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Pump Cleaning KitFor Applied Biosystems 3500 Dx and 3500 Series Genetic Analyzers

Protocol

For research use only. Not intended for any animal or human therapeutic or diagnostic use, unless otherwise indicated.

Information in this document is subject to change without notice.

APPLIED BIOSYSTEMS DISCLAIMS ALL WARRANTIES WITH RESPECT TO THIS DOCUMENT, EXPRESSED OR IMPLIED, INCLUDING BUT NOT LIMITED TO THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. TO THE FULLEST EXTENT ALLOWED BY LAW, IN NO EVENT SHALL APPLIED BIOSYSTEMS BE LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY, OR UNDER ANY STATUTE OR ON ANY OTHER BASIS FOR SPECIAL, INCIDENTAL, INDIRECT, PUNITIVE, MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING BUT NOT LIMITED TO THE USE THEREOF, WHETHER OR NOT FORESEEABLE AND WHETHER OR NOT APPLIED BIOSYSTEMS IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

TRADEMARKS

The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners.

© 2010 Life Technologies Corporation. All rights reserved.

Part Number 4414004 Rev. B02/2010

Contents

3Pump Cleaning Kit Protocol

About This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Safety information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5Safety alert words . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5SDSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

PROTOCOL Pump Cleaning Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

Product information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Purpose of the product . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7Kit contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7When to use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Pump assembly care . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8Avoiding damage to the pump assembly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Safety alert lead-in . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Cleaning the pump assembly through the check valve fitting (CVF) . . . . . . . . . . . . . . . . 9Cleaning the pump assembly through the array port . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

APPENDIX A Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16General chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16SDSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16Chemical waste safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Biological hazard safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

General safety alerts for all chemicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

4 Pump Cleaning Kit Protocol

Contents


About This Guide

Purpose

The Pump Cleaning Kit for Applied Biosystems 3500 Dx and 3500 Series Genetic Analyzers protocol provides reference information for the Pump Cleaning Kit and describes how to prepare, maintain, and troubleshoot the system.

Safety information

Note: For general safety information, see this section and Appendix A, “Safety” on page 15. When a hazard symbol and hazard type appear by a chemical name or instrument hazard, see the “Safety” Appendix for the complete alert on the chemical or instrument.

Safety alert words

Four safety alert words appear in Applied Biosystems user documentation at points in the document where you need to be aware of relevant hazards. Each alert word—IMPORTANT, CAUTION, WARNING, DANGER—implies a particular level of observation or action, as defined below:

IMPORTANT! – Indicates information that is necessary for proper instrument operation, accurate chemistry kit use, or safe use of a chemical.

CAUTION! – Indicates a potentially hazardous situation that, if not avoided, may result in minor or moderate injury. It may also be used to alert against unsafe practices.

WARNING! – Indicates a potentially hazardous situation that, if not avoided, could result in death or serious injury.

DANGER! – Indicates an imminently hazardous situation that, if not avoided, will result in death or serious injury. This signal word is to be limited to the most extreme situations.


About This GuideSafety information

SDSs

The Safety Data Sheets (SDSs) for any chemicals supplied by Applied Biosystems or Ambion are available to you free 24 hours a day. For instructions on obtaining SDSs, see “SDSs” on page 16.

IMPORTANT! For the SDSs of chemicals not distributed by Applied Biosystems or Ambion contact the chemical manufacturer.


PROTOCOL

Pump Cleaning Kit

Product information

Overview

Cleaning the Applied Biosystems 3500 Dx and 3500 Series Genetic Analyzer pump assemblies will ensure efficient mechanical operation of the pump system. To perform this cleaning, the following parts are required. The parts are provided in a complimentary Pump Cleaning Kit (4414007).

