Affymetrix GeneChip Fluidics Station 450 User manual

P/N 08-0295 Rev. A
June, 2008
Affymetrix®GeneChip®Fluidics Station
450 User’s Guide for AGCC

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
Products may be covered by one or more of the following patents and/or sold under
license from Oxford Gene Technology:
Arrays products may be covered by one or more of the following patents: U.S. Patent
Nos. 5,445,934; 5,744,305; 5,945,334; 6,140,044; 6,261,776; 6,291,183; 6,346,413;
6,399,365; 6,420,169; 6,551,817; 6,610,482; 6,733,977; 6,955,915 and D430,024 and
other U.S. or foreign patents. Products are manufactured and sold under license
from OGT under 5,700,637 and 6,054,270.
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
and other U.S. or foreign patents.
Fluidics Stations 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.
AutoLoaders 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.
Copyright
© 2008 Affymetrix Inc. All rights reserved.
Manufactured by
Affymetrix, Inc.
West Sacramento, CARobin Bjorgan
®

i
Contents
CHAPTER 1 The Fluidics Station 450 3
Introduction 5
Instrument Components 10
Accessory Items 12
How the Fluidics Station Works 13
CHAPTER 2 Using the Fluidics Station 450 15
Introduction 17
Starting the Fluidics Station 17
Handling the Probe Array Cartridge 18
Setting Up an Experiment 19
Defining the Experiment 19
Priming the Fluidics Station 19
Running a Protocol on a Probe Array 21
Customizing the Protocol 32
Shutting Down 33
CHAPTER 3 Instrument Care and Maintenance 35
Introduction 37
Fluidics Station Bleach Protocol 38
Troubleshooting and Assistance 50
When to Contact Technical Support 59
APPENDIX A Customer Module Replacement Procedure 61
Introduction 63
New Module Installation 70

ii GeneChip®Fluidics Station 450 for AGCC User’s Guide
APPENDIX B Using More Than One Fluidics Station 75
Introduction 77
APPENDIX C Specifications 79
Introduction 81
APPENDIX D Warranty 83
Warranty 85
APPENDIX E Parameters and Messages 87
Introduction 89
LCD Messages 90
INDEX 95

Chapter 1The Fluidics Station 450

Chapter 1

5
Introduction
1
This chapter introduces the Affymetrix®GeneChip®Fluidics Station 450 and its
components, gives an overview of how the fluidics station works, and covers the
safe use of the fluidics station.
We have written this user guide to be used in tandem with the Affymetrix®
GeneChip®Command Console™ (AGCC) User’s Guide (P/N 702569).

6GeneChip®Fluidics Station 450 for AGCC User’s Guide
FS450 FEATURES
Table 1.1
FS-450 Features
Feature Description Benefit
3 position sampling
with individual vial
detection
• System will accept 1 to 3 vials.
• System can detect the
presence/absence of vials in the
3 loading positions.
• Flexible loading and operation to
meet script and user
requirements.
Unattended operation
(“Walk away
capability”)
• System will automatically
sample from up to 3 vials based
on defined protocol.
• No interruptions to operator
during the protocol – simply
“load and go.”
• Labor savings.
Modular design • Individual faceplates and blanks
provide the possibility to offer
fluidics stations with two or four
modules.
• Fluidics processing capability
can grow with GeneChip probe
array usage.
• The operator can replace a failed
module.
New probe array
cartridge loading
• Linear (versus angular)
movement of the cartridge to
engage fluidic connections.
• Features on the probe array
housing used to align fluid
needles with cartridge.
• Easier cartridge loading.
• Secure fluidic connection.
• Reduced potential for leaks.
New fluid detection
sensor
• Presence/absence of fluid
detected by measuring
resistance across the needles
that penetrate the GeneChip
cartridge septa.
• Detection path automatically
replaced by loading cartridge.
• Robust performance.
• Elimination of false positive and
false negative missing fluid
errors caused by sample
carryover.
Leak path isolation • All potential leak paths are
funneled into a single channel.
• Critical fluidic components are
protected from potential
damage.
• Should leaks occur, single
channel enables rapid
identification and resolution by
user.
Improved user
diagnostics
• Introduction of new error codes
to software.
• User can quickly identify/ correct
faults on their own to get
running without need for service
call.

chapter 1 | The Fluidics Station 450 7
WARNINGS AND PRECAUTIONS
• The fluidics station 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 adherence to the OSHA Blood Borne Pathogens
Standard (29 CFR 1910.1030) 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 fluidics station.
• 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 fluidics station in ways not specified by Affymetrix. Doing so
may impair the protections provided by the fluidics station.
• The fluidics station 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 FS450 is intended for indoor, laboratory use in a controlled environment.
Do not place hands or fingers inside the cartridge holder. Under
fault conditions, the area behind the cartridge holder can have
temperatures that rise to 100°C or higher.

