust 5. Fluidics Station Circuit Breaker Button 7. Fluidics Station Clean Dry Air Supply 8. Fluidics Station USB Cable for Data Communications 9. Fluidics Station Power Cable Figure 2.3 The GeneTitan Instrument rear connections Figure 2.4 shows the workstation and UPS connections. 1. The power cord to the workstation 2. The firewire cable from the scanner 3. The server cable (for those systems with a server connection) 4. USB cables (one for the scanner, one for the fluidics station and other USB cables depending upon the system configuration) 5. USB cable from the UPS 6. USB connection on the UPS 7. UPS power outlets to workstation, fluidics station, scanner and other devices depending upon configuration. 8. UPS power supply 9. Fluidics station power cable

26 chapter 2 The GeneTitan Instrument Workstation Power Cord 2. Firewire Cable to Scanner 3. Server Cable 6. USB Cable to Workstation 7. Power Outlets 4. USB Cables to Scanner and Fluidics Station 5. USB Cable to UPS 8. UPS Power Cord Figure 2.4 The workstation and UPS connections IMPORTANT: The Firewire (IEEE 1394 High Speed Serial Bus) cable is not a locking connector. Insure that the Firewire cable is plugged securely and in the correct orientation in both the scanner and the workstation. Avoid snagging or pulling this cable during the scanner operation. Maintain adequate (6, cm) distance in the rear.

27 24 GeneTitan Instrument User s Guide The USB cable is not a locking connector. Insure that the USB cable is plugged securely and in the correct orientation in both the scanner and the workstation. Avoid snagging or pulling this cable during the scanner operation. Maintain adequate (6, cm) distance in the rear. Indicator Lights and Power Buttons The GeneTitan Instrument has three indicator lights and two buttons. (Figure 2.5). 1. GeneTitan Plate Confirmation Button to open/close drawers 2. GeneTitan Instrument Status (Green) 3. Scanner Warm up/standby (Yellow) 4. Scanner Operating (Green) 5. Scanner I/O Button (not used) Figure 2.5 Lights and buttons of the instrument 1. The fluidics station confirmation button. In accordance with the AGCC software message, press this to open and close a drawer. 2. The fluidics station status light.

28 chapter 2 The GeneTitan Instrument 25 A. Green: On = Activation at powerup, System Ready 3. The scanner yellow light. This indicates that the scanner is warming up and/or is in standby mode. 4. The scanner yellow green light. This indicates that the scanner is operating 5. The scanner power button. Enables manual control of some components in the instrument (use not recommended). The I/O switch enables you to turn on some circuits in the instrument without turning on the software. It does not turn on the entire instrument. Affymetrix recommends using the software to turn on the instrument and against using the I/O switch. All power to the instrument is turned on when the AGCC GeneTitan Control software is started and turned off when the software is shut down. The I/O switch on the front of the instrument is inoperative when the instrument is being controlled using the software. IMPORTANT: If you press the I/O switch first, before turning on the software, only the switched components will turn on. The complete instrument will not power up until you start the AGCC GeneTitan Control software. When you shut the software down, the circuits controlled by the I/O switch will not be turned off until you press the I/O button again. Affymetrix recommends against using the I/O switch. Principles of Operation This section describes the GeneTitan Instrument system and principles of operation. Translation Stage The fluidics station has a 3-axis translation stage that holds the 96-well plate. This has sufficient travel in X, Y and Z in order to reach all tray locations during the operation to process the array plate. In case of power interruption or cycling of the power of the instrument or if you reboot the workstation or application, all stages in the instrument will stop immediately and hold on to their positions Plate Gripper The plate gripper holds the array plate. The plate gripper consists of a motorized gripper capable of handling the array plate, tray cover, array plate / hybridization tray, and array plate /scan tray. The plate gripper transfers the array plate from one location to another with in the instrument.

29 26 GeneTitan Instrument User s Guide The plate gripper has three position sensors. These include open, closed with part present, and closed with part absent. The plate gripper can center the array plate front to back, top to bottom while it is handling the array plate. It can maintain the parallelism of the array against the liquid surface in the Stain tray, Wash A station, and Wash B station while it is handling the array plate In the event of power interruption, the plate gripper will hold a plate in the closed position. You can manually open the plate gripper to perform a recovery procedure of the array plate. Input/Output Drawers The fluidics station has six input/output drawers which accept array plates/array plate covers, array plates/hybridization tray, array plates/scan tray combinations, stain trays, and scan trays. See Figure 2.2 on page 21. A software enacted command opens and closes the input/output drawers via the gripper. Each input/output drawer holds two trays. Each tray sits in its tray pocket on the drawer. Each input/output drawer has a locking mechanism to secure the drawer when it fully retracts inside of the instrument. Each of the input/output drawer can collect a small volume spillage to ensure the spillage does not drip to other drawers below it. Each of the input/output drawers has an optical sensor to detect the present or absence of a tray on the drawer. Each of the input/output drawers has fiducial pins that work in conjunction with the optical sensor of the plate gripper to define the position of the drawer relative to the home position of the stage in X, Y and Z axes. During the operation of the instrument calibration, the software records this position into a configuration file. Each of the input/output drawers has a stationary flag to work in conjunction with the optical sensors on the plate gripper to provide a means of recovering the instrument from a power interruption. The instrument has a lighted circular confirmation button. This button has a flashing blue light when an Input/Output drawer is open to indicate action is required. The light shall be off when Input/Output drawer is closed. Bulk Fill / Drain System Bulk Fill/Drain system comprises the Wash A buffer, Wash B buffer, de-ionized water and waste bottles. This system enables the instrument to fill and drain from two different sources of buffer solution automatically during the operation. See Figure 2.2 on page 21. The bottles are on the left side of the instrument. You must maintain a minimum about for fluid in each of bottles. Table 3.1 on page 35 shows the minimum volumes of buffer and rinse required to process an array plate on the GeneTitan instrument. Wash A Buffer The Wash A buffer has the following characteristics:

30 chapter 2 The GeneTitan Instrument 27 Inside the fluidics station, a wash reservoir holds the Wash A buffer. The wash reservoir accepts the array while it being handled by the plate gripper. This wash reservoir has a fluid level sensor to ensure the level and presence/absence of liquid during the fill cycle. This reservoir has a Wash A buffer source. A three-liter bottle located next to the fluidics station instrument contains this buffer source. The Wash A buffer shares the same waste collection source with the Wash B buffer. A five-liter bottle next to the fluidics station collects the waste. Wash B Buffer The Wash B buffer has the following characteristics: Inside the fluidics station, a wash reservoir holds the Wash B buffer. The Wash B buffer has a DI water source in a one-liter bottle next to the fluidics station. This contains the rinse water. The wash reservoir can direct any overflow of buffer to the waste line. The Wash B station has a heater to heat the wash B buffer inside the wash reservoir up to a specific temperature set point. You cannot set this specific temperature setpoint. A software protocol file controls the temperature. The Wash B station has a lid, which has a built in heater to warm up the lid to minimize the condensation of the buffer during the operation. You cannot set this specific temperature setpoint. A software protocol file controls the temperature. The Wash B station has a Wash B buffer source. A one-liter bottle contains this buffer source. Fluidics Bottle Rack The bottle rack contains all the buffer solution, the rinse, and the waste collection sources of the instrument. It is located outside on the left side of the instrument. See Figure 2.2 on page 21. CDA Interface The instrument has an inlet port 3/8 inches OD to receive the facility clean dry air supply (CDA) supply source. This port is located at the back of the instrument. See item 13 in Figure 2.3 on page 22. Scanner Handoff Station The fluidics station can accept the load drawer from the scanner automatically without user intervention.

31 28 GeneTitan Instrument User s Guide Clamp/Unclamp Station The fluidics station has a motorized clamp/unclamp station that allows the plate gripper to place or remove the array plate / hybridization tray. The clamp/unclamp station has sensors to detect presence/absence of hybridization tray. Hybridization Oven The fluidics station has an on-board, integrated hybridization oven. This oven has the following characteristics: The hybridization oven can hold up to two array plate/hybridization tray combinations. You can program, via the software interface, the hybridization oven to any temperature set points from 37.0 to 70.0 C in 0.1-degree increments. The hybridization oven can ramp up to the temperature set point within 15 minutes. The oven temperature employs a USB enabled temperature control. Each shelf of the hybridization oven has a sensor to detect the presence/absence of trays. Trash Station The fluidics station has a trash station which allows the plate gripper to throw away tray covers whenever they are no longer needed during the operation of the array plate processing. See Figure 2.2 on page 21. The trash station accepts Affymetrix tray covers. The trash station has optical sensors to detect whether the bin is empty or full. The system alerts you to empty the bin if the sensors detect that the bin is not empty at the beginning of each run. Notification The System can notify a user or a group of users, via , regarding changes in the state of the system. The system can configure which system events shall initiate an notification and to which user(s) this notification shall be sent. The notification system is compatible with standard SMTP systems only. The trash station has a sensor to ensure that the trash bin is fully inserted into the instrument. The trash station also has a locking mechanism to secure the trash bin after it is fully inserted in to the instrument. The software controls this locking mechanism to prevent you from accidentally unloading the bin during operation.

32 chapter 2 The GeneTitan Instrument 29 The Scanner The UPS Unit The array plate scanner is an integral part of the GeneTitan Instrument. It automatically receives and scans a 96-well GeneTitan array plate after processing by the GeneTitan Instrument. This requires no user intervention. The system also uses an uninterruptible power supply (UPS, Figure 2.6 and Figure 2.4 on page 23). This UPS can maintain power to the workstation, the gantry and the I/O modules of the fluidics station, and the gantry of scanner for approximately 2 to 5 minutes to safely perform the array plate recovery and the shutdown procedure in case of an power interruption. The software/system provides the following functionality when attached to the UPS: When the instrument control software detects loss of main power, the software shall log any power interruptions and messages to the log files. The software monitors the power loss for at least 1 minute before triggering any recovery procedure to recover the instrument or the array plate. During the power interruption event, the UPS will provide enough power for the 96 Fluidics instrument to complete the appropriate recovery procedure. After completion of the operation(s), the software will hold all loaded plates on the drawers, ready for unload when you respond to and initiate the unload operation. The software provides an alert when the battery level on the UPS falls to a critical level and will send an to notify the user.

33 30 GeneTitan Instrument User s Guide UPS Unit CDA Unit Clean Dry Air Supply Software Interface Figure 2.6 The USP and CDA units The GeneTitan Instrument system requires a clean dry air (CDA) source to 70 psi. You are required to furnish this. The Figure 2.6 shows the CDA regulator and source that Affymetrix uses. This need not be the same as yours and is for illustration purposes only. See the Site Preparation Guide Affymetrix GeneTitan Instrument (P/N ) for preparing your facility for GeneTitan Instrument installation. The GeneTitan Instrument instruments operate under the Affymetrix GeneChip Command Console (AGCC). The AGCC Launcher opens the user applications. See the AGCC Installation Instructions (P/N ) for software installation instructions if you need to re-install the software and the Affymetrix GeneChip Command Console User s Guide (P/N ) for instructions on using the software. All DAT files generated from the scanner are compatible with the AGCC software and imported automatically into AGCC for analysis in the AGCC image viewer.

