[PDF] DYEnamic ET Terminator用Instructions

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1 for Model 373 DNA Sequencer ABI PRISM 377 DNA Sequencer ABI PRISM 310 Genetic Analyzer ABI PRISM 3100 Genetic Analyzer ABI PRISM 3700 DNA Analyzer DYEnamic ET Terminator Cycle Sequencing Kit Model 373 / ABI PRISM 377 DNA Sequencer, ABI PRISM 310 / 3100 Genetic Analyzer, ABI PRISM 3700 DNA AnalyzerApplied Biosystems

2 2DYEnamic ET Terminator Cycle Sequencing Kit Mobility filematrix file 1Model 373 DNA Sequencer / ABI PRISM 377 DNA Sequencer...1 2ABI PRISM 310 Genetic Analyzer...7 3ABI PRISM 3100 Genetic Analyzer ABI PRISM 3700 DNA Analyzer...17 DYEnamic ET Terminator Cycle Sequencing Kit DYEnamic ET Terminator

3 DYEnamic ET Terminator Cycle Sequencing Kit ABI Model 373 / ABI PRISM 377 ABI Model 373 / ABI PRISM 377 Mobility filematrix file ABI Mobility file Matrix file Mobility filematrix file () Matrix file DataUtilityMatrix file 1

4 ABI for 377_373.sit 1 DYEnamic ET Terminator Matrix StandardUS80860) Red loading dyeus ul DYEnamic ET Terminator Cycle Sequencing KitFormamide loading dye Mobility filematrix file 3 StuffIt Expander for377_373.sit for377_373.sitstuffit Expander 3 3for377_373 DYEnamic ET Term.{US80872} Mobility file 4 DYEnamic ET Terminator Matrix file 5 Read Me 4 Mobility fileet Terminator dye 5 Matrix file DNA 6 ABIMacintoshSystem DYEnamic ET Term.{US80872}DYEnamic ET Terminator ABIMacintoshSystem 6 2

5 ABI 377 ABI DyeSet/PrimerDYEnamic ET Term.(US80872) Instrument FilenoneABI 377 ET Term matrix T, A, C, G Matrix file DYEnamic ET Terminator ABI ABI 377ABI 373 Run ModuleAE Sample Sheet1ET Term matrix ABI 377Instrument Filenone ABI 373Instrument FileDYEnamic ET Terminators Auto Analyzeoff 48 cm A 1,200 Formamide loading dyematrix Standards 4Matrix Standards 3. 4ACGTFormamide loading dye 4 µl 2434 µl 3623 µl 482 µl 3

6 ABI Matrix file Matrix file ABI Raw Data 1RunMatrix Standards4 2Raw Data 1 DataUtility MacintoshFile DataUtility 2.Matrix file 1Sequense AnalysisDataUtility 1 2UtilityMake Matrix 2 Matrix Standards HD377Run Matrix StandardsRun 3 T7 Terminator Matrix file 3Make MatrixCAGT 4 23 CT AA GC T G 4Make Matrix T7 Terminator Matrix 4 Comment 5Update File 4 6SystemABI DYEnamic ET Terminators 7OK OK 8YES Make Matrix successfully completed 5 Matrix Standards 9OK Matrix file 57 6 Raw Data Start atpoints Matrix Standards DataUtility Raw Data No 7 Matrix file 4

7 Matrix Standards DYEnamic ET Terminator Cycle Sequencing Kit Matrix file DyeSet/Primer filedyenamic ET Term. (US80872) Matrix filedyenamic ET Terminators ABI Matrix Standards AE Run ModuleSeq Run - Seq Run - Instrument FileDYEnamic ET Terminators AE Auto Analyze DyeSet/Primer filedyenamic ET Term. (US80872) Matrix filedyenamic ET Terminators 5

8 ABI Matrix file 1. Matrix Standard Matrix Standards Matrix file 2. Raw DataRaw Data , UtilityMake Matrix 6. Make MatrixStart at Matrix Standards 4 Matrix file 1. Matrix file 2. Dye Terminator Matrix Taq Terminator Matrix 1.T7 Terminator MatrixMatrix file T7 Terminator Matrix Matrix file DYEnamic ET Terminators BigDye Matrix file 1. Matrix filedyenamic ET Terminators Matrix filebigdye Matrix file Matrix Standards Matrix file AE 6

