affymetrix genechip® array station user's...

P/N 701859 Rev. 4June 2006

Affymetrix GeneChip® Array StationUser’s Guide

701859.book Page i Friday, June 2, 2006 9:42 AM

ii

For Research Use Only. Not for Use in Diagnostic Procedures.

TrademarksAffymetrix®, GeneChip®, ®, HuSNP®, GenFlex®, Flying Objective™, CustomExpress®, CustomSeq®, NetAffx™, Tools To Take You As Far As Your Vision®, The Way Ahead™, Powered by Affymetrix™, and GeneChip-compatible™, are trademarks of Affymetrix, Inc.

Caliper® and Twister® are trademarks of Caliper Life Sciences, Inc.All other trademarks are the property of their respective owners.

Limited LicenseSubject 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.

Copyright©2005-2006 Affymetrix, Inc. All Rights Reserved

701859.book Page ii Friday, June 2, 2006 9:42 AM

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Contents

CHAPTER 1 Array Station System Description 3

INTRODUCTION 5

SYSTEM DESCRIPTION 5Intended Use 5

SAFETY 5

REGULATORY COMPLIANCE 7

TECHNICAL SUPPORT CONTACT INFORMATION 8

ARRAY STATION SUBSYSTEMS 9Mechanical Subsystems 10Recovery from an Emergency Shutdown 17Caliper Twister II Robotic Arm and Storage Rack 18The Bio-Rad DNA Engine Thermal Cycler 20The Watlow Temperature Control 21

USER DOCUMENTATION 22

CHAPTER 2 Maintenance and Troubleshooting 23

PREVENTATIVE MAINTENANCE 25Daily 25Weekly 25Monthly 25Quarterly 26

ARRAY STATION TROUBLESHOOTING 27

E-MAIL NOTIFICATION 30Alternative E-Mail Configuration 33

INDEX 37

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Chapter 1 Array Station System Description

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Chapter 1


5

Introduction

Welcome to the Affymetrix GeneChip® Array Station. This system uses robotic technology to automate many of the labor intensive tasks routinely used in target preparation.

This user’s manual provides a general overview of the Array Station, recommendations for maintenance, and troubleshooting tips.

System Description

Affymetrix has developed the GeneChip Array Station to deliver a complete, flexible solution for increased productivity and standardization. The system automates target preparation and processing of GeneChip® arrays in a standard 96-well format. Proven GeneChip arrays, optimized assays and reagents, flexible instrumentation, and an open software architecture together provide you with an integrated system that delivers the most accurate and reproducible data possible.

INTENDED USE

Designed with multiple capabilities, this system also provides scalable and flexible options for meeting both your current and future research requirements. The GeneChip Array Station has been designed and optimized for use with the current GeneChip system. The automated target preparation method produces hybridization cocktail that is ready to load into cartridge arrays. As such, it can be easily and conveniently added to your existing workflow.

Safety

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.

CAUTION


6 GeneChip® Array Station User’s Guide

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.

If you use the Array Station in a manner not specified in this user guide,you may impair the protection provided by the equipment.

The thermocycler methods have been preset at the factory and shouldnot be modified.


chapter 1 | Regulatory Compliance 7

Regulatory ComplianceWe, Affymetrix, 4G Crosby Drive, Bedford, MA 01730, USA

declare under sole responsibility that the Affymetrix GeneChip® Array Station 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.

Regulatory Agency Certification

Compliant with directive 2002/96/EC (WEEE)



Technical Support Contact InformationAffymetrix provides technical support to all licensed users via phone or E-mail. To contact Affymetrix Technical Support:

Affymetrix, Inc.3420 Central ExpresswaySanta Clara, CA 95051 USATel: 1-888-362-2447 (1-888-DNA-CHIP)Fax: 1-408-731-5441

[email protected]

Affymetrix UK Ltd.,Voyager, Mercury Park,Wycombe Lane, Wooburn Green,High Wycombe HP10 0HHUnited Kingdom

UK and Others Tel: +44 (0) 1628 552550France Tel: 0800919505Germany Tel: 01803001334Fax: +44 (0) 1628 552585

[email protected]@affymetrix.com

Affymetrix Japan, K. K.Mita NN Bldg16 Floor, 4-1-23 Shiba,Minato-ku, Tokyo 108-0014Japan

Tel: (03) 5730-8200Fax: (03) 5730-8201

www.affymetrix.com


chapter 1 | Array Station Subsystems 9

Array Station SubsystemsThe Array Station is composed of both hardware and software subsystems. Figure 1.1 illustrates the core mechanical components of the Array Station including the Caliper Sciclone, Bio-Rad DNA Engine Thermal Cycler, and Twister II.

