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®
GenePix
Autoloader 4200AL
MICROARRAY SCANNER
User's Guide
Part Number 2500-0165 Rev B August 2005 Printed in USA
Copyright 2005 Axon Instruments / Molecular Devices Corp.
No part of this manual may be reproduced, stored in a retrieval system, or
transmitted, in any form or by any means, electronic, mechanical, photocopying,
microfilming, recording, or otherwise, without written permission from Molecular
Devices Corp.
QUESTIONS? See Axon's Knowledge Base: http://support.axon.com
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Inhaltszusammenfassung für Axon GenePix Autoloader 4200AL

  • Seite 1 User’s Guide Part Number 2500-0165 Rev B August 2005 Printed in USA Copyright 2005 Axon Instruments / Molecular Devices Corp. No part of this manual may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from Molecular Devices Corp.
  • Seite 3 !!!!! SAFETY LEASE READ There are important safety issues that you must take into account when using this instrument. Please carefully read the safety warnings starting on page 45 before you use this instrument. VERIFICATION This instrument is extensively tested and thoroughly calibrated before leaving the factory.
  • Seite 5 Table of Contents • iii Table of Contents Chapter 1 Introduction ..................1 Chapter 2 Installation .................... 3 About This User’s Guide..................3 Computer Requirements..................3 Setting Up and Moving the GenePix Scanner............4 Preparing to Install the GenePix Scanner.............. 5 Quick Overview of Hardware and Software Installation ........
  • Seite 6 Dynamic Range and Detection Limit ..............32 Specifications ...................... 33 Technical Assistance....................35 Warranty and Repair Service ................37 Licensing Notice..................... 41 Declaration of Conformity..................43 Important Safety Information................45 Index ........................65 GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 7 Introduction • 1 Chapter 1 Introduction The GenePix Autoloader 4200AL is the latest microarray scanner from Axon Instruments, Inc. It has several enhanced features for high-performance quantitative imaging set by the benchmark GenePix 4000 series scanners. Key features of the 4200AL are: •...
  • Seite 8 Acuity Microarray Informatics software. Axon Instruments has consulted widely among the scientific pioneers of microarray techniques to produce an instrument that fulfills all their image acquisition and primary analysis needs. GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 9 GenePix Pro Software User’s Guide, and the on-line Help in GenePix Pro (press <F1>). For information on setting up your GenePix Autoloader 4200AL scanner and software, please refer to this chapter. For a guided tutorial on scanning your first slide, see Chapter 3 of this manual, and Chapter 4 of the GenePix Pro Software User’s Guide.
  • Seite 10 Setting Up and Moving the GenePix Scanner Placement Place the GenePix Autoloader 4200AL scanner on a secure laboratory bench top or reinforced table. The scanner weighs more than 50 kg (110 lb) and requires two people to lift it. There are four recessed hand spaces underneath the scanner to assist lifting.
  • Seite 11 Installation • 5 Failure to park the scanner before moving it may cause misalignment or damage to the optical system. Preparing to Install the GenePix Scanner If you have purchased a GenePix scanner without the optional host computer please follow the instructions below. If you purchased a GenePix scanner with a bundled host computer, the necessary hardware and software are already installed.
  • Seite 12 Win-ASPI compliant. You must also ensure that you have the proper cabling to connect the SCSI card to the GenePix scanner. While it is possible that an existing GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 13 Installation • 7 SCSI card may work with the GenePix scanner, technical support is provided only for the SCSI card that is bundled with the GenePix. If you are using the GenePix scanner on a computer with multiple SCSI devices please ensure that there are no SCSI ID conflicts.
  • Seite 14 The data cable between the computer and the scanner is securely connected. • The GenePix scanner has power (the green power light at the front of the scanner will be glowing). • The SCSI card is operational (see above). GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 15 Installation • 9 • The GenePix SCSI ID 4 does not conflict with any other SCSI devices that you may have already installed on your computer (e.g., a Jaz drive). • The scanner power was turned on before booting the computer. Chapter 2...
  • Seite 17 Operation The Shipping-lock Slide Carrier The GenePix Autoloader 4200AL scanner is delivered to you in the “Park” position, using a slide carrier modified specifically to secure the robot arm for shipping. This shipping-lock slide carrier has a plastic slide glued into position 36.
  • Seite 18 However, the quickest position for single slide scanning is position 36. After scanning, multiple slide carriers can be stacked for easy storage of each batch. GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 19 Operation • 13 Note: Over time the sharp edges of glass slides may etch the inside surfaces of the plastic slide carrier. If you begin to see handling failures in specific slide positions, you should replace the slide carrier. We recommend replacing slide carriers after approximately 30 batches.