9 DYEnamic ET Terminator Cycle Sequencing Kit ABI PRISM 310 ABI PRISM 310 Mobility filematrix file Moblity filematrix filemacintosh4 Matrix file ABI 310 Mobility filematrix file Mobility filematrix file POP4 () Matrix file DataUtilityMatrix file 7

10 for310.sit 1 DYEnamic ET Terminator Matrix StandardUS80860) 1 Matrix StandardsTSRApplied Biosystems ABI 310 Mobility filematrix file 2 StuffIt Expander for310.sit for310.sitstuffit Expander 2 for3103 DYEnamic ET Term.POP6 Mobility file 3 DYEnamic ET Terminators Matrix file 4 Read Me 3 Mobility fileet Terminator dye 4 Matrix file DNA 5 ABIMacintoshSystem DYEnamic ET Term.POP6DYEnamic ET Terminators ABIMacintoshSystem 5 8

11 1. DyeSet/PrimerDYEnamic ET Term.POP6 Matrixnone ET Term matrix T, A, C, G Matrix file DYEnamic ET Terminator ABI Sample Sheet1ET Term matrix Module Auto Analyzeoff POP6 A POP4 ABI 310TSR TSRMatrix Standards 4Matrix Standards 3. TSR30 µl 9

12 Matrix file Matrix file 1.Raw Data 1RunMatrix Standards4 2Raw Data ABI DataUtility MacintoshFile DataUtility 2 Matrix Standards HD377Run Matrix StandardsRun 3 Matrix file 2.Matrix file 1Sequense AnalysisDataUtility 1 2UtilityMake Matrix 3Make MatrixCAGT RunMatrix Standards 23 CT AA GC T G 4Make Matrix T7 Terminator Matrix 4 Matrix Standards 5Update File 4 6SystemABI DYEnamic ET Terminators 7OK OK 8YES Make Matrix successfully completed 5 Raw Data Start atpoints Matrix Standards DataUtility Raw Data 9OK Matrix file 56 6 Matrix file No 10

13 DYEnamic ET Terminator Cycle Sequencing Kit Matrix Standards AE ABI 310 DyeSet/Primer filedyenamic ET Term.POP6 Matrix filedyenamic ET Terminators ModuleSeq POP6ASeq POP6E AE Auto Analyze ABI 310 BasecallerABI-CE1 DyeSet/Primer filedyenamic ET Term.POP6 Matrix filedyenamic ET Terminators 11

14 Matrix file Matrix Standards Matrix file 1. Matrix Standard 2. Raw DataRaw Data ABI , UtilityMake Matrix 6. Make MatrixStart at Matrix Standards 4Matrix Standards Matrix file 1. Matrix file 2. A StandardC StandardG Standard T Standard4 Dye Terminator Matrix Taq Terminator Matrix 1.T7 Terminator MatrixMatrix file T7 Terminator Matrix Matrix file DYEnamic ET Terminators BigDye Matrix file 1. Matrix filedyenamic ET Terminators Matrix filebigdyematrix file 12

15 DYEnamic ET Terminator Cycle Sequencing Kit ABI PRISM 3100 ABI PRISM 3100Mobility file Spectral Calibration Mobility file Mobility file Spectral Calibration Matrix Standards ABI 3100 Spectral Calibration Override matrix 13

16 POP650 cmdt3100pop6et50cm.zip 1 POP636 cmdt3100pop6et36cm.zip 1 DYEnamic ET Terminator Matrix Standard for ABI 3100 / 3700US84001 Hi Di FormamideApplied Biosystems POP5Mobility File Mobility file 2 WindowsWinZip zip WinZip Wizard 2 ABI Mobility fileet Terminator dye 4 Mobility file Mobility DT3100POP6{ET}50cm.mobDT3100POP6{ET}36cm.mob 3 DT3100POP6{ET}50cm.mobDT3100POP6{ET}36cm.mob Mobility file 4 D: Perkin-Elmer Abi Shared Analysis Bacecaller Mobility D: Appliedbiosystems Shared Analysis Bacecaller Mobility 14