• Array port cleaning tool• 20 mL Leur-Lok™ plastic syringe• Barbed fitting, Leur-Lok to 3/16-inch barb• Platinum-cured silicon tubing, 3/16-inch ID × 3/8 OD• Lint-free foam swabs

Applied Biosystems provides a complimentary pump assembly cleaning kit (PN 4414007) with your instrument.

Purpose of the product

The Pump Assembly Cleaning Kit (PN 4414007) allows you to clean the Applied Biosystems 3500 Dx and 3500 Series Genetic Analyzer pump assembly and Check Valve Fitting (CVF) assembly. The pump assembly consists of a pump unit and a lower block.

Kit contents

The kit contains:

Item Part Number

Array port cleaning tool 4445057

Lint-free swabs 201587

Syringe assembly, consisting of: 4415483

Syringe 4427171

Fitting 4415488

Tubing 4428056


Pump Cleaning KitPump assembly care

When to use

In nearly all circumstances, the Water Wash Wizard is very effective in cleaning the pump assembly. Occasionally, a situation in which the Water Wash Wizard is not sufficiently effective may arise. In the following situations, use this kit to thoroughly clean the pump assembly:

• Polymer has dried in the channels of the lower block due to maintenance oversight.Mechanical malfunctions may cause dried polymer to appear in the pump assembly. Washing with either the Water Wash Wizard or this kit may not remove dried polymer – replacing the lower block may be necessary.

• Some contaminant in the pump assembly is suspected of causing problems. The CVF might be clogged or contaminated.

Note: Problems such as electrical arcing require parts to be replaced by a service engineer. Please contact your service engineer or Life Technologies.

Pump assembly care

Avoiding damage to the pump assembly

The pump assembly can be irreversibly damaged if:

• Polymer dries in the polymer channels of the pump assembly.• The inside surface of the channel is scratched.• The pump assembly is exposed to organic solvent.• The pump assembly is exposed to temperatures greater than 40 °C.• There is arcing in the pump assembly.

IMPORTANT! To minimize background fluorescence, use clean, powder-free, silicone-free latex gloves whenever you handle the pump assembly or any item in the polymer path.


Pump Cleaning KitProcedures

Procedures

Safety alert lead-in

For the following hazards, see the complete safety alert descriptions in “General safety alerts for all chemicals” on page 18:

WARNING! CHEMICAL HAZARD. Anode Buffer Container, POP-4™, POP-6™, POP-7™ polymers, and 1✕ GA Buffer/EDTA.

Cleaning the pump assembly through the check valve fitting (CVF)

Figure 1 Setup for cleaning the pump assembly

Clean the pump assembly:

• Through the CVF.• Through the pump chamber.• Past the array port.• Through the pump upper channel.• Through the lower block.• Past the buffer pin.• Into the ABC.

Syringe

Check Valve Fitting (CVF)

Array port plug

Anode Buffer Container

(ABC)

Buffer pin

Array port

Capillary array



To clean the pump assembly:

1. Power off the instrument by unplugging the power cord.

2. Remove the capillary array. For array removal instructions, see the Applied Biosystems 3500/3500xL Genetic Analyzer User Guide (PN 4401661) and Applied Biosystems 3500Dx/3500xL Dx Genetic Analyzer User Guide (PN 4401688).

3. Install the array port plug (where the array was installed) into the array port of the pump assembly and turn the array port lever clockwise (¼ turn) to lock the plug into place.

4. Install an empty Anode Buffer Container (ABC).

IMPORTANT! Do not use deionized water warmer than 40 °C to rinse the pump assembly. Water above 40 °C will damage internal components of the pump.

IMPORTANT! Do not disassemble the pump assembly.

5. Remove the polymer pouch.

6. Fill the 20-mL silicone-free plastic syringe (provided) with deionized water (40 °C or colder).

7. Fit the plastic tubing onto the CVF.

8. Dispense several syringe volumes of deionized water (40 °C or colder) through the pump channel.

9. Inspect the channels for dried polymer, which appears as white residue. Wash partially obstructed channels with water (40 °C or colder) until the dried polymer is removed.Verify that all polymer is removed before proceeding.