  • Seite 20 Because the scanner maps the slide carrier, it scans only those positions containing slides. Configuring a Batch Scan There are two types of settings that you can make on the Batch Scan tab: GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 21 Operation • 15 • For each slide in the slide carrier, you can specify hardware (scanner) settings and analysis settings. • For the entire batch scan, you can specify file naming and saving options, and Workflow options. For Each Slide To scan it as part of the batch process, you must select the slide and select the Include in Data Scan button.
  • Seite 22 The GAL/GPS file does not need to be aligned to features, but it does need to be roughly near the features on the array. See the GenePix Pro Help for more on Auto PMT. GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 23 You can open this file by selecting Open Batch Scan Log from the File menu. The log file is saved by default in the …\Axon\Data\ directory, but you can specify where it is saved in the Options / Folders dialog box.
  • Seite 24 Diagnostics Report every two hours during operation. Installing Additional Filters Your GenePix Autoloader 4200AL scanner comes with one standard filter for each installed laser. The standard filters are not accessible by the user. You can install additional filters in any of the twelve remaining filter positions. The installation process involves two steps: 1.
  • Seite 25 Operation • 19 2. Turn the wheel to align any open position with the hole in the top of the filter cartridge. The number of that filter position is visible in the smaller adjacent hole. Note the number of the filter position you will use: this number must be recorded in GenePix Pro (see below).
  • Seite 26 2. Record the information for the new filters in GenePix Pro 1. Turn on the scanner and computer. If GenePix Pro is running, shut it down. 2. From the Windows Start menu, go to Programs / Axon Laboratory / GenePix Pro / Filter Tool.
  • Seite 27 Operation • 21 3. In the Filter Tool program, click the checkbox for the filter position you are adding. The Filter Wavelength dialog box will appear (Figure 7). Figure 7. Mid-point wavelength editor. 4. Enter the midpoint of the wavelength range that is transmitted by the filter. For a band-pass filter, a 530DF30 filter, for example, transmits a 30 nm band of light centered at 530 nm (i.e., it transmits 515 –...
  • Seite 28 Release Magazine Lock Important: The Release Magazine Lock utility should only be used under the supervision of Axon Technical Support. Improper use of this utility may cause damage to your scanner and/or slides. GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 29 Operation • 23 Open Robot Grippers Important: The Open Robot Grippers utility should only be used under the supervision of Axon Technical Support. Improper use of this utility may cause damage to your scanner and/or slides. Calibrate Focus Focus calibration works with the GenePix 4000B only.
  • Seite 31 Imaging System Hardware • 25 Chapter 4 Imaging System Hardware The GenePix Autoloader 4200AL scanner is one of the most sensitive scanners currently available. This chapter introduces some of the fundamental hardware concepts needed to understand the operation of the GenePix scanner.
  • Seite 32 Excitation laser light is directed onto the slide after passing through a series of filters and mirrors. While laser light is by definition very narrow band, the GenePix scanner employs additional optical filters to ensure that no GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 33 Imaging System Hardware • 27 spurious excitation light is directed onto the slide. If the laser light impinges on an appropriate fluorophore bound on the slide, emission light of a longer wavelength is emitted (the difference between the emission and excitation wavelengths is called the Stokes shift).
  • Seite 34 28 • Imaging System Hardware Emission filters are located in a sixteen-position filter wheel that is readily accessible in the GenePix Autoloader 4200AL. Four positions in the filter wheel are reserved for the standard emission filters (red, yellow, green, blue) and are installed at the factory and are not accessible. The remaining twelve positions are available to the user for custom filter installation (see below).
  • Seite 35 The filter information is stored in the PC board of the scanner (not the computer). After each filter installation or change is made, turn on the scanner and open the Filter Tool program, located in the Axon Laboratory / GenePix Pro 5 folder of the start menu. Activate the filter position by pressing on the check box, and enter a description that will help you identify the filter.
  • Seite 36 When using such a mechanical device, one must be able to monitor the variability in the performance of its mechanical components. The GenePix scanner has been designed with a number of optimizations to ensure that variability in the mechanical GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 37 Axon Instruments is the world leader in the design and construction of low-noise amplifiers. Our amplifiers are used around the world by researchers in the neuroscience community.
  • Seite 38 Furthermore, while an instrument may have a large dynamic range, one may not be able to use the whole range reliably if the response is non-linear. Therefore when GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 39 Imaging System Hardware • 33 rating an instrument one must consider the range over which its response remains linear. For the GenePix scanner, the dynamic range is 10 The dynamic range of an instrument is often considered in conjunction with its detection limit.