17 Spectral Calibration Hi Di Formamide Matrix Standards 1.Matrix Standards 15 µlmatrix StandardsHi Di Formamide195 µl 296A1H1A2H21610 µl A X B X C X D X E X F X G X H X X X X X X X X X ABI Data Collection Matrix standards 3100 Data Collection 1Plate ViewNew Plate Editor 2Plate Name 3ApplicationSpectral Calibration 4Plate Type96-Well 5Finish Plate Editor 6A1H216Sample Name 7Dye SetF 8Spectral Calibration Run Module 36 cmspect36_pop6defaultmodule 50 cmspect50_pop6defaultmodule 9Spectral Calibration ParametersSeqStd{AnyDyeSet}.par 10OK Plate SetupPending Plate Records Spectral Calibration Result ABI CalibrationOK 15

18 4.Spectral Calibration Spectral Profile 1FileOverride Spectral Calibration Select the dye set to display 2FOK Spectral Calibration Profile for F ABI Spectral Calibration ProfileSpectral Profile 4 5.Override matrix 5.Override matrix 1ProfileOverride matrix from another source From Capillary 2ProfileOverride cap 6.Spectral Calibration Data Spectral Calibration DataSpectral Calibration Data D: Perkin-Elmer Abi 3100 DataCollection SpectralCalLogs D: Appliedbiosystems 3100 DataCollection SpectralCalLogs 16

19 DYEnamic ET Terminator Cycle Sequencing Kit ABI PRISM 3700 ABI PRISM 3700Mobility file Spectral Calibration Mobility file Mobility file Spectral Calibration Matrix Standards Spectral Calibration Override matrix ABI

20 POP5DT3700POP5ET.zip 1 POP6DT3700POP6ET.zip 1 DYEnamic ET Termiantor Matrix Standard for the ABI 3100 / 3700 (US84001) Hi Di FormamideApplied Biosystems Mobility file 2 WindowsWinZip zip WinZip Wizard *2 3 Mobility fileet Terminator dye 4 Mobility file Mobility DT3700POP5{ET}.mobDT3700POP6{ET}.mob DT3700POP5{ET}.mobDT3700POP6{ET}.mobMobility file *4 D: Prekin-Elmer Abi Shared Analysis Bacecaller Mobility D: Appliedbiosystems Shared Analysis Bacecaller Mobility ABI

21 Spectral Calibration Hi Di Formamide Matrix Standards 1.Matrix Standards 1Matrix Standard40 µl 2Matrix Standard360 µlhi Di Formamide 3400 µlmatrix Standard 0.2 ml 2200 µl 2. 1ABI Data Collection 2 3Matrix Standard Right-Bar910 LEFT BAR RIGHT BAR Matrix standards 3700 Data Collection POP5 1ABI 3700 Data CollectionRun SetupSpectral Run Select the calibration module and dye set 2 Calibration Module : SpectSQ1_1POP-5DefaultModule DyeSet : F Parameter : SeqStd(AnyDyeSet).par 3OK Run SetupRun Tablespectral runstart Run 4Start Run CalibrationSpectral Calibration Result OK 5OK ABI 3700 POP6 1ABI 3700 Data CollectionInstrument UtilitiesModule Editor 2OthersSpectSQ1_1POP6-DefaultModule 3Run Time2700sec4000sec 4Save AsSpectSQ1_1POP6-Extended 5OKDone 6Run SetupSpectral Run Select the calibration module and dye set 19

22 7 Calibration Module : SpectSQ1_1POP6-Extended DyeSet : F Parameter : SeqStd(AnyDyeSet).par 8OK 9POP53 4.Spectral Calibration Spectral Profile 1Data CollectionData AcquisitionOverride Spectral Calibration Select the dye set to display 2FOK Spectral Calibration Profile for F 3Spectral Calibration ProfileSpectral Profile 4 5.Override matrix ABI Override matrix 1ProfileOverride matrix from another source From Capillary 2ProfileOverride cap 6.Spectral Calibration Data Spectral Calibration DataSpectral Calibration Data D: Perkin-Elmer Abi 3700 DataCollection SpectralCalLogs D: Appliedbiosystems 3700 DataCollection SpectralCalLogs 20

