Site Preparation Guide. GeneAtlas System

Transcription

1 Site Preparation Guide GeneAtlas System P/N Rev. C June 2010

2 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, GeneChipcompatible, Command Console, GeneTitan, DMET, Axiom and GeneAtlas are trademarks of Affymetrix Inc. All other trademarks are the property of their respective owner Limited License Subject to the Affymetrix terms and conditions that govern your use of Affymetrix products, Affymetrix grants you a nonexclusive, 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, 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. Fluidics Stations 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. imaging devices 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 Station 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. Array Plates Products may be protected by one or more of the following patents: U.S. Patent Nos. 5,445,934; 5,744,305; 6,261,776; 6,291,183; 6,346,413; 6,399,365; 6,610,482; 6,733,977; and other U.S. or foreign patents. Products are manufactured and sold under license from OGT under 5,700,637 and 6,054,270. Copyright 2010 Affymetrix Inc. All rights reserved.

3 Contents i Contents GeneAtlas System Site Preparation Guide The GeneAtlas System and Components Laboratory Requirements Recommended Bench Placement Electrical Outlets Network Requirements and Software Capability Electromagnetic Compatibility (EMC) Receiving Inspection Initial Inspection Unpacking GeneAtlas System Specifications Computer Workstation Specifications Work Environment Required Lab Equipment and Supplies Certification GeneAtlas Fluidics Station GeneAtlas Imaging Station Safety Information and Warnings Hazards Technical Support

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5 GeneAtlas System Site Preparation Guide Affymetrix, Inc. developed this document to help you through the process of preparing your laboratory to ensure a prompt and successful installation and verification of the GeneAtlas System. In preparing your site for the installation of the GeneAtlas System, please note the following points: Suitable preparation of your laboratory is essential to a successful installation and verification. You may wish to work with your facilities personnel to ensure that your laboratory meets the minimum electrical and other environmental requirements as outlined in this document. You may wish to notify your IT department about networking the workstation if desired. You will need equipment required to perform the target preparation. Adequate space for the dimensions of the GeneAtlas System and bench top support to sustain the total weight are allocated with available service access. The GeneAtlas System and Components The GeneAtlas System comprises several components for processing GeneAtlas array strips. Affymetrix will provide the following system components (Table 1). Table 1 GeneAtlas System Components Component GeneAtlas Fluidics Station GeneAtlas Imaging Station GeneAtlas Hybridization Station Workstation and monitor External barcode reader Installation kit

6 4 GeneAtlas System Site Preparation Guide Laboratory Requirements The GeneAtlas System requires a laboratory workbench with a hard surface. Do not place the instrument on a rolling cart or a workbench with a soft surface such as wood. The workbench surface must be level (front and back) to within ±0.5. This means that the maximum allowable workbench tilt from front to back of the instrument must not exceed ± 0.5 degrees. The workbench must be capable of bearing the weight of the instrument including the Hybridization Station, a workstation monitor and keyboard. The workbench surface must be constructed of material that will not bend or deform under the weight of the instrument. Recommended Bench Placement 1. The instrument should be placed on a bench that can support at least 50 Kg of weight. 2. Additional clearance 12" (30.48 cm) to the right and 6" (15.24 cm) to the back. There should be 24" (61 cm) space to the left of the instrument adjacent to the GeneAtlas Fluidics Station for the 20" workstation monitor, keyboard, mouse and external barcode reader. 3. The workstation should be placed near the GeneAtlas Fluidics Station within the length of the provided USB Cable, but should not be in immediate contact with the Fluidic Station. The Hybridization Station is not connected to the workstation and thus need not be on the same bench. REAR 6" (15.24 cm) Clearance Direction of the Fluidics Station Air Vent Direction of the Imaging Station Air Vent 28" (71.1 cm) Clearance (for workstation, monitor, mouse, keyboard and external barcode reader) 17.2" (43.7 cm) Fluidics Station Imaging Station Hyb Station 10.4" (26.4 cm) 18.9" (48.0 cm) 8.9" (22.6 cm) 7.9" (20.0 cm) 24" (61 cm) FRONT

7 Electrical Outlets 5 Electrical Outlets Wall outlets: five separate, dedicated grounded outlet within 4 ft. (1.22 m) of the instrument. This should be sufficient for the GeneAtlas Fluidics Station, the GeneAtlas Imaging Station, the Hybridization Station and the workstation and monitor Network Requirements and Software Capability You can connect the workstation to a compatible network to transfer data or access data share remotely. You will need to supply your own network cable for this purpose. IMPORTANT: To prevent any disruption to the array processing and scanning, you must turn off all automatic software updates (such as Windows software updates, antivirus-updates, etc.). Electromagnetic Compatibility (EMC) A good EMC environment is critical to the instrument since large noises may lead to unpredictable results. Please consider the following cautions: Keep the instrument away from high dischargeable equipment, such as pacemakers, electric welding equipment, etc. Keep the instrument away from frequently starting-up high power consuming equipment, such as refrigerators, centrifuges, etc. Keep the instrument away from any strong magnetic field. Do not connect many power cables to the junction box to which the instrument is connected. Do not plug in or pull out any other equipment to the same junction box while the instrument is running. Receiving Inspection Your site receiving and inspection must provide suitable safeguards and inspection to receive the GeneAtlas System. Initial Inspection If any external damage is noticed, please indicate the damage on the shipping receipt when you sign for the system. If any internal or sealed damage is noticed when the carton is opened, please contact both the shipping agent and Affymetrix, Inc. immediately.

