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abi PRISM 377, User Manual

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abi PRISM 377 User Manual Download Page 22

Software and Firmware

3-1

Software and 
Firmware

3

Overview

In This Chapter

The following topics are covered in this chapter.

Topic

See Page

Software

3-2

Firmware

3-5

3

Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

Summary of Contents for PRISM 377

Page 1: ...utilized and idle equipment along with credit for buybacks and trade ins Custom engineering so your equipment works exactly as you specify Critical and expedited services Leasing Rentals Demos In stock Ready to ship TAR certified secure asset solutions Expert team I Trust guarantee I 100 satisfaction All trademarks brand names and brands appearing herein are the property of their respective owners...

Page 2: ...ABI PRISM 377 DNA Sequencer 96 Lane Upgrade User s Manual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 3: ... and certain other countries ABI AFLP Plant Mapping AmpFlSTR AmpFlSTR Profiler AmpFlSTR Profiler Plus ApliTaq Gold Applied Biosystems BigDye Primer BigDye Terminator and True Allele are trademarks of PE Corporation or its subsidiaries in the U S and certain other countries All other trademarks are the sole property of their respective owners Artisan Technology Group Quality Instrumentation Guarant...

Page 4: ...1 Overview 2 1 Preparing Gels 2 2 Setting Run Conditions 2 5 Loading Gels 2 7 3 Software and Firmware 3 1 Overview 3 1 Software 3 2 Firmware 3 5 4 Troubleshooting 4 1 Overview 4 1 Troubleshooting 4 2 A Filter Set Dye Combinations A 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 5: ...t Numbers C 1 ABI PRISM 377 DNA Sequencer Parts C 1 ABI PRISM DNA Fragment Analysis Kits and Reagents C 3 ABI PRISM DNA Sequencing Kits and Reagents C 8 User s Manuals C 12 Part Number Updates C 12 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 6: ...PRISM 377 DNA Sequencer User s Manual Technical Support Contacts For technical support contact information refer to the ABI PRISM 377 DNA Sequencer User s Manual In This Chapter The following topics are covered in this chapter Topic See Page Upgrade Overview 1 2 Important Upgrade Notes 1 3 Kit Configurations 1 4 1 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisa...

Page 7: ...t Tracker decreasing labor to process gels Increased comb thickness in loading area to 0 4 mm while using 0 2 mm gel for electrophoresis causing no change in run time Improved comb durability and geometry allowing easier loading of volumes up to 1 5 µL Added position based CCD integration with time scaling allowing collection while accelerating the stage which minimizes noise Upgraded instruments ...

Page 8: ...xtensions It is important to turn off these extensions before beginning any 96 lane run From the Extensions Manager window turn off the following extensions Open Tpt Modem Open Tpt Remote Access Open Tpt Serial Arbitrator Computer Notes Can Run on Any Macintosh Computer 96 lanes can be run on any Macintosh computer supplied with the 377 instrument Processor Speed The processor speed does not impac...

Page 9: ...ane upgrade 4305423 1 1 1 1 1 1 Clamps glass 2 in 4305386 3 3 3 3 3 3 Comb 100 well shark s tooth cast 0 4 mm 1 8 mm center 4305385 2 2 2 2 2 2 Kit EEPROM 96 lanes 1 1 1 1 1 1 PCA tested 16 MHz 377XL 1 1 Upgrade 8 MB Power Mac RAM SIMM 2 Upgrade 8 MB Power Mac RAM DIMM 2 2 1 Mac OS 8 1 1 1 1 1 1 Seq Anal 3 2b 1 1 1 1 1 1 GeneScan 3 0b 1 1 1 1 1 1 a Spacers are 48 cm and need to be cut to size befo...

Page 10: ...is Chapter The following topics are covered in this chapter Topic See Page Preparing Gels 2 2 Setting Run Conditions 2 5 Loading Gels 2 7 2 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 11: ...aled or absorbed through the skin Effects are cumulative When handling always wear personal protection i e lab coat safety glasses and chemical resistant gloves and use in a well ventilated area Thoroughly clean surfaces subject to contamination i e binder clips combs and glass plates 2 Clamp the gels as shown below Use three stainless steel bulldog binder clips P N 4305386 on the top IMPORTANT To...