34 chapter 2 The GeneTitan Instrument 31 Barcode Reader Workstation You can view the status of the array plate process through all instruments steps during a plate run from the GeneTitan Instrument user interface. This includes the status of hybridization, fluidic wash and stain, and scanning. You can view the composite.cel file (all sub-array.cel files of an array) after scanning is completed using AGCC Image Viewer. You can also view the individual sub array.dat file and be able to tile all the sub array.dat files of an array in a single screen view. The fluidics station uses a barcode reader to read the barcode labels on the array plate. The GeneTitan Instrument is equipped with a Dell workstation with Windows XP and the AGCC software application installed. System Workflows After target preparation, the system workflow consists of three major steps. They are the hybridization step, the fluidic step (wash and stain) and the scanning step. The hybridization and fluidic steps take place on the fluidic instrument. The scanning step takes place on the scanner. Figure 2.8 shows a typical process workflow of a plate after the sample has undergone hybridization and before scanning.

35 32 GeneTitan Instrument User s Guide After Hybridization 1 st Wash A Parameters: Time, number of Mixes*, and number of Cycles** Values: 4.5 minutes, 108 mixes, 2 cycles Wash B Parameters: Temperature, and Time Values: 43 C, 15 minutes 1 st SAPE Stain Parameter: Time Value: 10 minutes 2 nd Wash A Parameters: Time, number of Mixes*, and number of Cycles** Values: 4.5 minutes, 108 mixes, 2 cycles AB Stain Parameter: Time Value: 10 minutes 3 rd Wash A Parameters: Time, number of Mixes*, and number of Cycles** Values: 4.5 minutes, 108 mixes, 2 cycles 2 nd SAPE Stain Parameters: Time Value: 10 minutes 4 th Wash A Parameters: Time, number of Mixes*, and number of Cycles** Values: 4.5 minutes, 108 mixes, 2 cycles Ready to scan Figure 2.7 The system workflow from hybridization to scan ready The instrument can complete any process workflow in a 9 AM to 5 PM work day and five days a week. The workflow of the instrument ensures that every plate undergoes the identical process when it is processed through all instruments.

36 chapter 2 The GeneTitan Instrument 33 Figure 2.8 shows a typical five - day workflow to process plates through one GeneTitan instrument using various starting amounts of target preparation. Table A shows a schedule that runs one plate per day starting with target preparation followed by hybridization, washing, staining and scanning on the GeneTitan Instrument. Table B shows a schedule that runs one plate per day using only one liquid handler on the high throughput array plate processing system followed by hybridization, washing, staining and scanning on the GeneTitan Instrument. Table C shows a schedule that runs two plates per day using two liquid handlers on the high throughput array plate processing system followed by hybridization, washing, staining and scanning on the GeneTitan Instrument.

37 34 GeneTitan Instrument User s Guide A. Typical 5 - day week workflow for IVT Express Assay Assay with 50 ng starting material using two plates, one plate per day Day 1 Day 2 Day 3 Day 4 Day 5 Plate 1 Target Prep 1 2 Plate 2 Array Plate Processing Integrated Hyb, Wash-Stain Scan 1 2 B. Typical 5 - day week workflow with IVT Express Assay assay > 100 ng of starting material using four plates, one plate per day Target Prep on 1st liquid handler Array Plate Processing Hyb, Wash Stain Scan 4 Day 1 Day 2 Day 3 Day 4 Day (The following Monday) Plate 1 Plate 2 Plate 3 Plate 4 C. Typical 5 - day week workflow with IVT Express Assay assay > 100 ng of starting material using six plates, two plates per day Day 1 Day 2 Day 3 Day 4 Day 5 Target Prep on 1st liquid handler Plate 1 Target Prep on 2nd liquid handler Plate 2 Plate 3 Array Plate Processing 2 plates/day Hyb Wash-Stain Scan Plate 4 Plate 5 Plate 6 Notes: The GeneTitan Instrument can process 2 plates of 24 or 96 IVT samples in 24 hours. The target prep with IVT 1.0 requires 1.25 days. Use of a second liquid handler doubles the throughput. Figure 2.8 A typical five-day workflow to process two, four and six plates from target preparation through hyb, wash, stain, scan. Table C illustrates a run using two plates simultaneously.

38 Chapter3 OPERATING THE GENETITAN INSTRUMENT Setting Up the Instrument The Affymetrix field service technicians will have set up and tested the instrument before your running an array plate. One of your responsibilities will be to ensure that the instrument is properly connected and that the fluid levels are within the proper levels. Maintaining Proper Fluid Levels Before starting the instrument, you must ensure that you have the proper levels of Wash A, Wash B and Rinse fluids. The instrument detects if there is no fluid coming from the source bottle. However, to successfully run the GeneTitan instrument and to ensure there is no splashing of the fluid onto the array plates, you must maintain a minimum of 150 ml buffer (Wash A and Wash B) and DI water in the appropriate bottles. Table 3.1 shows the minimum volumes of buffer and rinse required to process an array plate on the GeneTitan instrument. IMPORTANT: You must maintain a minimum level of 150 ml of fluid in the bottles even when not running an array. This volume of fluid is required to cover the dip tube filter to prevent splashing when the instrument pumps air into the bottle. Table 3.1 Minimum Volumes of fluids Fluid Type Amount required in the bottle to process one HT array plate Amount required in the bottle to process two HT array plates Rinse 350 ml+ 550 ml Wash A 1500 ml 2500 ml Wash B 300 ml 450 ml+