23 DYEnamic ET Terminator Cycle Sequencing Kit US US ,000 US , DYEnamic ET Terminator

24 1. DYEnamic ET Terminator Cycle Sequencing Kit US81050 Sequencing reagent premix Control DNAM13 mp18 50 µl 0.2 µg / µl Control primeruniversal cycle primer 23 mer 100 µl 0.5 pmol / µl 5'-GTTTTCCCAGTCACGACGTTGTA-3 sodium acetate / EDTA buffer 1.5 M sodium acetate >ph 8250 mm EDTA Formamide loading dye US81060US DYEnamic ET Terminator Cycle Sequencing Kit Model 373ABI PRISM 377 DNA Sequencer500 base 3. Material Safety Data Sheet Material Safety Data Sheet Material Safety Data Sheet 22

25 4. DDW 5 pmol 260 nmod 260N pmol / µl pmol / µlod N N 100 %70 % ) AutoSeq G mm EDTA AutoSeq G-50Na 2EDTA 372 mg80 mlnaohph ml ABI Model 373ABI PRISM 377 ABI Model 373 DNA Sequencer, ABI PRISM 377 DNA Sequencer, ABI PRISM 310 Genetic Analyzer, ABI PRISM 3100 Genetic Analyzer, ABI PRISM 3700 DNA Analyzer

26 5. DYEnamic ET Terminator DYEnamic ET Terminator Cycle Sequencing KitThermo Sequenase II DNA ddntp21 Ar 488 nmdonor dye Acceptor dyeenergy TransferddGddAddTddC4 Donor dyeacceptor dyeacceptor dye Acceptor dye 1 3Energy Transfer4 Acceptor dyetaq dye terminatorrhodamine dye (rhodamine 110 rhodamine-6-gtetramethly rhodaminerhodamine X) Acceptor dyerhodamine Taq dye terminator ditpdgtpditp DNA DYEnamic ET Terminator Cycle Sequencing Kit2Thermo Sequenase II DNA 5 ditp GCDNA DNADNA DNADNA DDW0.1 mmedtadnaedta µl8 µl 3. sodium acetate / EDTA buffer 1.5 M >ph 8250 mm EDTA Thermo Sequenase II DNA

27 7. DNA 1Preparation of the sequencing reaction 1. DNA pmol 1, 2, 4 x µl 5 pmol 13 y µl 8 µl H 2O z µl Total 20 µl DNA M13mp18DNA200 ng 1 µl 2 pmol 1 4 µl 8 µl H 2O 7 µl Total 20 µl sec sec 2530 cycles min 1DNA0.1 mmedta10 mm Tris-HCl (ph 8.5)0.1 mm EDTA(TEEDTA) EDTADNA pmol ngdnam13dyenamic ET Terminator M13mp1810 ng4 fmol 335 pmol 4 1, DYEnamic ET Terminator Tm 2 7 Thermo Sequenase II DNA1DNAdITPThermo Sequenase II DNA

28 2Post reaction clean-up AutoSeq G-50 AutoSeq G mm EDTA100 µl 1.5 ml12,000g 1.5 ml 12,000g DNA ABI Model 373ABI PRISM 377 AutoSeq G-50Formamide loading dye ABI PRISM 310 AutoSeq G-50 ABI PRISM 3100 / 3700 AutoSeq G µl 20 µl 2 µlsodium acetate / EDTA buffer 1 80 µl95 % (75 %) 2 15DNA 12,000 rpm µl70 %DNA (35) µlformamide loading dye µltsr l 3734 µl µl µl 1 sodium acetate / EDTA buffer dyesodium acetate / EDTA buffer1.5 M >ph 8250 mm EDTAsodium acetate / EDTA buffer 2 75 %70 %80 % dye ,500g g µl38450 µl70 % 26