8 6 GeneAtlas System Site Preparation Guide IMPORTANT: If you detect any apparent damage to the system, do not plug it into the power line. Unpacking Take care when unpacking the system and placing it on a laboratory bench. Rough handling and shock may damage or misalign components of the instrument. GeneAtlas System Specifications Table 2, Table 3, and Table 4 list the important instrument specifications. \ Table 2 GeneAtlas Specifications Specifications Hybridization Station Fluidics Station Imaging Station Temperature range Ambient +5º to 150ºC Ambient +5º to 60ºC N/A Temperature resolution 0.1ºC 0.1ºC N/A Temperature uniformity ±0.2ºC 0.1ºC N/A Temperature accuracy ±0.3ºC ±0.1ºC N/A Excitation Wavelengths (nm) N/A N/A 530 * Autofocus Wavelengths (nm) N/A N/A 590* Effective Resolution N/A N/A 1 μm x 1 μm Digital Resolution N/A N/A 12 bits Effective Dynamic Range N/A N/A 14 bits File Format N/A N/A DAT Sensitivity N/A N/A 0.1fluors/μm² Readout Noise N/A N/A 10 Electrons Active Pixels N/A N/A 1344 (H) x 1024 (V)* Maximum Frame Rate N/A N/A 43 fps Exposure Time (Min.) N/A N/A 0.01 msec. Exposure Time (Max.) N/A N/A 1.0 sec. Array Strip Capacity 4 1/run 1/run Run Time/Strip (hours) Length 20" (265 mm) 16.8" (428 mm) 15.3" (389 mm) Width 7.9" (200 mm) 16.5" (420 mm) 6.4" (164 mm)

9 Computer Workstation Specifications 7 Table 2 GeneAtlas Specifications (Continued) Specifications Hybridization Station Fluidics Station Imaging Station Height 3.3" (3.3 (83 mm) 14.3" (364 mm) 11.9" (303 mm) Noise(dB) <56 <56 <56 Weight (Kg) 5.7* 12* 11* Power Supply Voltage V (± 10%) V (± 10%) V (± 10%) Voltage Current 1.41A Maximum* 1.50A Maximum* 1.00A Maximum* Line Frequency Hz Hz Hz * Unique feature Computer Workstation Specifications Table 3 Computer Workstation Specifications * Base unit Dell OptiPlex 760 Processor Memory Keyboard Hard drive Operating system Mouse CD-ROM or DVD-ROM drive IEEE 1394 card Monitor Barcode scanner Intel Core 2 Duo Processor E8400 (3.0 GHz, 6M cache, 1333 FSB) 2GB USB keyboard 250 GB Microsoft Windows XP Professional with SP3 USB two-button optical mouse with scroll 8X DVD+/RW Onboard Dell 19-inch flat panel monitor Handheld Work Environment * Workstation specifications are for representative purposes and are subject to change Table 4 GeneAtlas Work Environment Parameter Clearance Temperature Specification 6" (15.24 cm) in rear 59 F - 86 F (15 C - 30 C) Relative humidity 10-90%

10 8 GeneAtlas System Site Preparation Guide Table 4 GeneAtlas Work Environment Parameter Pollution degree Specification 2 environment Altitude <2000m Required Lab Equipment and Supplies You must have the following reagents, instruments and supplies in order to perform the operational verification and target preparation protocols on the GeneAtlas System. Table 5 lists these components. Table 5 Lab Equipment and suppliers required to operate the GeneAtlas System Material Source P/N Required Equipment Thermal Cycler with heated Lid (capable of holding 0.2 ml tubes for reaction incubations and with appropriate adaptors to accommodate strip tubes) Heat block Microcentrifuge (with an adapter for the PCR striptubes or plates supplied with the kit) Vortex Mixer (with flat top adaptor to accommodate strip tubes) Spectrophotometer (e.g., NanoDrop ND-8000 UV-Vis Spectrophotometer) Orbital shaker for 96-well plates (e.g., Barnstead/Lab-Line Titer Plate Shaker) Magnetic Stand for 96-well plate used with the IVT Target Prep Assay (96-well Magnetic Stand) Magnetic Stand for 96-well plate used with the WT Target Prep Assay (Magnetic Stand-96) Miscellaneous Supplies NanoDrop Technologies Ambion Ambion ND-8000 AM10050 AM % Ethanol (ACS Grade or equivalent) 100% Isopropanol (ACS Grade or equivalent Pipette for 0.1 to 2 μl * Rainin L-2 Pipette for 2 to 20 μl* Rainin L-20 Pipette for 20 to 200 μl* Rainin L-200 Pipette for 100 to 1000 μl* Rainin L-1000 Sterile-barrier, RNase-free Pipette Tips