39 36 GeneTitan Instrument User s Guide Filling the Reagent Bottles The AGCC software will ask you to refill the reagent bottles at the beginning of every run (Figure 3.1). The bottles have color coded caps and labels that provide information on the paticular reagent that goes into the bottle. You must remove the cap from the reagent bottle. The instrument has a place holder behind the bottle to place the cap with the tube. This will prevent any reagent buffers in the tubes from leaking onto the table. The excess fluid in the tube attached to the cap drains into the bottle holder. Upon filling the bottle with the appropriate amount of reagent buffer, and after draining the waste bottle, you must then tighten the cap on the bottles. IMPORTANT: The instrument pressurizes the reagent buffer bottles during operation. Tighten the caps firmly but gently. Open the bottles only when the instrument indicates that they are no longer pressurized. 8. Waste Bottle 9. Wash A Bottle 10. Wash B Bottle 11. Rinse Bottle (DI Water) Figure 3.1 The GeneTitan Instrument reagent bottles

40 chapter 3 Operating the GeneTitan Instrument 37 Starting the Instrument This section shows you how to launch the AGCC software and turn on the GeneTitan Instrument. NOTE: Launching the AGCC Instrument Control software will turn on the integrated fluidics station and establish connection with the scanner. You cannot run the scanner without turning on the GeneTitan Instrument. Power On/Off Procedure 1. To power on the system, turn the workstation on. 2. Using the user interface, log into the computer. 3. Launch the AGCC application. Click Microsoft Windows Start button Programs Affymetrix Command Console AGCC GeneTitan Control or click the AGCC GeneTitan Control icon,, on the AGCC Launcher. The following operations then occur: The AGCC GeneTitan Control window opens (Figure 3.2). The software turns on high power to the GeneTitan Instrument. All stages, subsystem, components in both the fluidics and scanner then initialize to their default state to ensure that each component in the instrument is functioning properly. All stages of both fluidics and scanner instruments performs its homing routine to find its home position. The Hybridization oven turns on and warms up to either to the initial temperature set point of 48 C or the temperature of the last executed protocol - which may differ from 48 C). If any of the steps above fail to execute during the startup procedure, the software shall not complete its startup procedure. The software shall prompt the error dialog box to state the failure modes.

41 38 GeneTitan Instrument User s Guide Figure 3.2 The AGCC GeneTitan Control widow 4. To power off the GeneTitan Instrument, run the shutdown procedure, exit and close the GeneTitan Control application. During the closing or exiting of the AGCC application, the software moves all the stages to their safe position. The software then closes. IMPORTANT: If you press the I/O switch first, before turning on the software, only the switched components will turn on. The complete instrument will not power up until you start the AGCC GeneTitan Control software. When you shut the software down, the circuits controlled by the I/O switch will not be turned off until you press the I/O button again. Affymetrix recommends against using the I/O switch.

42 chapter 3 Operating the GeneTitan Instrument 39 Processing an Array Plate This section tells you how to run an array plate from hybridization through the various modes of operation: Hyb-Wash-Scan Wash-Scan Hyb-Wash Scan Hyb-Wash-Scan Mode The Hyb-Wash-Scan Mode of operation performs the hybridization, wash-stain, and scan processes of an array plate through the instrument from start to finish without user intervention. You can specify either one or two plates to be processed through the instrument using this mode of operation. This section provides a summary of the operations for hybridization, wash, stain and scan. You must follow the directions in the Affymetrix GeneChip Command Console User s Guide (P/N ) for detailed instructions. Process Description Hyb-Wash-Scan Mode The fluidic step (wash-stain) of the hyb-wash-scan Mode follows a pre-determined fluidic protocol. This protocol has eight sequential steps that are described in the flowchart in Figure 3.3. There are adjustable or user selectable parameters associated with each step; however, all process time dependent parameters shall not be adjustable. IMPORTANT: Only an approved Affymetrix product development team can change all the parameters in the fluidic protocol.

43 40 GeneTitan Instrument User s Guide After Hybridization 1 st Wash A Parameters: Time, number of Mixes*, and number of Cycles** Values: 4.5 minutes, 108 mixes, 2 cycles Wash B Parameters: Temperature, and Time Values: 43 C, 15 minutes 1 st SAPE Stain Parameter: Time Value: 10 minutes 2 nd Wash A Parameters: Time, number of Mixes*, and number of Cycles** Values: 4.5 minutes, 108 mixes, 2 cycles AB Stain Parameter: Time Value: 10 minutes 3 rd Wash A Parameters: Time, number of Mixes*, and number of Cycles** Values: 4.5 minutes, 108 mixes, 2 cycles 2 nd SAPE Stain Parameters: Time Value: 10 minutes 4 th Wash A Parameters: Time, number of Mixes*, and number of Cycles** Values: 4.5 minutes, 108 mixes, 2 cycles Ready to scan Figure 3.3 The eight sequential steps in the fluidic step (Wash-Stain) of the Hyb-Wash-Scan protocol * Every mix is an up and down movement of the array plate in the reservoir of the Wash A station ** Every cycle is a fill and drain of the wash buffer in the reservoir of the Wash A station

44 chapter 3 Operating the GeneTitan Instrument 41 Hyb-Wash-Scan Mode Procedure for Running a Plate Setting Up the Instrument Refer to Affymetrix GeneChip Command Console User s Guide (P/N ) for detailed information on this procedure. 1. Start the run by launching the Affymetrix GeneChip Command Console (AGCC) from the workstation of the instrument. 2. Register the sample to the AGCC using the AGCC Portal option from the AGCC Launcher. 3. Start the instrument control interface from the AGCC Launcher. The instrument shall go through its initialization procedure to ensure all the components function properly. 4. Select the Hyb-Wash-Scan Mode to process the array plate from the setup page of the instrument user application. 5. Enter the array plate barcode. There are two methods of doing this. A. Let the GeneTitan Instrument automatically read the plate barcode. B. As an option, you can manually enter a plate s barcode using either a USB external barcode reader or the keyboard. Place the cursor in the barcode field, and scan the barcode using the barcode reader or you can manually enter the barcode. Click Next to continue to the next step. 6. The application instructs you to load the tray in the available position on the drawer. 7. The application prompts you to refill the buffer bottles. Refill them if necessary then press the configuration button (Figure 3.4) to continue to the next step.