Page 12: ...pry the casting comb 5 Using a razor blade scrape off all excess acrylamide from the glass in the loading area 6 Using a squirt bottle rinse the loading area with dH2O and dry with at lint free tissue 7 Using a syringe add 1x TBE in to the loading area Note Adding TBE eases the insertion of the comb IMPORTANT Be very careful not to introduce bubbles They are very difficult to remove once the comb ...

Page 13: ... depress the surface of the gel d Teeth should just barely indent the surface of the gel If the surface of the gel is not completely flat in the loading region insert some of the teeth below the surface of the gel up to 0 5 mm so that all of the teeth touch the gel surface e If a tooth has penetrated the gel surface do not attempt to withdraw the comb This will cause sample to leak into adjacent w...

Page 14: ...ode and 36 lane gels run in Full Scan mode Any deviation from the default is likely to confuse the tracker resulting in mistracked lanes Setting Run Conditions To set gel run conditions No of Lanes Comb Run Mode 24 Shark s tooth Full Scan 24 Square tooth Full Scan 32 Shark s tooth Full Scan 34 Square tooth Full Scan 36 Shark s tooth Full Scan 36 Square tooth Full Scan 48 Shark s tooth XL Scan 50 S...

Page 15: ...rresponds to your desired filter set from the appropriate pulldown menus c Select the proper instrument file matrix for your run IMPORTANT The tracker will not function unless the matrix file was selected before starting the run d Select the proper sample sheet 5 Perform the plate check prerun and run procedures as instructed in the ABI PRISM 377 DNA Sequencer User s Manual Step Action Artisan Tec...

Page 16: ...asons of loading speed and accuracy Applied Biosystems highly recommends using a two pitched eight channel loader to load 96 lane gels Two Pitch Eight Channel Loader The following schematics depict generic two pitched eight channel loaders in their closed position Note For specific vendor information see Two Pitch Eight Channel Loader Suppliers on page B 1 Distance between needles 9 mm in closed p...

Page 17: ...the suggested load volumes for GeneScan Note For more details refer to the GeneScan Reference Guide and the LMS v 2 User s Manual No of Wells Resuspension Vol µL a a 5 1 Deionized formamide to 50 mg blue dextran mL in 25 mM EDTA Loading Vol µL 24 36 6 9 1 5 48 2 4 1 0 1 5 64 2 4 1 0 1 5 96 2 4 1 0 1 5b b Loading 1 5 µL requires a syringe with a 0 2 mm tip to facilitate loading at the bottom of the...

Page 18: ...der Notes Loading in staggered format with a two pitch eight channel loader takes 12 loading steps Load No 1 12 The number in each well represents the respective gel lane position Odd lane loading positions are color coded on the comb Gel lane position Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 19: ...eth which could cause leakage 3 Using the two pitch eight channel loader draw 2 µL of sample into the needles 4 Clear any air gaps in the needles by dispensing 0 5 µL of sample or by dispensing until sample is visible in the tips of the syringe 5 Using the comb markers as a guide align the needles into their respective lanes 6 Very slowly dispense up to 1 5 µL of samples into the wells Load the od...

Page 20: ... 9 Electrophorese for 2 min 10 Repeat steps 2 7 to load the even lanes 11 End the prerun and begin the run Step Action Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 21: ...2 12 Gels Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 22: ...ftware and Firmware 3 Overview In This Chapter The following topics are covered in this chapter Topic See Page Software 3 2 Firmware 3 5 3 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 23: ...ing or GeneScan run modules and sample sheets are maintained in the Preference file CCD Pixel Position The instrument is shipped with the correct CCD pixel position value in memory When a run is started the software checks for a value greater than zero If the value is lost from memory an error message is displayed at the beginning of the run as shown below The CCD pixel position value may become c...