The Sciclone control software provides a graphical user interface (GUI) to run and track the various mechanical components that comprise the application. The Sciclone software has integrated all instrument control panels (ICP's) into one GUI, thus enhancing software ease of use. See Figure 1.2 for a schematic of the software product configuration for the array station.

Figure 1.1The GeneChip® Array Station

DI Water

Caliper®

Sciclone

Workstation

Caliper® Sciclone Head

Twister® II

Plate Stacker

Waste

LiquidComputer

Terminal

The Bio-Rad® DNA

Engine Thermal

Cycler is located

behind the Twister

unit. The thermal

cycler controller and

spectrophotometer

are located below

the Array Station.

Twister® II

Robot Arm

Caliper® Sciclone

Workstation Deck

EMERGENCY STOP

BUTTON

DI Water

®



MECHANICAL SUBSYSTEMS

The Array Station comprises the following mechanical subsystems:

1. Caliper Sciclone (See Figure 1.1 on page 9.)2. Caliper Twister II (See Figure 1.9 on page 18.)3. Bio-Rad DNA Engine Thermal Cycler (See Figure 1.11 on page

20.)4. Watlow Temperature Control (See Figure 1.12 on page 21.)

Caliper Sciclone

The primary mechanical subsystem is the Caliper Sciclone liquid handling robotic system. The robotic system is designed to perform rapid high-precision liquid transfers between 96-well and 384-well microplates. This workstation is combined with a Twister II plate stacker to provide a complete plate storage, transfer, and dispensing system.

The sub-components of the Caliper Sciclone are:

1. High Volume Head (HVH)—capable of pipetting volumes of up to 200 μL to 96 samples at once. Note that the type of tip will determine the actual volume dispensed (Figure 1.3).

Figure 1.2 The Caliper Sciclone 4.0 software for the GeneChip® Array Station



Figure 1.3Array Station High Volume Head



2. Z8 Pipette Head — capable of pipetting independent volumes up to 100 μL from 1 to 8 samples. Note that the type of tip will determine the actual volume dispensed (Figure 1.4).

Figure 1.4The Z8 Pipette Head



3. Bulk Reagent Dispensing Head - capable of bulk dispensing reagents into plates on the system (Figure 1.5).

Figure 1.5The Bulk Reagent Dispensing Head



4. Caliper Sciclone Gripper - capable of moving plates within the deck of the Caliper Sciclone and lidding/delidding plates (Figure 1.6).

Figure 1.6The Caliper Sciclone Gripper



5. Active Locator Plate - actively indexes plates placed in this deck positioner (Figure 1.7).

6. Clamp Release - facilitates removal of HT Array Plate from Hybridization Plate (Figure 1.8).

Figure 1.7 The Active Locator Plate

Figure 1.8 The Clamp Release



The Caliper Sciclone robotic workstation and the Twister II robotic armare equipped with safety interlocked doors and an emergency STOPswitch located on the front and rear of the Caliper Sciclone. Theinterlocked doors must be closed to operate the Caliper Sciclone andthe Twister II robotic arm. If you open the doors to either the CaliperSciclone or the Twister II robot, the corresponding robot will stopimmediately and display an error message at the console. Once youclose the doors, you will then have the option to “retry method step,”“skip method step,” or “stop execution” from the console to recoverfrom the error. If you “pause” the Caliper Sciclone or Twister II robot,or if the Array Station pauses between method steps, you can open andclose the doors safely without generating an error. However, if the dooris open when you, or the software, command the robot to resume, thesystem will generate an error and the Caliper Sciclone or Twister IIrobot will not move.

Under no circumstances are you to override this safety interlock!Serious injury can result.

Do not place your hands inside the robotic deck or inside theTwister II shields while the system is in operation. Twister II robotstackers must also be in place for operation.



RECOVERY FROM AN EMERGENCY SHUTDOWN

To recover from an emergency shutdown, follow these steps.

1. Turn the stop button clockwise until it raises.

If unsure about the position of the stop button, press the stop button until it is firmly depressed and then turn the red portion clockwise until the button comes back up.

2. Power off the Caliper Sciclone (ensure that the Caliper Sciclone gantry is supported; otherwise, the head will slowly descend).

3. Remove anything from the Twister II robot's metal gripper and ensure that the grippers are supported; otherwise, the gripper will slowly descend.

4. Power off the Twister II robot.5. Power off the computer. 6. Power on all components and restart the computer.

IF NECESSARY, PRESS THE EMERGENCY STOP BUTTON TOIMMEDIATELY SHUT DOWN THE SYSTEM. This removes all powerto the Caliper Sciclone Robot and the Twister II Robot.