45 42 GeneTitan Instrument User s Guide Confirmation Button (to open/close drawers) Figure 3.4 The Confirmation button 8. The application automatically displays the Plate Type field and the Protocol field based on the information of the barcode number of the array plate. 9. The application prompts you to empty the cover trash bin. Open the trash bin door (Figure 3.5), remove and empty the trash bin, return the trash bin then press the configuration button (Figure 3.4) to continue to the next step.

46 chapter 3 Operating the GeneTitan Instrument 43 Figure 3.5 Unloading the trash bin 10. The application prompts you to unload plates from a previous run from the instrument, remove any plate or plate receptacle from the drawer (Figure 3.6) then press the confirmation button (Figure 3.4) to continue to the next step. The software will, in some cases, direct you to leave the empty blue plate cover on Drawer #6 since it may be used as a temporary holding location for subsequent plate processing steps.

47 44 GeneTitan Instrument User s Guide Figure 3.6 Remove any plate or receptacle from the drawer Loading the Instrument The application prompts you to load the plates into the instrument. Perform the following sequence of events to load all the appropriate plates into the instrument. 1. The application opens the Input/Output Drawer #2 and prompts you to load the scan tray with cover (Figure 3.7). Load the scan tray containing array holding buffer and its cover into the left position on the drawer then click the Confirmation button (Figure 3.4) on the front of the instrument to close the drawer.

48 chapter 3 Operating the GeneTitan Instrument 45 Figure 3.7 Loading the scan tray into Draw #2 2. The application opens the Input/Output Drawer #3 and prompts you to load the SAPE stain solution tray with cover (Figure 3.8). Load the stain tray containing SAPE solution and its cover into the left position on the drawer then click the Confirmation button (Figure 3.4) on the front of the instrument to close the drawer.

49 46 GeneTitan Instrument User s Guide Figure 3.8 Loading the SAPE stain tray into Draw #3 3. The application opens the Input/Output Drawer #4 and prompts you to load the AB stain solution tray with cover (Figure 3.9). Load the stain tray containing AB solution and its cover to the left position on the drawer then click the Confirmation button (Figure 3.4) on the front of the instrument to close the drawer.

50 chapter 3 Operating the GeneTitan Instrument 47 Figure 3.9 Loading the stain tray with AB buffer into Draw #4 4. The application opens the Input/Output Drawer #5 (Figure 3.10) and prompts you to load the SAPE stain tray with cover. Load the stain tray containing SAPE stain in the left drawer of Drawer #5 then click the Confirmation button (Figure 3.4) on the front of the instrument to close the drawer.

51 48 GeneTitan Instrument User s Guide Figure 3.10 Loading the stain tray with SAPE stain into Draw #5 5. The application opens the Input/output Drawer #6 and asks you to load the array plate with the protective cover on to the left position and the hybridization tray containing the prepared hybridization solution on to the right position (Figure 3.11 and Figure 2.2 on page 21). Load the array plate and the hybridization tray into its appropriate location on the drawer then click the Confirmation button (Figure 3.4) on the front of the instrument to close the drawer. The application reads the barcode number of the array plate then compares it with the barcode number and the plate type specified in the Barcode field and Plate Type field on the Setup page. If the information is correct, the application allows you to proceed to the next step. If not, the application will prompt you to load correct plate into the instrument.

52 chapter 3 Operating the GeneTitan Instrument 49 Figure 3.11 Loaded array plate with cover (left) and hybridization tray (right) in Drawer #6 6. The application prompts you to review the setup of the instrument (review the sections, Setting Up the Instrument, on page 41 and Loading the Instrument, on page 44) then click the Start button to start the run. The Instrument Performs the Hybridization Procedure The procedures are fully automatic, and there is no user interaction until the instrument completes the hybridization, wash, stain and scan protocols. The instrument performs the following operations. A. The GeneTitan Instrument automatically fills the Wash B reservoir with the wash B buffer and warms it up to the temperature set point in the protocol file. This occurs approximately 30 minutes before the hybridization step is completed. B. The GeneTitan Instrument automatically fills the Wash A station with wash A buffer before the hybridization is complete. C. The GeneTitan Instrument will also remove the covers immediately before the stain step. D. Once the hybridization is completed, the oven door of the GeneTitan Instrument opens automatically.