8GeneChip®Fluidics Station 450 for AGCC User’s Guide
Caution Notices:
REGULATORY
This device complies with Part 15 of the 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 undesirable operation.
Compliant with Directive 2002/96/EC (WEEE).
Compliant with EU Directive 89/336/EEC (EMC)
Compliant with EU Directive 73/23/EEC (LVD)
CAUTION
• You must have read and understood the contents of
this manual before attempting to operate this fluidics
station.
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 général. La prise de courant doit être
située ou installée à proximité du matériel 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.

chapter 1 | The Fluidics Station 450 9
CUSTOMER SUPPORT INFORMATION
Affymetrix, Inc.
3420 Central Expressway
Santa Clara, CA 95051
USA
E-mail: [e-mail]
Tel: [phone] (1-888-DNA-CHIP)
Fax: [phone]
Affymetrix UK Ltd
Voyager, Mercury Park,
Wycombe Lane, Wooburn Green,
High Wycombe HP10 0HH
United Kingdom
E-mail: [e-mail]
Tel: [phone]
Fax: [phone]
Affymetrix Japan, K. K.
Mita NN Bldg
16 Floor, 4-1-23 Shiba,
Minato-ku, Tokyo 108-0014
Japan
Tel: [phone]
Fax: [phone]
www.affymetrix.com

10 GeneChip®Fluidics Station 450 for AGCC User’s Guide
Instrument Components
The GeneChip®Fluidics Station 450 contains four modules. Each module can hold
one GeneChip®probe array cartridge and up to three 1.5 mL vials. The
Affymetrix®GeneChip®Command Console™ (AGCC) software on the computer
workstation, which is connected to the instrument, can control each of the four
modules independently of the others. A single computer workstation can control as
many as eight fluidics stations. You can use any or all of the modules at the same
time. You can also choose a different protocol for each module as long as each uses
the same Wash A and Wash B reagents. The modules are numbered 1 through 4
near the LCD window.
The GeneChip Fluidics Station 450 includes the following components. See Figure
1.1 on page 11.
1. Sample Holders — holds up to three sample vials
2. Module Door — protective cover for the peristaltic pump on the module
3. Cartridge Holder — holds the cartridge during fluidics operation
4. Washblock — part of the cartridge holder that completes the fluid path
when a cartridge is not in place (used for cleaning out or draining the
fluidics station)
5. Cartridge Lever — engages or releases the cartridge holder
6. Needle Lever — inserts the needles into the sample vials
7. LCD Window — displays messages during processes
8. Wash Bottles (2) — hold wash buffers and tubing that draws buffer
through system
9. DI Water Bottle — holds deionized water and tubing that draws water
through system
10. Waste Bottle — collects waste from hybridizations and washes
11. Sample or Vial Needles — extend into the sample vials and draw fluid.

chapter 1 | The Fluidics Station 450 11
Figure 1.1
The GeneChip®Fluidics Station 450 and components
7. LCD Window
1. Sample Holder
10. Waste Bottle
5. Cartridge Lever
9. DI Water
Bottle
3 & 4. Wash block
and Cartridge Holder
8. Wash A
Bottle
8. Wash B
Bottle
6. Needle Lever
2. Module Door 11. Sample Needles (extended)

12 GeneChip®Fluidics Station 450 for AGCC User’s Guide
Accessory Items
Affymetrix provides the following accessories for Fluidics Station 450.
Table 1.2
FS-450 accessories list
Part Number Description Quantity
340011 Assy, Terminator Plug 1
350001 Assy, cable, CPU, DBP9,3/F 1
350014 Cord Power 1
370013 Fuse 4A, 5X20mm, Type F, 250V 2
400110 Tubing, Silicone Peristaltic, 8.5 4
08-0295 Fluidics 450 for AGCC User's Guide 1
400118 Media Bottle, SQ, 500 mL Fluidics DI water/buffer 3
400119 Media Bottle, SQ, 1000 mL Bottle 1
400137 Bottle cap, Pre-drilled 4
410016 Needle, Sample 1
500321 Datum, Chip_49*
*Chip_49 is a blank probe array for testing purposes.
4
08-0093 FS450 Quick Reference Card 1
700357 MSDS Buffer, SSPE 20x 1
08-0099 Module Replacement Quick Reference Card 1
08-0076 Tough-Spot Quick Reference Card 1
610175 CD, Library files, Fluidics Station 450 Scripts 1