29 6 7 DNAloading dye DNA (1020)loading dye 3Gel electrophoresis and Data analysis ABI 310 DyeSet/Primer filedyenamic ET Term.POP6 Matrix filedyenamic ET Terminators Run ModuleSeq POP6ASeq POP6E Instrument FileDYEnamic ET Terminators AE Matrix Standards BasecallerABI-CE1 DyeSet/Primer filedyenamic ET Term.POP6 Matrix filedyenamic ET Terminators ABI-CE1BasecallingABI-CE2 ABI DyeSet/Primer filedyenamic ET Term. (US80872) Matrix filedyenamic ET Terminators Run ModuleSeq Run A- Seq Run E- Instrument FileDYEnamic ET Terminators AE Matrix Standards DyeSet/Primer filedyenamic ET Term. (US80872) Matrix filedyenamic ET Terminators ABI 3100 Plate Editor DyeSetF Mobility FileDT3100pop6{ET}50cm.mob DT3100pop6{ET}36cm.mob ABI 3700 Plate Editor DyeSetF Mobility FileDT3700pop5{ET}.mob DT3700pop6{ET}.mob 27

30 8. 8 µl DNA pmol x µl 5 pmol y µl H 2O z µl Total 20 µl 10 µl sec sec 2530 cycles 60 1 min AutoSeq G mm EDTA100 µl 1.5 ml12,000g 1.5 ml 12,000g DNA Formamide loading dye µl 20 µl sodium acetate / EDTA buffer 2 µl 95 % 80 µl75 %) ,000 rpm15 () 70 % µl 12,000 rpm35 () Formamide loading dye 4 µl 310 TSR 1225 µl µl µl µl µl 28

31 9. 1DNA pmoldna DYEnamic ET Terminators DNA1010,000 ng4 fmol4 pmolm13mp18 DNAABI PRISM pmol ngdna bp0.1 3,800 bpdna380 ng DNA ng pmol DNADNA 140 PCR1,000 bp DNA(ng) ,000 (bp) 1,400 PCR1,000 bp 1,200 1,000 DNA(ng) ,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10,000 (bp) DNA50 DNA 1,500DNA PCR DNA 29

32 DNA DNA0.1 mmedta10 mm Tris-HCl (ph 8.5)0.1 mm EDTAEDTATE EDTA DNA DYEnamic ET Terminator Cycle Sequencing Kit DNA DNA M13-DNA 1213 DNA DNAcaesium chloridepeg DNADNADNA pmol bp cliff effect 5 pmol EDTA0.1 mm260 nmod 260N pmol / µl pmol / µlod 260 /0.01N N TmPCR 1825 mer3' 3' 3 DYEnamic ET Terminator Cycle Sequencing Kit Thermo Sequenase II DNA 30

33 1DNA 2 3 DYEnamic ET Terminator Cycle Sequencing Kit8 µl 20 µl DYEnamic ET Terminator Dilution Buffer DYEnamic ET Terminator Dilution BufferUS ML US MLDYEnamic ET Terminator Dilution Buffer NOTE DYEnamic ET Terminator Dilution Buffer1 / 2DYEnamic ET Terminator Cycle Sequencing Kit 20 µl 4 µl4 µldyenamic ET Terminator Dilution Buffer20 µl 6 µl2 µl Thermo Sequenase II DNA Tm 2 Thermo Sequenase II DNADNAdITP

34 DNAPCR2530 Bacterial Artificial ChromosomesBACDNA 5BAC BAC10 kb DNA100 kbbac 0.15 pmoldna10 µg DNA DNABAC 1 µgdnabacdna1 µg pmol DNA DNA9598 DNA5 DNA µl216 µl 40 µl2 6 sodium acetate / EDTA buffer sodium acetate / EDTA 85 % 80 % 75 % 70 % 65 % 60 % 1.5 M sodium acetate / 250 mm EDTA Blobs Good Good Good Delayed Delayed 7.5 M ammonium acetate Blobs Blobs Blobs Good Delayed Delayed 7.5 M ammonium acetate / 60 mm EDTA Blobs Blobs Good Good Delayed Delayed 1.5 M sodium acetate Blobs Good Good Delayed Delayed Delayed No Salt Blobs Blobs Blobs Blobs Blobs Blobs 20 µl1 / 10 2 µl95 % Blobs70 % GoodBlobs Delayed 32

35 10. ) GAT2001,000 C3350 % EDTA DNA DNA DNA 75 % DNA DNA DNA 5 pmol DNA 350 DNA DNA DNA DNAPCRddNTP350 base DNA1 pmol 5 pmol 24 DNA EDTAsodium acetate / EDTA buffer 33