53 50 GeneTitan Instrument User s Guide The Instrument Performs the Wash and Stain Procedure The GeneTitan Instrument then performs the wash and stain procedure in the following manner. There is no user interaction during this procedure. A. The plate gripper moves the combination of the array plate and the hybridization tray from the oven to the Clamp/Unclamp station. B. The oven immediately closes the door after the plate gripper is retracted. C. The plate gripper unloads the combination of the array plate and hybridization tray into the Clamp/Unclamp station. The Clamp/Unclamp station executes the unclamp command to separate the array plate from the hybridization tray. D. The plate gripper removes the array plate from the hybridization tray and moves the array plate from the Clam/Unclamp station to the Wash A station with prefilled wash A buffer for the first and second wash A steps. E. The GeneTitan Instrument cycles the array plate with an up and down motion while immersed in the buffer solution. The fluidic protocol file specifies the time duration for agitation and the number of buffer drain and fill cycles. F. The plate gripper transfers the array plate to the Wash B station for its stringent wash step. The wash B buffer of this station has already warmed up to the temperature set point. G. The plate gripper immerses the array plate into the Wash B buffer solution for the time specified in the fluidic protocol. H. The plate gripper transfers the array plate to Drawer #6 left side blue cover. After removing the SAPE stain tray cover, the plate gripper transfers the array plate to the SAPE stain tray where the first stain step takes place at ambient temperature. The plate gripper immerses the array plate in the stain solution for the time specified in the fluidic protocol file. I. The plate gripper transfers the array plate to the Wash A station with pre-filled wash A buffer for the third and fourth wash A step. J. The GeneTitan Instrument cycles the array plate up and down while immersed in the buffer solution. The fluidic protocol file specifies the time duration for agitation and the number of buffer drain and fill cycles. K. The plate gripper transfers the array plate to Drawer #6 left side blue cover. After removing the SAPE stain tray cover, the plate gripper transfers the array plate to the AB stain tray where the second stain step takes place at ambient temperature. The fluidic protocol file specifies the immersion time of the array plate in the stain solution. L. The plate gripper transfers the array plate to the Wash A station with pre-filled wash A buffer for its fifth and sixth wash A steps. M. The GeneTitan Instrument cycles the array plate up and down while it is immersed in the buffer solution. The fluidic protocol file specifies the time duration time for agitation and the number of buffer drain and fill cycles.

54 chapter 3 Operating the GeneTitan Instrument 51 N. The plate gripper transfers the array plate to Drawer #6 left side blue cover. After removing the SAPE stain tray cover, the plate gripper transfers the array plate to the SAPE tray for its third stain step at ambient temperature. The fluidic protocol file specifies the immersion time for the array plate in the stain solution. O. The plate gripper transfers the array plate to the Wash A station with pre-filled wash A buffer for its seventh and eighth wash A step. P. The GeneTitan Instrument cycles the array plate up and down while immersed in the buffer solution. The fluidic protocol file specifies the time duration time for agitation and the number of buffer drain and fill cycles. Q. The plate gripper transfers the array plate to the scan tray with pre-filled array holding buffer and unloads the array plate on the scan tray. R. The plate gripper moves the hyb tray from the unclamp station to the output location on Drawer #1. S. The GeneTitan Instrument performs the Wash A and Wash B reservoir cleanup operation. The Instrument Performs the Scan Procedure A. The load drawer of the scanner extends into the GeneTitan Instrument at the scanner handoff position. B. The plate gripper of the GeneTitan Instrument transfers the array plate/scan tray to the scanner handoff position and unloads them on the load drawer of the scanner. C. The plate gripper of the GeneTitan Instrument retracts from the scanner handoff station. D. The load drawer of the scanner retracts and carries the plate into the scanner. E. The plate gripper of the GeneTitan Instrument transfers the hybridization tray from the Clamp/Unclamp station to the hybridization tray output left position on the input /output Drawer #1. F. The scanner executes the scan process of the array plate automatically using the appropriate media files associated with specific probe array type. The output files from the scanner are automatically converted to the format that is compatible with AGCC. G. Once the scanner completes its scanning of the array plate, the load drawer of the scanner transfers the combination of the array plate and scan tray into the GeneTitan Instrument at the scanner hand-off position. H. The plate gripper of the GeneTitan Instrument moves the array plate/scan tray to the Input/Output Drawer #2 and unloads them to appropriate position on the drawer.

55 52 GeneTitan Instrument User s Guide Wash-Scan Mode The Wash-Scan Mode of operation allows you to bypass the hybridization step and begin processing the array plate from the Wash-Stain and Scan steps without any user intervention. In this mode of operation, you can process one array plate at a time. You must follow the directions in the Affymetrix GeneChip Command Console User s Guide (P/N ) for detailed instructions. Wash-Scan Mode Process Description You can use this Wash-Scan Mode to process the array plate if you performed the hybridization step of the array plate in an offline oven. Wash-Scan Mode Procedure for Running a Plate Refer to Affymetrix GeneChip Command Console User s Guide (P/N ) for detailed information on this procedure. Setting Up the Instrument Refer to Affymetrix GeneChip Command Console User s Guide (P/N ) for detailed information on this procedure. 1. Start the run by launching the GeneTitan Affymetrix GeneChip Command Console (AGCC) from the workstation of the instrument. 2. Register the sample to the AGCC using the AGCC Portal option from the AGCC Launcher. 3. Start the instrument control interface from the AGCC Launcher. The instrument shall go through its initialization procedure to ensure all the components function properly. 4. Select the Wash-Scan mode to process the array plate from the setup page of the instrument user application. 5. Enter the array plate barcode. There are two methods of doing this. A. Let the GeneTitan Instrument automatically read the plate barcode. B. As an option, you can manually enter a plate s barcode using either a USB external barcode reader or the keyboard. Place the cursor in the barcode field, and scan the barcode using the barcode reader or you can manually enter the barcode. Click Next to continue to the next step. 6. The application instructs you to load the tray in the available position on the drawer. 7. The application prompts you to refill the buffer bottles. Refill them if necessary then press the configuration button (Figure 3.4 on page 42) to continue to the next step.

