Thermo Fisher Scientific Array Station User guide

P/N 701859 Rev. 4

June 2006

Affymetrix

GeneChip

®

Array Station

User’s Guide

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

ii

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™, 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 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.

Copyright

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I

Contents

CHAPTER 1 Array Station System Description 3

INTRODUCTION 5

SYSTEM DESCRIPTION 5

Intended Use 5

SAFETY 5

REGULATORY COMPLIANCE 7

TECHNICAL SUPPORT CONTACT INFORMATION 8

ARRAY STATION SUBSYSTEMS 9

Mechanical Subsystems 10

Recovery from an Emergency Shutdown 17

Caliper Twister II Robotic Arm and Storage Rack 18

The Bio-Rad DNA Engine Thermal Cycler 20

The Watlow Temperature Control 21

USER DOCUMENTATION 22

CHAPTER 2 Maintenance and Troubleshooting 23

PREVENTATIVE MAINTENANCE 25

Daily 25

Weekly 25

Monthly 25

Quarterly 26

ARRAY STATION TROUBLESHOOTING 27

E-MAIL NOTIFICATION 30

Alternative E-Mail Configuration 33

INDEX 37

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II

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Chapter 1Array Station System Description

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Chapter 1

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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

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6GeneChip® 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 should

not be modified.

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chapter 1 | Regulatory Compliance 7

Regulatory Compliance

We, 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)

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8GeneChip® Array Station User’s Guide

Technical Support Contact Information

Affymetrix provides technical support to all licensed users via phone or E-mail. To

contact Affymetrix Technical Support:

Affymetrix, Inc.

3420 Central Expressway

Santa Clara, CA 95051 USA

Tel: 1-888-362-2447 (1-888-DNA-CHIP)

Fax: 1-408-731-5441

support@affymetrix.com

Affymetrix UK Ltd.,

Voyager, Mercury Park,

Wycombe Lane, Wooburn Green,

High Wycombe HP10 0HH

United Kingdom

UK and Others Tel: +44 (0) 1628 552550

France Tel: 0800919505

Germany Tel: 01803001334

Fax: +44 (0) 1628 552585

[email protected]

Affymetrix Japan, K. K.

Mita NN Bldg

16 Floor, 4-1-23 Shiba,

Minato-ku, Tokyo 108-0014

Japan

Tel: (03) 5730-8200

Fax: (03) 5730-8201

www.affymetrix.com

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chapter 1 | Array Station Subsystems 9

Array Station Subsystems

The 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 1.1

The GeneChip® Array Station

DI Water

Caliper®

Sciclone

Workstation

Caliper® Sciclone Head

Twister® II

Plate Stacker

Waste

Liquid

Computer

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

®

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10 GeneChip® Array Station User’s Guide

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

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chapter 1 | Array Station Subsystems 11

Figure 1.3

Array Station High Volume Head

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12 GeneChip® Array Station User’s Guide

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 1.4

The Z8 Pipette Head

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chapter 1 | Array Station Subsystems 13

3. Bulk Reagent Dispensing Head - capable of bulk dispensing

reagents into plates on the system (Figure 1.5).

Figure 1.5

The Bulk Reagent Dispensing Head

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14 GeneChip® Array Station User’s Guide

4. Caliper Sciclone Gripper - capable of moving plates within the

deck of the Caliper Sciclone and lidding/delidding plates (Figure

1.6).

Figure 1.6

The Caliper Sciclone Gripper

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chapter 1 | Array Station Subsystems 15

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

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16 GeneChip® Array Station User’s Guide

The Caliper Sciclone robotic workstation and the Twister II robotic arm

are equipped with safety interlocked doors and an emergency STOP

switch located on the front and rear of the Caliper Sciclone. The

interlocked doors must be closed to operate the Caliper Sciclone and

the Twister II robotic arm. If you open the doors to either the Caliper

Sciclone or the Twister II robot, the corresponding robot will stop

immediately and display an error message at the console. Once you

close the doors, you will then have the option to “retry method step,”

“skip method step,” or “stop execution” from the console to recover

from the error. If you “pause” the Caliper Sciclone or Twister II robot,

or if the Array Station pauses between method steps, you can open and

close the doors safely without generating an error. However, if the door

is open when you, or the software, command the robot to resume, the

system will generate an error and the Caliper Sciclone or Twister II

robot 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 the

Twister II shields while the system is in operation. Twister II robot

stackers must also be in place for operation.

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chapter 1 | Array Station Subsystems 17

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 TO

IMMEDIATELY SHUT DOWN THE SYSTEM. This removes all power

to the Caliper Sciclone Robot and the Twister II Robot.

Please note that the entire run will be lost if the emergency stop

button is depressed.

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18 GeneChip® Array Station User’s Guide

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

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Thermo Fisher Scientific Array Station User guide

Thermo Fisher Scientific Array Station User guide

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