Page 24: ...0 GS PR 36A 1200 CHILLER GS PR 36A 2400 GS PR 36A 2400 CHILLER GS PR 36C 1200 GS PR 36C 1200 CHILLER GS PR 36C 2400 GS PR 36C 2400 CHILLER GS PR 36D 1200 GS PR 36D 1200 CHILLER GS PR 36D 2400 GS PR 36D 2400 CHILLER GS PR 36E 1200 GS PR 36E 1200 CHILLER GS PR 36E 2400 GS PR 36E 2400 CHILLER GS PR 36F 1200 GS PR 36F 1200 CHILLER GS PR 36F 2400 GS PR 36F 2400 CHILLER GS Run 12A 1200 GS Run 12A 1200 C...

Page 25: ...36A 2400 Seq PR 36A 2400 CHILLER GS Run 36D 1200 CHILLER Seq Run 36A 1200 Seq Run 36A 1200 CHILLER Seq Run 36A 2400 Seq Run 36A 2400 CHILLER Seq Run 36E 1200 Seq Run 36E 1200 CHILLER Seq Run 36E 2400 Seq Run 36E 2400 CHILLER Seq Run 48A 1200 Seq Run 48A 1200 CHILLER Seq Run 48B 1200 CHILLER Seq Run 48E 1200 Seq Run 48E 1200 CHILLER GS Run 60W D CHILLER GS Run 2140V A CHILLER GS Run 2140V C CHILLER...

Page 26: ...nded Scan Region The 96 Lane Scan mode uses a larger scan region to accommodate the increased comb size The stage travels farther towards the edge on each side and accelerates at a faster pace as it reenters the scan region This offsets the increased number of collection channels so that the integration time per channel remains approximately that of an XL scan As a result there is no loss of sensi...

Page 27: ...nstrument memory This is indicated by the instrument status lights changing from green ready to flashing yellow After a total reset a new copy of the firmware will be downloaded to the instrument when you relaunch the ABI PRISM 377 96 Collection software To reset the firmware image with a total reset Step Action 1 Exit Collection 2 Press the reset button on the back of the 377 instrument 3 Immedia...

Page 28: ...rences For more information on troubleshooting refer to the following manuals GeneScan Reference Guide ABI PRISM 377 DNA Sequencer User s Manual Topic See Page Gels 4 2 Thermistors 4 3 Results 4 3 377 96 Error Messages 4 4 Glass Plates 4 6 4 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 29: ...kinked or damaged spacers Replace the spacers Error Your CCD offset is too high I will reset it to zero The CCD reading is below zero during calibration scan Reset the CCD offset value a Open 377 96 Collection b In the Run window select the Run module c Double click the small document icon next to the Run Module pulldown menu d Change the CCD offset value to zero e Click Save as Default Comb is di...

Page 30: ...ven lanes overlap Running too long between staggered loadings Shorten the run time between loadings Too much salt in the sample Resuspend samples in formamide only Perform extra 70 ethanol rinse of samples if precipitated may lead to slight loss in signal Signal showing up in neighboring lanes Leaky lanes Check clamps and comb fit Signal intensity very high and signal is being detected in neighbor...

Page 31: ...viation Exceeds Tolerance The EP voltage deviated outside its tolerance range The instrument operation is paused Call service Warning Plate Out Thermistor P43 J43 Open Short Circuit Warning Plate In Thermistor P44 J44 Open Short Circuit Warning Possible Heater Thermistor Open Short Circuit Indicates one of the following Possible open or short circuit exists with the thermistor cableconnected to J4...

Page 32: ...re Occurs after the pump was turned on and off three times to see if coolant flow was detected Open the Manual Control window and try to turn on the pump manually If the problem persists call service No flow detected Attempted Pump Restart Indicates the coolant pump was turned on but no coolant flow was detected by the flow switch Check the reservoir to see if there is liquid in the cooler Scanner...