56 chapter 3 Operating the GeneTitan Instrument The application automatically displays the Plate Type field and the Protocol field based on the information of the barcode number of the array plate. 9. The application prompts you to empty the cover trash bin. Open the trash bin door (Figure 3.5 on page 43), remove and empty the trash bin, return the trash bin then press the configuration button (Figure 3.4 on page 42) to continue to the next step. 10. The application prompts you to unload plates from a previous run from the instrument, remove any plate or plate receptacle from the drawer (Figure 3.6 on page 44) then press the confirmation button (Figure 3.4 on page 42) to continue to the next step. Procedure 1. The application prompts you the system is warming the Wash B buffer to the preset temperature. Click the Next button to proceed to the next step. 2. The application prompts you to load the plates into the instrument using the same procedure specified in the section, Loading the Instrument, on page 44 with the exception that you load the array plate/ hybridization tray to the right position of the Input/Output Drawer #6 (Figure 3.12). A blue protective cover plate is also required on the left side (with no array plate loaded on it)

57 54 GeneTitan Instrument User s Guide Figure 3.12 Loading array plate and hyb tray on the right position in Drawer #6 3. The application prompts you to review the setup of the instrument then click the Start button to start the run. Once the preset temperature of the Wash B buffer is reached, the plate gripper transfers the array plate/hybridization tray to the Clamp/Unclamp station. The Clam/Unclamp station executes the unclamp command to eject the array plate from the hybridization tray. 4. The instrument performs the same procedures as those specified in the section, The Instrument Performs the Wash and Stain Procedure, on page 50 to the completion of scanning as specified in the section, The Instrument Performs the Scan Procedure, on page 51 to complete the array plate processing.

58 chapter 3 Operating the GeneTitan Instrument 55 Hyb-Wash Mode Hyb-Wash Mode Process Description The Hyb-Wash mode of operation enables you to start the array process with the hybridization step and end the process with Wash-Stain step. This mode allows to bypass the Scan step of the process workflow. You can process one array plate at a time. Hyb-Wash Mode Procedure for Running a Plate Refer to Affymetrix GeneChip Command Console User s Guide (P/N ) for detailed information on this procedure. Setting Up the Instrument 1. Start the run by launching the GeneTitan Affymetrix GeneChip Command Console (AGCC) from the workstation of the instrument. 2. Register the sample to the AGCC using the AGCC Portal option from the AGCC Launcher. 3. Start the instrument control interface from the AGCC Launcher. The instrument shall go through its initialization procedure to ensure all the components function properly. 4. Select the Hyb-Wash mode to process the array plate from the setup page of the instrument user application. 5. Enter the array plate barcode. There are two methods of doing this. A. Let the GeneTitan Instrument automatically read the plate barcode. B. As an option, you can manually enter a plate s barcode using either a USB external barcode reader or the keyboard. Place the cursor in the barcode field, and scan the barcode using the barcode reader or you can manually enter the barcode. Click Next to continue to the next step. 6. The application instructs you to load the tray in the available position on the drawer. 7. The application prompts you to refill the buffer bottles. Refill them if necessary then press the configuration button (Figure 3.4 on page 42) to continue to the next step. 8. The application automatically displays the Plate Type field and the Protocol field based on the information of the barcode number of the array plate. 9. The application prompts you to empty the cover trash bin. Open the trash bin door (Figure 3.5 on page 43), remove and empty the trash bin, return the trash bin then press the configuration button (Figure 3.4 on page 42) to continue to the next step.

59 56 GeneTitan Instrument User s Guide 10. The application prompts you to unload plates from a previous run from the instrument, remove any plate or plate receptacle from the drawer (Figure 3.6 on page 44) then press the confirmation button (Figure 3.4 on page 42) to continue to the next step. Loading the Instrument The application prompts you to load the plates into the instrument. Perform the following sequence of events to load all the appropriate plates into the instrument. 1. The application opens the Input/Output Drawer #2 and prompts you to load the scan tray with cover (Figure 3.7 on page 45). Load the scan tray containing array holding buffer and its cover into the left position on the drawer then click the Confirmation button (Figure 3.4 on page 42) on the front of the instrument to close the drawer. 2. The application opens the Input/Output Drawer #3 and prompts you to load the SAPE stain solution tray with cover (Figure 3.8 on page 46). Load the stain tray containing SAPE solution and its cover into the left position on the drawer then click the Confirmation button (Figure 3.4 on page 42) on the front of the instrument to close the drawer. 3. The application opens the Input/Output Drawer #4 and prompts you to load the AB stain solution tray with cover (Figure 3.9 on page 47). Load the stain tray containing AB solution and its cover to the left position on the drawer then click the Confirmation button (Figure 3.4 on page 42) on the front of the instrument to close the drawer. 4. The application opens the Input/Output Drawer #5 (Figure 3.10 on page 48) and prompts you to load the SAPE stain tray with cover. Load the stain tray containing SAPE stain in the left drawer of Drawer #5 then click the Confirmation button (Figure 3.4 on page 42) on the front of the instrument to close the drawer. 5. The application opens the Input/output Drawer #6 and asks you to load the array plate with the protective cover on to the left position and the hybridization tray containing the prepared hybridization solution on to the right position (Figure 3.11 and Figure 2.2 on page 21). Load the array plate and the hybridization tray into its appropriate location on the drawer then click the Confirmation button (Figure 3.4 on page 42) on the front of the instrument to close the drawer. The application reads the barcode number of the array plate then compares it with the barcode number and the plate type specified in the Barcode field and Plate Type field on the Setup page. If the information is correct, the application allows you to proceed to the next step. If not, the application will prompt you to load correct plate into the instrument.