IMPORTANT! Some time may be required for the deionized water to clear the obstruction. Do not use any pointed or sharp objects to clear the channel, even if the channel is completely obstructed with dried polymer.

10. Remove the syringe assembly from the CVF.

11. Use deionized (40 °C or colder) water and the supplied lint-free swabs to clean out any dried residue around the buffer pin and array port.

12. Wipe the CVF and exterior surfaces of the pump assembly with lint-free lab wipes.

IMPORTANT! Do not use compressed gas to blow water from the channels, valve, or any part of the pump assembly.

13. Reinstall the polymer pouch or, if the instrument is not to be used immediately, leave the conditioning pouch on to prevent the CVF from drying out.



When reinstalling the polymer pouch, run the Bubble Remove Wizard before proceeding:

a. From the Maintenance Wizards screen, click Remove Bubbles.

Note: The Bubble Remove Wizard takes 5 to 15 minutes to complete.

b. Follow the prompts in the Bubble Remove Wizard window.

c. Check the Quick View section of the Dashboard for the updated status of the polymer pouch after removing bubbles from the polymer pump fluid path.

14. Rinse and dry the syringe assembly.

Cleaning the pump assembly through the array port

Clean the pumps upper channel from the array port to the ABC.

IMPORTANT! Do not use deionized water warmer than 40 °C to rinse the pump assembly. Water above 40 °C damages the internal components of the pump.

IMPORTANT! Do not disassemble the pump assembly.

To clean the pump assembly through the array port:

1. Power off the instrument by unplugging the power cord.

2. Remove the capillary array. For array removal instructions, see the Applied Biosystems 3500/3500xL Genetic Analyzer User Guide (PN 4401661) and Applied Biosystems 3500Dx/3500xL Dx Genetic Analyzer User Guide (PN 4401688).

3. Install an empty ABC.

4. Fill the 20-mL silicone-free plastic syringe (provided) with deionized water (40 °C or colder).



5. Install the array port cleaning tool (provided) into the plastic tubing as shown:

6. Insert the array port cleaning tool into the array port of the pump assembly as shown:

7. Tighten the array port ¼ turn.

8. Dispense several syringe volumes of deionized water (40 °C or colder) through the pump channel.

9. Inspect the channels for dried polymer, which appears as white residue, and/or bubbles, which may be stuck to the wall of the channels. Partially wash obstructed channels with water (40 °C or colder) until dried polymer and/or bubbles are removed.

10. Remove the syringe assembly from the array port.

Array port cleaning tool, PN 4445057(provided)

Plastic tubing(provided)

20-mL Syringe(provided)

Array port

Syringe assembly



11. Immediately reinstall the array:

a. From the Maintenance Wizards screen, click Install Capillary Array.

Note: The Install Capillary Array Wizard takes 15 to 45 minutes to complete.

b. Follow the prompts in the Install Capillary Array Wizard window.

c. Check the Quick View section of the Dashboard for the updated status of the capillary array.

12. Empty the ABC.

13. Use deionized water (40 °C or colder) and the supplied lint-free swabs to clean out any dried residue around the buffer pin and array port.

14. Install the conditioning pouch.

15. Proceed with the Water Wash Wizard.

16. Rinse and dry the syringe assembly. If the instrument is not to be used immediately, leave the conditioning pouch on to prevent the CVF from drying out.


APPENDIX A

Safety

This appendix covers:

Chemical safety. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16General chemical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16SDSs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16Chemical waste safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17Biological hazard safety. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

General safety alerts for all chemicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18


Appendix ASafetyChemical safety

Chemical safety

General chemical safety

Chemical hazard warning

WARNING! CHEMICAL HAZARD. Before handling any chemicals, refer to the Safety Data Sheet (SDS) provided by the manufacturer, and observe all relevant precautions.