11 Required Lab Equipment and Supplies 9 Table 5 Lab Equipment and suppliers required to operate the GeneAtlas System (Continued) Material Source P/N 8-strip PCR tubes and caps (0.2 ml) Non-stick RNase-free microfuge tubes, 0.5 ml Non-stick RNase-free microfuge tubes, 1.5 ml Optional Reagents, Equipment & Supplies Vacuum Centrifuge Concentrator Reagents and apparatus for preparation and electrophoresis of agarose gels Quant-iT RiboGreen RNA Reagent Quant-iT PicoGreen RNA Reagent Invitrogen Invitrogen RNaseZap RNase Decontamination Ambion AM9780 (250 ml) AM9784 (4.0 L) The RNA Storage Solution Ambion Ambion AM7000 (10 x 1.0 ml) AM7001 (50 ml) Bioanalyzer 2100 Agilent RNA 6000 Nano Kit Agilent Technologies Network cable (for connecting the workstation to your network and to the internet for software updates and data transfer) * or equivalent Tips must be pointed, not rounded, for efficient use with the probe arrays. Beveled pipette tips may cause damage to the array septa and cause leakage.

12 10 GeneAtlas System Site Preparation Guide Certification GeneAtlas Fluidics Station EMC Directive 89/336/EEC Low Voltage Directive 73/23/EEC DRPF134: The instrument shall meet the following North American EMC and Safety Regulations: ICES-003, Industry Canada, Interference-Causing Equipment Standard, Digital Apparatus, Class A (Canada) FCC Part 15 Radio Frequency Emissions for Class A Equipment (USA) CAN/CSA-C22.2 No (Canada) as harmonized to IEC UL (USA) as harmonized to IEC Compliant with directive 2002/96/EC (WEEE) (WEEE German Registration) WEEE Registration France Complies with requirements of Radio communications (Electromagnetic Compatibility) Standard 2008 GeneAtlas Imaging Station EMC Directive 89/336/EEC Low Voltage Directive 73/23/EEC DRPS0190: The instrument shall meet the following North American EMC and Safety Directives: ICES-003, Industry Canada, Interference-Causing Equipment Standard, Digital Apparatus, Class A (Canada) FCC Part 15 Radio Frequency Emissions for Class A Equipment (USA) CAN/CSA-C22.2 No (Canada) as harmonized to IEC UL (USA) as harmonized to IEC Compliant with directive 2002/96/EC (WEEE) (WEEE German Registration) WEEE Registration France

13 Safety Information and Warnings 11 Complies with requirements of Radio communications (Electromagnetic Compatibility) Standard 2008 Safety Information and Warnings WARNING: Use of controls or adjustments or performance of procedures other than those specified in installation guide and user manual may result in damage to the instrument, loss of data, invalid data, hazardous radiation exposure, LED light, hazardous voltage, moving parts, or even cause fire. Exposure to the hazards may cause severe or fatal injury. v WARNING: Users are not allowed to gain access to the interior of the GeneAtlas Instrument through any other openings except that is needed to perform operations related with consumables Removing the housing may damage the instrument components and result in hazardous exposure to LED light, hazardous voltage, or moving parts. If the protective housing is damaged, users are not allowed to operate the instrument any more. Hazards Table 6 summarizes possible hazards. Table 6 GeneAtlas System Hazards Hazard Present? Description Chemical No Control No Control software Electrical Yes V power Ergonomic Yes User interface Gas No Mechanical Yes instrument weight (heavy instrument) Laser Noise No No Temperature Yes Hybridization Station and Fluidics Station Ultrasonic No

14 12 GeneAtlas System Site Preparation Guide Table 6 GeneAtlas System Hazards (Continued) Hazard Present? Description Vibration E-Fields H-Fields No No No

15 Technical Support 13 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. Affymetrix, Inc Central Expressway Santa Clara, CA USA Tel: (1-888-DNA-CHIP) Fax: Affymetrix UK Ltd., Voyager, Mercury Park, Wycombe Lane, Wooburn Green, High Wycombe HP10 0HH United Kingdom UK and Others Tel: +44 (0) France Tel: Germany Tel: Fax: +44 (0) Affymetrix Japan, K. K. ORIX Hamamatsucho Bldg, 7F Hamamatsucho, Minato-ku Tokyo Japan Tel: Fax:

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