Pump Cleaning Kit For Applied Biosystems 3500 Dx and 3500 Series Genetic Analyzers. Protocol
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1 Pump Cleaning Kit For Applied Biosystems 3500 Dx and 3500 Series Genetic Analyzers Protocol
2 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 Life Technologies Corporation. All rights reserved. Part Number Rev. B 02/2010
3 Contents About This Guide Purpose Safety information Safety alert words SDSs PROTOCOL Pump Cleaning Kit Product information Overview Purpose of the product Kit contents When to use Pump assembly care Avoiding damage to the pump assembly Procedures Safety alert lead-in Cleaning the pump assembly through the check valve fitting (CVF) Cleaning the pump assembly through the array port APPENDIX A Safety Chemical safety General chemical safety SDSs Chemical waste safety Biological hazard safety General safety alerts for all chemicals Index Pump Cleaning Kit Protocol 3
4 Contents 4 Pump Cleaning Kit Protocol
5 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. Pump Cleaning Kit Protocol 5
6 About This Guide Safety 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. 6 Pump Cleaning Kit Protocol
7 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 ( ). 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 ) with your instrument. Purpose of the product The Pump Assembly Cleaning Kit (PN ) 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 Lint-free swabs Syringe assembly, consisting of: Syringe Fitting Tubing Pump Cleaning Kit Protocol 7
8 Pump Cleaning Kit Pump 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. 8 Pump Cleaning Kit Protocol
9 Pump Cleaning Kit Procedures 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 Array port Capillary array Buffer pin Array port plug Check Valve Fitting (CVF) Anode Buffer Container (ABC) Syringe 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. Pump Cleaning Kit Protocol 9
10 Pump Cleaning Kit Procedures 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 ) and Applied Biosystems 3500Dx/3500xL Dx Genetic Analyzer User Guide (PN ). 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. 10 Pump Cleaning Kit Protocol
11 Pump Cleaning Kit Procedures 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 ) and Applied Biosystems 3500Dx/3500xL Dx Genetic Analyzer User Guide (PN ). 3. Install an empty ABC. 4. Fill the 20-mL silicone-free plastic syringe (provided) with deionized water (40 C or colder). Pump Cleaning Kit Protocol 11
12 Pump Cleaning Kit Procedures 5. Install the array port cleaning tool (provided) into the plastic tubing as shown: Array port cleaning tool, PN (provided) Plastic tubing (provided) 20-mL Syringe (provided) 6. Insert the array port cleaning tool into the array port of the pump assembly as shown: Array port Syringe assembly 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. 12 Pump Cleaning Kit Protocol
13 Pump Cleaning Kit Procedures 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. Pump Cleaning Kit Protocol 13
14 Pump Cleaning Kit Procedures 14 Pump Cleaning Kit Protocol
15 APPENDIX A Safety This appendix covers: Chemical safety General chemical safety SDSs Chemical waste safety Biological hazard safety General safety alerts for all chemicals Pump Cleaning Kit Protocol 15
16 Appendix ASafety Chemical 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 lowdensity 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 SDSs About SDSs 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. 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. 16 Pump Cleaning Kit Protocol
17 Appendix ASafety Chemical safety Obtaining SDSs Each time you receive a new SDS packaged with a hazardous chemical, be sure to replace the appropriate SDS in your files. The SDS for any chemical supplied by Applied Biosystems is available to you free 24 hours a day. To obtain SDSs: Chemical waste safety 1. Go to 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 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 lowdensity 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. Pump Cleaning Kit Protocol 17
18 Appendix ASafety General safety alerts for all chemicals Waste disposal Biological hazard safety 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. 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. 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 ; bmbl5toc.htm). Occupational Safety and Health Standards, Bloodborne Pathogens (29 CFR ; 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: General safety alerts for all chemicals Read the SDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves. 18 Pump Cleaning Kit Protocol
19 Index Index B biohazardous waste, handling 18 C caring for the pump assembly 8 CAUTION, description 5 chemical safety 16 chemical waste safety 17 cleaning procedure 9 D DANGER, description 5 E equipment, required 8 G guidelines chemical safety 16 chemical waste disposal 17 chemical waste safety 17 R radioactive waste, handling 18 required equipment 8 materials 8 S safety biological hazards 18 chemical 16 chemical waste 17 guidelines 16, 17, 18 SDSs about 6 description 16 obtaining 17 W WARNING, description 5 waste disposal, guidelines 18 waste profiles, description 18 H hazards. See safety I IMPORTANT, description 5 K kit M contents 7 purpose 7 materials, required 8 P part numbers 7 procedure, pump cleaning 9 product information 7 product, purpose of 7 Pump Cleaning Kit 19
20 Part Number Rev. B 02/2010 Headquarters 850 Lincoln Centre Drive Foster City, CA USA Phone Toll Free International Sales For our office locations please call the division headquarters or refer to our Web site at
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