WARNING! CHEMICAL HAZARD. All chemicals in the instrument, including liquid in the lines, are potentially hazardous. Always determine what chemicals have been used in the instrument before changing reagents or instrument components. Wear appropriate eyewear, protective clothing, and gloves when working on the instrument.

WARNING! CHEMICAL HAZARD. Four-liter reagent and waste bottles can crack and leak. Each 4-liter bottle should be secured in a low-density polyethylene safety container with the cover fastened and the handles locked in the upright position. Wear appropriate eyewear, clothing, and gloves when handling reagent and waste bottles.

WARNING! CHEMICAL STORAGE HAZARD. Never collect or store waste in a glass container because of the risk of breaking or shattering. Reagent and waste bottles can crack and leak. Each waste bottle should be secured in a low-density polyethylene safety container with the cover fastened and the handles locked in the upright position. Wear appropriate eyewear, clothing, and gloves when handling reagent and waste bottles.

Chemical safety guidelines

To minimize the hazards of chemicals:

• Read and understand the Safety Data Sheets (SDSs) provided by the chemical manufacturer before you store, handle, or work with any chemicals or hazardous materials. (See “About SDSs” on page 16.)

• Minimize contact with chemicals. Wear appropriate personal protective equipment when handling chemicals (for example, safety glasses, gloves, or protective clothing). For additional safety guidelines, consult the SDS.

• Minimize the inhalation of chemicals. Do not leave chemical containers open. Use only with adequate ventilation (for example, fume hood). For additional safety guidelines, consult the SDS.

• Check regularly for chemical leaks or spills. If a leak or spill occurs, follow the manufacturer’s cleanup procedures as recommended in the SDS.

• Comply with all local, state/provincial, or national laws and regulations related to chemical storage, handling, and disposal.

SDSs

About SDSs Chemical manufacturers supply current Safety Data Sheets (SDSs) with shipments of hazardous chemicals to new customers. They also provide SDSs with the first shipment of a hazardous chemical to a customer after an SDS has been updated. SDSs provide the safety information you need to store, handle, transport, and dispose of the chemicals safely.


Appendix ASafetyChemical safety

Each time you receive a new SDS packaged with a hazardous chemical, be sure to replace the appropriate SDS in your files.

Obtaining SDSs

The SDS for any chemical supplied by Applied Biosystems is available to you free 24 hours a day. To obtain SDSs:

1. Go to www.appliedbiosystems.com, click Support, then select SDS.

2. In the Keyword Search field, enter the chemical name, product name, SDS part number, or other information that appears in the SDS of interest. Select the language of your choice, then click Search.

3. Find the document of interest, right-click the document title, then select any of the following:

• Open – To view the document• Print Target – To print the document• Save Target As – To download a PDF version of the document to a

destination that you choose

Note: For the SDSs of chemicals not distributed by Applied Biosystems, contact the chemical manufacturer.

Chemical waste safety

Chemical waste hazards

CAUTION! HAZARDOUS WASTE. Refer to Material Safety Data Sheets and local regulations for handling and disposal.

WARNING! CHEMICAL WASTE HAZARD. Wastes produced by Applied Biosystems instruments are potentially hazardous and can cause injury, illness, or death.

WARNING! CHEMICAL STORAGE HAZARD. Never collect or store waste in a glass container because of the risk of breaking or shattering. Reagent and waste bottles can crack and leak. Each waste bottle should be secured in a low-density polyethylene safety container with the cover fastened and the handles locked in the upright position. Wear appropriate eyewear, clothing, and gloves when handling reagent and waste bottles.

Chemical waste safety guidelines

To minimize the hazards of chemical waste:

• Read and understand the Safety Data Sheets (SDSs) provided by the manufacturers of the chemicals in the waste container before you store, handle, or dispose of chemical waste.