Please note that the entire run will be lost if the emergency stopbutton is depressed.



Caliper Twister II Robotic Arm and Storage Rack

The Twister II is responsible for moving material between the deck, the storage racks and the thermocycler (Figure 1.9). The Twister II robotic arm transports the pipette tips from the storage racks to the deck. The storage racks (Figure 1.10) hold nested pipette tip boxes for use on the deck.

Figure 1.9 The Caliper Twister II



Figure 1.10 The Caliper Twister II tip storage racks



The Bio-Rad DNA Engine Thermal Cycler

The Bio-Rad DNA Engine Thermal Cycler (from Bio-Rad Laboratories, Inc.) is a component that is necessary for certain assay steps, e.g., incubation, fragmentation, denaturing, etc. See Figure 1.11.

Figure 1.11The Bio-Rad DNA Engine Thermal CyclerWARNING: The thermocycler methods have been preset at the factory and should not be modified!



The Watlow Temperature Control

The Watlow temperature control unit is necessary to set the temperature of the reagent cold block on the deck and for controlling the temperature of the high stringent wash buffer. See Figure 1.12.

Figure 1.12The Watlow® Temperature Control



User DocumentationThe operation of the Array Station robotic system requires familiarity with the user documentation. Those manuals that are relevant for you will depend on your system configuration. For the Array Station configuration, refer to the following documents.

1. GCOS User’s Guide (P/N 701439): if you are using Affymetrix GeneChip® analysis software, you should be familiar with Affymetrix’ GeneChip® Operating System in order to interpret the assay results.

2. Array Station Site Prep Guide (P/N 702020)

3. HT Scanner Site Prep Guide (P/N 702021)

4. Array Station Deck Layout Quick Reference Card (P/N 702013)

5. GeneChip® Array Station Reagent Preparation for Cartridge Arrays Quick Reference Card (P/N 702032)

6. HT Scanner User’s Guide (P/N 701978)

7. GeneChip® Expression Analysis Technical Manual For Cartridge Arrays Using the GeneChip Array Station (P/N 702064)

8. HT Image Reader User’s Manual details the use of the HT Image Reader analysis software. In order to analyze the assay results, you must be familiar with HT Image Reader software.

The following manuals are for operator reference only. You should never tamper or alter the initial Affymetrix protocols or scripts.

1. Caliper® Sciclone User’s Manual (from Caliper Life Sciences).

2. MJ Thermal Cycler ICP Guide (from Bio-Rad Laboratories, Inc.).


Chapter 2 Maintenance and Troubleshooting


Chapter 2


chapter 2 | Maintenance and Troubleshooting 25

Preventative MaintenancePreventative maintenance as part of a routine schedule is the most effective way to ensure the system remains in good condition. Use the guidelines provided in this section for daily, weekly, monthly, and quarterly maintenance activities.

DAILY

• Clean up liquid and tip waste containers.

• Change the tip base in the A5 position after every wash/stain run.

• Reboot computer before every run.

• If running plates, ensure that the levels of the buffers are sufficient.

• Clean up any liquid spills at the end of a run.

• Look for air bubbles in the visible portion of the lines and in the Z8 and bulk dispense syringes while the priming method is running.

WEEKLY

• Change the “P” pads on the lids after every 15 runs.

• Wipe-down of the deck and deck locators with water to remove any buffer salt buildup or spills followed by conditional washes if needed (for example, with RNase or DNase wash, etc.). Remove deck locators to clean underneath as well.

• Prime pumps with DI water weekly when not being used. Prime bulk reagent dispenser and Z8 with DI water.

• Check and replace the gripper pads as needed on both the Sciclone gripper and the Twister II gripper.

MONTHLY

• Check the plastic tubing ferrules (clear & black) going into the Z8 pump and make sure they are finger tight.

• Check the plastic tubing ferrules (clear) going into the bulk reagent pump and make sure they are finger tight.

• Clear out instrument log folders. These folders are located at:

(C:\Affymetrix\Logs\Execution)



QUARTERLY

• Bleach the Z8 and bulk dispense lines.

• Lubricate the cannula block with the silicone oil provided.



Array Station TroubleshootingWhen errors are encountered while the system is running, a window will appear on the screen allowing you to determine the next step.

For example, the software will generate an error if the Caliper Sciclone head moves to an improper position. In Sciclone 4.0, the Alarm Manager window (Figure 2.1) is embedded into the GUI. If an error were to occur, you would click the Alarms tab for immediate help in correcting the problem. The top panel displays the error description followed by recovery options. The Alarm Manager window (Figure 2.1) presents you with several options to determine the best course of action.