60 chapter 3 Operating the GeneTitan Instrument 57 Figure 3.13 Loaded array plate with cover (left) and hybridization tray (right) in Drawer #6 6. The application prompts you to review the setup of the instrument then click the Start button to start the run. The Instrument Performs the Hybridization Procedure The procedures are fully automatic, and there is no user interaction until the instrument completes the hybridization, wash, stain and scan protocols. The instrument performs the following operations. A. The GeneTitan Instrument automatically fills the Wash B reservoir with the wash B buffer and warms it up to the temperature set point in the protocol file. This occurs approximately 30 minutes before the hybridization step is completed. B. The GeneTitan Instrument automatically fills the Wash A station with wash A buffer five minutes before the hybridization is complete. C. The GeneTitan Instrument will also remove the covers immediately before the stain step. D. Once the hybridization is completed, the oven door of the GeneTitan Instrument opens automatically. The Instrument Performs the Wash and Stain Procedure The GeneTitan Instrument then performs the wash and stain procedure in the following manner. There is no user interaction during this procedure.

61 58 GeneTitan Instrument User s Guide A. The plate gripper moves the combination of the array plate and the hybridization tray from the oven to the Clamp/Unclamp station. B. The oven immediately closes the door after the plate gripper is retracted. C. The plate gripper unloads the combination of the array plate and hybridization tray into the Clamp/Unclamp station. The Clamp/Unclamp station executes the unclamp command to separate the array plate from the hybridization tray. D. The plate gripper removes the array plate from the hybridization tray and moves the array plate from the Clam/Unclamp station to the Wash A station with prefilled wash A buffer for the first and second wash A steps. E. The GeneTitan Instrument cycles the array plate with an up and down motion while immersed in the buffer solution. The fluidic protocol file specifies the time duration for agitation and the number of buffer drain and fill cycles. F. The plate gripper transfers the array plate to the Wash B station for its stringent wash step. The wash B buffer of this station has already warmed up to the temperature set point. G. The plate gripper immerses the array plate into the Wash B buffer solution for the time specified in the fluidic protocol. H. The plate gripper transfers the array plate to Drawer #6 left side blue cover. After removing the SAPE stain tray cover, the plate gripper immerses the array plate in the stain solution for the time specified in the fluidic protocol file. I. The plate gripper transfers the array plate to the Wash A station with pre-filled wash A buffer for the third and fourth wash A step. J. The GeneTitan Instrument cycles the array plate up and down while immersed in the buffer solution. The fluidic protocol file specifies the time duration for agitation and the number of buffer drain and fill cycles. K. The plate gripper transfers the array plate to Drawer #6 left side blue cover. After removing the SAPE stain tray cover, the plate gripper transfers the array plate to the AB stain tray where the second stain step takes place at ambient temperature. The fluidic protocol file specifies the immersion time of the array plate in the stain solution. L. The plate gripper transfers the array plate to the Wash A station with pre-filled wash A buffer for its fifth and sixth wash A steps. M. The GeneTitan Instrument cycles the array plate up and down while it is immersed in the buffer solution. The fluidic protocol file specifies the time duration time for agitation and the number of buffer drain and fill cycles. N. The plate gripper transfers the array plate to Drawer #6 left side blue cover. After removing the SAPE stain tray cover, the plate gripper transfers the array plate to the SAPE tray for its third stain step at ambient temperature. The fluidic protocol file specifies the immersion time for the array plate in the stain solution.

62 chapter 3 Operating the GeneTitan Instrument 59 O. The plate gripper transfers the array plate to the Wash A station with pre-filled wash A buffer for its seventh and eighth wash A step. P. The GeneTitan Instrument cycles the array plate up and down while immersed in the buffer solution. The fluidic protocol file specifies the time duration time for agitation and the number of buffer drain and fill cycles. Q. The plate gripper of the GeneTitan Instrument then transfers the hybridization tray from the Clamp/Unclamp station to the Hybridization tray output left position on the Input /Output Drawer #1. R. The plate gripper moves the hyb tray from the unclamp station to the output location on Drawer #1. S. The GeneTitan Instrument performs the Wash A and Wash B reservoir cleanup operation. Scan Mode Scan Mode Process Description The Scan mode of operation allows you to scan the array plate on the high throughput array scanner. This mode allows you to bypass the hybridization and wash-stain step of the process workflow. You can scan only one array plate at a time. Scan Mode Procedure for Running a Plate Refer to Affymetrix GeneChip Command Console User s Guide (P/N ) for detailed information on this procedure. 1. Perform the same procedure as specified in the section, Setting Up the Instrument, on page The application prompts you to unload plates from the previous run from the instrument then click the Next button to continue to the next step 3. The application prompts you to load the plates into the instrument. The application opens the Input/Output Drawer #2 and prompts you to load the array plate/scantray on the drawer. Load the array plate/scantray into the left side of the drawer then click the Confirmation button on the front of the instrument to close the drawer.

63 60 GeneTitan Instrument User s Guide Figure 3.14 Loading the scan tray on the left into Draw #2 4. The application prompts you to select the array to be scanned. The application makes the default selection based on the barcode number of the array plate. You can select the specific array to scan by overwriting the default selection. 5. The application prompts you review the setup of the instrument then click the Start button to start the run. A. The application reads the barcode number of the array plate then compares it with the barcode number and the plate type specified in the Barcode field and Plate Type field on the Setup page of the application. If this information is correct, the application allows you to proceed to the next step. If not, the application will prompt you to load correct plate into the instrument. B. The scanner extends its load drawer into the fluidic instrument at the scanner handoff position. C. The plate gripper transfers the array plate/scan tray to the scanner handoff position and places the array plate/scan tray into the load drawer of the scanner. D. The load drawer retracts into scanner and loads the array plate into the scanner. E. The scanner automatically scans the array plate. F. After the scan is completed, the load drawer transfers the array plate/scan tray to the GeneTitan Instrument.