chapter 1 | The Fluidics Station 450 13
How the Fluidics Station Works
The Fluidics Station 450 is used to hybridize, wash, and stain the GeneChip®probe
arrays (called arrays in this manual). The FS450 can independently process an
array using a different fluidics protocol in each of four different modules.
The AGCC Fluidics Control software is used to control the FS450 Fluidics Station.
A workstation with AGCC Fluidics Control software and a Sealevel card installed
can control up to eight different fluidics stations.
For further instructions, see Using the Fluidics Station 450 on page 15, and the
GeneChip®Expression Analysis Technical Manual, P/N 702232 (available at
www.affymetrix.com/support), for instructions on using the fluidics station with
individual protocols.
SAMPLE STAINING PROTOCOL
1. Use the Affymetrix®GeneChip®Command Console™ (AGCC) software
to define an experiment and start the fluidics station protocol. You can find
information regarding this software in the AGCC User’s Guide (P/N
702569).
2. After the hybridization of the labeled target to the probe array, place the
probe array cartridge into the cartridge holder on the selected module of
the fluidics station. Gently flip the cartridge lever to close the washblock
and engage the probe array.
3. Depending on the fluidics protocol for the array, place vials containing the
proper reagent in individual vials in the vial holders as indicated on the
fluidics station LCD. Please note that the indicated position may be
You must have the required fluidics protocols installed before using
the FS450. See the AGCC User Guide for more information (P/N
702569).
Before you use the fluidics station, check the fluidics station
configuration and prime the fluidics station with appropriate buffer.
See the AGCC User Guide for more information (P/N 702569).

14 GeneChip®Fluidics Station 450 for AGCC User’s Guide
different depending on the particular assay protocol used. Refer to the
GeneChip®Expression Analysis Technical Manual, P/N 700365, or the
applicable genotyping manual for details.
4. The fluidics station will perform the following actions to stain the bound
target on the cartridge and prepare it for scanning. The fluidics station will:
• wash the cartridge with wash solution (or solutions) at a selected
temperature;
• draw staining solution from the vial into the cartridge and mix it
by alternately draining and filling the cartridge at a selected
temperature;
• expel the staining solution to the waste line;
• fill the cartridge with wash solution for scanning;
• clean the module tubing and needles for the next cartridge to be
processed.
5. After washing and staining, the Affymetrix®GeneChip®Scanner 3000
scans the cartridge by laser light to obtain fluorescence intensity data.
For more information about how the scanner works, refer to the appropriate
scanner manual.
In addition to the preceding protocol, the fluidics station can perform
variations of the steps described in the protocol and can run other
protocols. For more information about the protocols that can be
performed on the fluidics station, please contact your Affymetrix®
Technical Support representative.

Chapter 2Using the Fluidics Station 450

Chapter 2

17
Introduction
This section describes how to use the Affymetrix®GeneChip®Fluidics Station 450
with fluidics protocols. For details using the Fluidic Station with the AGCC
software, refer to the AGCC User’s Guide (P/N 702569).
Starting the Fluidics Station
1. Check to ensure that the fluidics station is connected to the power main
through the power cord provided.
2. Check to ensure that the fluidics station is connected to the workstation.
CommLink connections are located on the back of the fluidics station
(Figure 2.1).
3. Flip the ON/OFF switch for the fluidics station to the ON position. The
switch is located on the left side of the fluidics station (Figure 2.1).
The LCD window should display the following:
4. Turn on the computer workstation and launch the AGCC software.
Power-On Done
NOT PRIMED 25°C

18 GeneChip®Fluidics Station 450 for AGCC User’s Guide
Handling the Probe Array Cartridge
The GeneChip®probe array comes mounted in a plastic package to form a cartridge
(Figure 2.2). The probe array chip contains a collection of oligonucleotide probes
that have been arrayed on the inner glass surface. A chamber in the plastic package
directly under the chip acts as a reservoir where hybridization, washing and
staining occur.
Although the inner glass surface is protected, any contamination or scratches on the
outer surface of the glass can compromise the integrity of the scan. Avoid touching
the surface of the chip with your fingers. Skin oils and other substances, such as
lotions or ink, can fluoresce. If the surface of the probe array chip is noticeably
dirty, you should carefully clean the chip with a nonabrasive laboratory tissue.
Figure 2.1
Location of the serial ports and ON/OFF switch
Power Cable
CommLink In
Connector
CommLink Out
Connector
(to terminator or
cable to next
fluidics station)
Lid Release
Buttons
(Note: these
buttons may
be present or
absent
depending on
the model of
the fluidics
station.)
ON/OFF
Switch
(Power Main)