• Provide primary and secondary waste containers. (A primary waste container holds the immediate waste. A secondary container contains spills or leaks from the primary container. Both containers must be compatible with the waste material and meet federal, state, and local requirements for container storage.)

• Minimize contact with chemicals. Wear appropriate personal protective equipment when handling chemicals (for example, safety glasses, gloves, or protective clothing). For additional safety guidelines, consult the SDS.

http://www.appliedbiosystems.com


Appendix ASafetyGeneral safety alerts for all chemicals

• Minimize the inhalation of chemicals. Do not leave chemical containers open. Use only with adequate ventilation (for example, fume hood). For additional safety guidelines, consult the SDS.

• Handle chemical wastes in a fume hood.• After emptying a waste container, seal it with the cap provided.• Dispose of the contents of the waste tray and waste bottle in accordance with

good laboratory practices and local, state/provincial, or national environmental and health regulations.

Waste disposal If potentially hazardous waste is generated when you operate the instrument, you must:

• Characterize (by analysis if necessary) the waste generated by the particular applications, reagents, and substrates used in your laboratory.

• Ensure the health and safety of all personnel in your laboratory.• Ensure that the instrument waste is stored, transferred, transported, and disposed

of according to all local, state/provincial, and/or national regulations.

IMPORTANT! Radioactive or biohazardous materials may require special handling, and disposal limitations may apply.

Biological hazard safety

General biohazard WARNING! BIOHAZARD. Biological samples such as tissues, body fluids, infectious agents, and blood of humans and other animals have the potential to transmit infectious diseases. Follow all applicable local, state/provincial, and/or national regulations. Wear appropriate protective equipment, which includes but is not limited to: protective eyewear, face shield, clothing/lab coat, and gloves. All work should be conducted in properly equipped facilities using the appropriate safety equipment (for example, physical containment devices). Individuals should be trained according to applicable regulatory and company/institution requirements before working with potentially infectious materials. Read and follow the applicable guidelines and/or regulatory requirements in the following: • U.S. Department of Health and Human Services guidelines published in

Biosafety in Microbiological and Biomedical Laboratories (stock no. 017-040-00547-4; bmbl5toc.htm).

•Occupational Safety and Health Standards, Bloodborne Pathogens (29 CFR§1910.1030; www.access.gpo.gov/ nara/cfr/waisidx_01/29cfr1910a_01.html).

•Your company’s/institution’s Biosafety Program protocols for working with/handling potentially infectious materials.

Additional information about biohazard guidelines is available at:www.cdc.gov

General safety alerts for all chemicals

Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.

http://www.cdc.gov/od/ohs/biosfty/bmbl5/bmbl5toc.htm

http://www.access.gpo.gov/nara/cfr/waisidx_01/29cfr1910a_01.html




http://www.cdc.gov

Index

19Pump Cleaning Kit

Index

Bbiohazardous waste, handling 18

Ccaring for the pump assembly 8CAUTION, description 5chemical safety 16chemical waste safety 17cleaning procedure 9

DDANGER, description 5

Eequipment, required 8

Gguidelines

chemical safety 16chemical waste disposal 17chemical waste safety 17

Hhazards. See safety

IIMPORTANT, description 5

Kkit

contents 7purpose 7

Mmaterials, required 8

Ppart numbers 7procedure, pump cleaning 9product information 7product, purpose of 7

Rradioactive waste, handling 18required

equipment 8materials 8

Ssafety

biological hazards 18chemical 16chemical waste 17guidelines 16, 17, 18

SDSsabout 6description 16obtaining 17

WWARNING, description 5waste disposal, guidelines 18waste profiles, description 18

Part Number 4414004 Rev. B 02/2010

International SalesFor our office locations please call the division headquarters or refer to our Web site atwww.appliedbiosystems.com/about/offices.cfm

Headquarters850 Lincoln Centre Drive | Foster City, CA 94404 USAPhone 650.638.5800 | Toll Free 800.345.5224www.appliedbiosystems.com

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