  • Seite 41 Technical Assistance • 35 Technical Assistance If you need help to resolve a problem, there are several ways to contact Axon Instruments / Molecular Devices: World Wide Web www.axon.com Phone (800) 635-5577 +1 (510) 675-6300 E-mail axontech@axon.com Questions? See Axon’s Knowledge Base: http://support.axon.com...
  • Seite 43 Products returned to our factory for repair should be properly packaged with transportation charges prepaid. Axon Instruments / Molecular Devices will pay for the return shipping of the product to the customer. If the shipment is to a location outside the United States, the customer will be responsible for paying all duties, taxes and freight clearance charges if applicable.
  • Seite 44 The GenePix 4200AL is a solidly built instrument designed to survive shipping around the world. However, in order to avoid damage during shipping, the GenePix 4200AL must be properly packaged. GenePix 4200AL User’s Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 45 If you need to ship the GenePix 4200AL to another location, or back to the factory, and you do not have a means to adequately package it, Axon Instruments / Molecular Devices can ship the proper packaging material to you for a small fee.
  • Seite 47 Licensing Notice • 41 Licensing Notice Axon Instruments / Molecular Devices is not licensed under any patents owned by Oxford Gene Technology Limited ("OGT"), covering oligonucleotide arrays and methods of using them to analyze polynucleotides. The purchase of Axon Instruments / Molecular Devices products does not convey any license under any of OGT’s patent rights, including any right to make or use oligonucleotide arrays...
  • Seite 48 This instrument is licensed by Affymetrix under 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; 6,262,838; 6,335,824; 6,403,320; 6,403,957, 6,407,858; 6,472,671; 6,490,533; 6,545,264; 6,597,000; 6,643,015; and 6,650,411. GenePix 4200AL User's Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 49 Declaration of Conformity • 43 Declaration of Conformity Manufacturer: Axon Instruments / Molecular Devices Corp. 3280 Whipple Road Union City, CA 94587 USA Type of Equipment: Microarray Scanner Model Number: GenePix Autoloader 4200AL Serial Number: _____________ Year of Manufacture: 2004...
  • Seite 51 Important Safety Information • 45 Important Safety Information The operator of the GenePix Autoloader 4200AL Microarray Scanner instrument is assumed to be trained in the correct operation of the instrument and the safety issues. Throughout the GenePix Autoloader 4200AL Microarray Scanner User’s Guide, the word “you”...
  • Seite 52 Do not stick anything into the openings or vents of the GenePix 4200AL, other than loading the slide. You may cause an interlock to fail. • Do not attempt to move any parts below the slideholder. You may cause an interlock to fail. GenePix 4200A User's Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 53 Use standard laboratory procedures and cautions when working with chemicals. Caution: Always follow the manufacturer’s precautions when working with chemicals. Axon Instruments is not responsible or liable for any damages caused by or as a consequence of the use of any hazardous material.
  • Seite 54 If a label becomes illegible or is missing for any reason, please contact Microarray System Technical Support for a free replacement label. While waiting for the replacement label, copy the label shown in this section and attach the copy of the label to the instrument. GenePix 4200A User's Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 55 Site Requirements The GenePix Autoloader 4200AL is designed to operate optimally if the site requirements are met. As with any precision optical instrument, care should be taken to maintain a low-dust, low-vibration environment. Temperature and humidity extremes may compromise performance.
  • Seite 56 : la porte coulissante bloque automatiquement l’émission des rayons lors de son ouverture. Il y a deux accès potentiels sous l’appareil qui ne possèdent pas cette GenePix 4200AL User's Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 57 Symptômes Liés aux Problèmes de Verrouillage Il est dangereux de continuer à utiliser le GenePix 4200AL si seul l’un des deux verrouillages de sécurité fonctionne. Prière de contacter Axon Instruments immédiatement à l’un des numéros indiqués à l’arrière du GenePix 4200AL.
  • Seite 58 Attention: Veillez à toujours suivre les consignes de sécurité du fabricant lors de la manipulation de produits chimiques. Axon Instruments ne peuvent être tenues pour responsables de dommages éventuels, directs ou indirects, causés par l’utilisation de substances dangereuses.
  • Seite 59 Informations de Sécurité Importantes • 53 Accès non verrouillés par la Double Protection Vue de l'avant et de l’arrière du GenePix 4200AL montrant les sept vis qui maintiennent le boîtier. NE PAS RETIRER CES VIS ! DANGER ! Radiation laser lorsque ouvert EVITER IMPERATIVEMENT L’EXPOSITION DIRECTE AUX RAYONS Don’t remove these screws.