Figure 2.1The Alarm Manager window



1. Click on the Alarm tab (Figure 2.1) to determine the issue.

The window will display a detailed description of the error encountered.

2. The Stop Alarm button silences the alarm that sounds during an error condition.

3. If the error is recoverable or fixable, you can continue to use the Recovery Options.

4. If the move was not completed (examples: plate did not make it to destination, lid was dropped, tips were not picked up, etc.), then reset the system to the point before the error happened and highlight RetryInstruction [the operation the system was attempting to execute] and push the Execute Selected Option button. The system will then retry the operation.

5. If the move was completed successfully but an error occurred at the end of the operation (examples: lid was dropped but dropped on destination, thought it did not pick up tips when in fact it did, etc.), highlight SkipInstruction [the operation the system was attempting to execute] and push the Execute Selected Option button. The system will then skip the attempted operation and proceed to the next step.

6. If the move has caused a severe error or is unrecoverable, highlight StopExecution and push the Execute Selected Option button. The system will immediately stop all operation.

7. To aid in the recovery of the system, you can press the Diagnose button (Figure 2.2) to initialize the system or components that may be causing the error.

Errors involving liquid handling are difficult to recover from andshould be done with the aid of a Technical Support Representative.See Technical Support Contact Information on page 8.



8. Use the tabs above to locate the problematic module and initialize.

Figure 2.2The Diagnose window



E-Mail NotificationYou can program the Caliper Sciclone software to send an e-mail notification to the system operator when an error occurs on the Array Station. This will alert you to the fact that the run has been interrupted and give you a chance to determine the proper corrective action.

You can also use an alternative in the e-mail configuration in the form of the Simple Mail Transfer Protocol (SMTP). In setting up SMTP, you will need to know the server address. See Alternative E-Mail Configuration on page 33.

Caliper has set up a Microsoft Hotmail Plus account that will allow the system to send Notification e-mails but not receive outside email. This account has the following parameters.

a. The Mail Service Provider is Hotmail.b. The e-mail address is: [email protected]. The password is 1MyZymark.

To enable E-mail Notification:

1. Open Caliper Sciclone Software.2. Go to Tools menu and select Options (Figure 2.3).3. Select the Notification Tab.

You must also configure the e-mail program on the computer toallow the system to send e-mails.



4. Check the Enable Notification on Alarm box and click on the Configure Notification button.

This User Notification window (Figure 2.4) enables you to select several options when an error is encountered on the system. The system can send an e-mail notification, call a phone number, or run an executable program.

5. Select the mode in which you would like the send your e-mail (Utilize Outlook Email or Utilize SMTP Server.

a. “Utilize Outlook Email” uses the Microsoft Outlook program to send e-mails

b. “Utilize SMTP Server” uses a server to send e-mails. Fill in the Server Address and Sending Email Address fields.

6. To send an e-mail notification, select the Email Values tab and enter the email address in the Addresses box.

Figure 2.3 The Notification tab in the Options window



7. Click OK to save and close box.8. Close the Caliper Sciclone Software window.

Figure 2.4 The e-mail User Notification window



ALTERNATIVE E-MAIL CONFIGURATION

1. Open Sciclone 4.0 software and switch to the Editor view (Figure 2.5).

2. Go to Tools menu and select Options (Figure 2.3).3. Select Notification Tab.4. Enable the Notification Alarm box. This will also enable the

check box underneath. Check both boxes.5. Then click on the Configuration Notification System Settings.6. Select SMTP Server under server type (Figure 2.6).

Figure 2.5 The Editor view window



7. Fill in the Server Address window.8. Fill in the Sending Email Address window.9. Select Email Values tab at the top and fill out the Addresses,

Subject, and Message box (Figure 2.7).10. You may now test the email system by selecting the Test Email

button.

Figure 2.6 The SMTP Server window



Figure 2.7 The Email Values window


Index


Index 39

AActive Locator Plate 15

Affymetrix Technical Support 8Alarm Manager 27

Array Station product software configuration 15

Array Station Subsystems 9

BBio-Rad DNA Engine Thermal Cy-

cler 20

Bulk Reagent Dispensing Head 13

CCaliper Sciclone 10

Caliper Sciclone Gripper 14

Clamp Release 15

Compliance 7

DDispensing Head 13

EE-Mail Notification 30

Email Values 34

Emergency Shutdown 17

GGripper 14

HHigh Volume Head 10

MMaintenance 25

Materials List 22

Mechanical Subsystems 10

Microsoft Hotmail Plus 30

SSafety 5

SMTP Server 33

Subsystems 9

System Description 5

TTechnical Support 8Troubleshooting 27

UUser Manuals 22

WWatlow Temperature Control 21

ZZ8 Pipette Head 12


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