36 Sanger, F. et al. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74, (1977). 2. Prober, J. M. et al. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science 238, (1987). 3. Lee, L. G. et al. DNA sequencing with dye-labeled terminators and T7 DNA polymerase: effect of dyes and dntps on incorporation of dye-terminators and probability analysis of termination fragments. Nucleic Acids Res. 20, (1992). 4. Ju, J. et al. Fluorescence energy transfer dye-labeled primers for DNA sequencing and analysis. Proc. Natl. Acad. Sci. USA 92, (1995). 5. Tabor, S. & Richardson, C. C. A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and dideoxyribonucleotides. Proc. Natl. Acad. Sci. USA 92, (1995). 6. Huibregtse, J. M. & Engelke, D. R. DNA and Protein Engineering Techniques 1, (1988). 7. McMahon, G. et al. Characterization of c-ki-ras oncogene alleles by direct sequencing of enzymatically amplified DNA from carcinogen-induced tumors. Proc. Natl. Acad. Sci. USA 84, (1987). 8. Carothers, A. M. et al. Point mutation analysis in a mammalian gene: rapid preparation of total RNA, PCR amplification of cdna, and Taq sequencing by a novel method. BioTechniques 7, , (1989). 9. Murray, V. Improved double-stranded DNA sequencing using the linear polymerase chain reaction. Nucleic Acids Res 17, 8889 (1989). 10. Levedakou, E. N. et al. A strategy to study gene polymorphism by direct sequence analysis of cosmid clones and amplified genomic DNA. BioTechniques 7, (1989). 11. Lee, J. S. Alternative dideoxy sequencing of double-stranded DNA by cyclic reactions using Taq polymerase. DNA Cell Biol. 10, (1991). 12. Messing, J. New M13 vectors for cloning. Methods Enzymol. 101, (1983). 13. Mead, D. A. & Kemper, B. in Vectors : A Survey of Molecular Cloning Vectors and Their Uses, Butterworth Publishers, Massachusetts USA (1986). 14. Dente, L. et al. pembl: a new family of single stranded plasmids. Nucleic Acids Res. 11, (1983). 15. Holmes, D. S. & Quigley, M. A rapid boiling method for the preparation of bacterial plasmids. Anal. Biochem. 114, (1981). 16. Carlson, A. & Messing, J. J. Biotechnology 1, 253 (1984). 17. Birnboim, H. C. & Doly, J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7, (1979). 34

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38 MEMO

39 All goods and services are sold subject to the terms and conditions of sale of the company within the General Electric Company group which supplies them. A copy of these terms and conditions is available on request. Thermo Sequenase is a trademark of GE Healthcare Bio-Sciences Ltd or its subsidiaries. ABI PRISM and BigDye are trademarks of The Applera Corporation. GE Healthcare is a trademark of General Electric Company. NOTICE TO PURCHASER ; LIMITED LICENSE These kits are sold pursuant to Authorization from PE Applied Biosystems under one or more of the following US Patents : 4,849,513; 5,015,733; 5,118,800; 5,118,802; 5,151,507; 5,171,534; 5,332,666; 5,242,796; 5,306,618; 5,366,860; 4,855,225 and corresponding foreign patents and patent applications. Further information on purchasing licenses to perform DNA sequence and fragment analysis may be obtained by contacting the Director of Licensing at PE Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404GE HEALTHCARE IS LICENSED AS A VENDER FOR AUTHORIZED SEQUENCING AND FRAGMENT ANALYSIS INSTRUMENTS. NOTICE TO PURCHASE ABOUT LIMITED LICENSE The purchase of these kit (reagent)s include a limited non-exclusive sublicense under certain patents* to use the kit (reagent) to perform one or more patented DNA sequencing methods in those patents solely for use with Thermo Sequenase DNA polymerase purchaced from GE Healthcare for research activities. No other license is granted expressly, impliedly or by estoppel. For information concerning availability of additional licenses to practice the patented methodologies, contact GE Healthcare Life Science, Inc., Director, Business Development, 2636 S.Clearbrook Dr., Arlington Heights, IL *US Patent number 4,962,020; 5,173,411; 5,409,811; 5,498,523. Patent Pending. TM 2001

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