  • Seite 60 Espace nécessaire: 65 cm × 43 cm × 34 cm, plus 15,2 cm (6 in) clair. Poids: Structure suffisante pour supporter un poids de 45 kg (99 lbs.) pratiquement sans vibration. GenePix 4200AL User's Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 61 Información Importante sobre la Seguridad • 55 Información Importante sobre la Seguridad Se asume que el operador del GenePix 4200AL Microarray Scanner está entrenado en las precauciones de seguridad a seguir y en la utilización correcta del instrumento. La palabra “usted” como se utiliza en esta guía del usuario del GenePix 4200AL Microarray Scanner se refiere a este operador entrenado.
  • Seite 62 Seguridad del Láser Precauciones • No inserte ningún objeto en las aperturas o respiraderos del GenePix 4200AL diferente de la placa. Puede ocasionar fallas en el circuito de seguridad. GenePix 4200AL User's Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 63 El usuario debe utilizar procedimientos y precauciones de laboratorio estandarizados cuando trabaja con productos químicos. Precaución: Utilice siempre las instrucciones de la fábrica cuando trabaje con productos químicos. Axon Instruments no son responsables legalmente por daños o lesiones ocasionados como consecuencia del uso de materiales peligrosos.
  • Seite 64 Si una etiqueta se hace ilegible o se pierde por algun motivo, por favor contacte el servicio técnico del sistema para obtener etiquetas sin costo alguno. Mientras espera por las etiquetas de reemplazo, copie las que aparecen en esta sección y pegue una copia en el instrumento. GenePix 4200AL User's Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 65 Información Importante sobre la Seguridad • 59 Explicaciones de los Símbolos El equipo está a la espera Registrando (“Scanning”). Expulse (“Eject”). (“Standby”). La platina está lista para descargar. La platina está lista en posición de cargar la diapositiva y empezar. Atención, Peligro al levanter! Atención,...
  • Seite 66 Schrauben befestigt sind. Diese können nur mit Hilfe eines Werkzeuges entfernt werden. Sie sind unten abgebildet. Entfernen Sie niemals die Schrauben, um das Gehäuse zu öffnen! GenePix 4200AL User's Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 67 Sicherheitsmassnahmen • 61 • Die im Gerät enstehenden Laserstrahlen können Ihre Augen beschädigen, bevor Sie Gelegenheit haben, sich zu schützen. • Im Gerät entstehen hohe Spannungen. • Es befinden sich im Gerät keine für den Nutzer justierbaren Teile. • Wenn Sie versuchen, das Schutzgehäuse zu öffnen, kann dies eine Beschädigung des Gerätes zur Folge haben. Hinweise auf ein Versagen der elektrischen Verriegelung Wenn eines der nachfolgenden Probleme auftritt, hat wahrscheinlich eine Verriegelung versagt.
  • Seite 68 Der Benutzer muss alle normalen Laboranweisungen und Sicherheitsvorkehrungen befolgen, wenn Chemikalien verwendet werden. Achtung: Befolgen Sie immer die Anweisungen der Hersteller, wenn Sie mit Chemikalien arbeiten. Axon Instruments übernehmen keine Verantwortung für Schäden, die durch den Missbrauch von gefährlichen Chemikalien verursacht werden.
  • Seite 69 Sicherheitsmassnahmen • 63 Geräteöffnungen Ohne Elektrische Verriegelung Ober- und Rückseitenansicht des GenePix 4200AL zeigt die sieben Schrauben die das Schützgehäuse befestigen. ENTFERNEN SIE DIESE SCHRAUBEN UNTER KEINEN UMSTÄNDEN! VORSICHT!! Laserbestrahlung wenn geöffnet!! VERMEIDEN SIE DIREKTEN KONTAKT MIT DEM LASERSTRAHL! Don’t remove these screws. Instandhaltung und Vorsorge Es ist keine Vorsorge durch den Benutzer nötig.
  • Seite 70 Platzvoraussetzung: 65 cm × 43 cm × 34 cm, Bitte, einen zusätzlichen Abstand von 15,2 Zentimeter (6 Zoll) frei zu lassen. Gewichtsvoraussetzung: Genug um 45 kg (99 Pfund) zu unterstützen mit minimalen Schwingu. GenePix 4200AL User's Guide, Copyright 2005 Axon Instruments / Molecular Devices Corp.
  • Seite 71 Index • 65 Index Alexa Fluor Dyes, 26 Quantum Efficiency, 30 Amplifiers, 31 Spatial Resolution, 31 Help Custom Filters, 28 On-Line, 3 Cy3, Cy5, 26 Image Data Scan, 31 Size, 32 Digitization, 1 Lasers Emission Filter, 27, 28 Temperature Fluctuations, 26 Filters On-line Help, 3 Installing, 18...