Page 33: ...n manufacturing glass plates to exact tolerances for slab gel electrophoresis for over 10 years Our plates are highly refined Third party plates are not made to our proprietary process tolerances and may exhibit variances from the necessary dimensions Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 34: ...ncing None None D GeneScan 6 FAM HEX NED ROX Linkage Mapping Set V 2 Sequencing None None E GeneScan None None Sequencing dR6G dTAMRA dR110 dROX BigDyeTM Terminator BigDyeTM Primer dRhodamine terminator F GeneScan 5 FAM JOE NED ROX AmpFlSTR ProfilerTM PCR Amplification Kit AmpFlSTR Profiler PlusTM PCR Amplification Kit Plus PCR Amplification Kit AFLPTM Plant Mapping Kit Sequencing None None A Arti...

Page 35: ...A 2 Filter Set Dye Combinations Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 36: ...pricing and technical information regarding these products Suppliers Inside the U S Supplier Supplier Headquarters Product Part No Kloehn Company 10000 Banburry Cross Dr Las Vegas NV 89134 USA Voice 702 243 7727 Fax 702 243 6036 World Wide Web http www kloehn com Outside U S offices are listed on the following page Loader 0 25 mm 18597 Loader 0 3 mm 18663 Needle 0 25 mm 8 18597 Needle 0 3 mm 8 186...

Page 37: ... Loader Gel Mate 96 Needle 0 25 mm 10 67124 Supplier Supplier Headquarters Product Part No Supplier Supplier Contact Geographic Areas Served Kloehn Europe Bahnhofstrasse 12 Postfach 55 CH 7402 Bonaduz Switzerland Voice 41 81 630 2303 Fax 41 81 641 3488 E mail kloehneurope bluewin ch Europe World Precision Instruments Inc Australia P O Box 1191 Glen Waverly Victoria 3150 Australia Voice 61 0 3 9887...

Page 38: ...Japan 1 4 2 702 Naka Meguro Meguro Tokyo 153 0061 Japan Voice 81 0 3 3760 5050 Fax 81 0 3 3760 5055 E mail wpi tkb att ne jp Japan World Precision Instruments Inc United Kingdom Astonbury Farm Business Centre Aston Stevenage Hertfordshire SG2 7EG England Voice 44 0 1438 880025 Fax 44 0 1438 880026 E mail wpi piuk demon co uk Belgium Denmark England Finland France Ireland Norway Portugal Scotland S...

Page 39: ...sota International Trade Center 175 Sarasota Center Blvd Sarasota FL 34240 9258 USA Voice 941 371 1003 Fax 941 377 5428 E mail wpi wpiinc com Areas not listed above Supplier Supplier Contact Geographic Areas Served Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 40: ... spacers 401877 12 cm Glass plates spacers kit Includes two sets of 12 cm well to read glass plates and gel spacers 401835 48 cm Rear glass plate 401838 48 cm Front glass plate 401837 48 cm Gel spacers 0 2 mm 2 401839 36 cm Rear glass plate 401840 36 cm Front glass plate 4305384 36 cm Front stepped plates 2 401833 12 cm Rear glass plate 401834 12 cm Front glass plate 4305384 36 cm Front stepped pl...

Page 41: ...pouring fixture 604014 Bottom pouring fixture 603873 Upper buffer chamber 603875 Lower buffer chamber 603822 Upper buffer electrode assembly 603823 Lower buffer electrode assembly 4303201 Front 36 cm well to read heat plate 4305386 Clamps glass 2 in Bulldog Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 42: ...n 500XL TAMRA 403039 GeneScan 500XL ROX 401098 GeneScan 1000 ROX 401100 GeneScan 2500 ROX 401545 GeneScan 2500 TAMRA 401144 Loading buffer P N Item Quantity 401894 F dUTP Set R110 R6G and TAMRA 3 3 and 12 nmol 3 x 30 µL 401896 R110 dUTP 6 nmol 2 x 30 µL 401897 R6G dUTP 6 nmol 2 x 30 µL 401895 TAMRA dUTP 24 nmola 2 x 30 µL a TAMRA dNTP is supplied at a concentration four times higher than R110 dNTP...

Page 43: ...08 0221 GeneAmp PCR Core Reagents with F dUTP Set N808 0222 GeneAmp Thermostable rTth Reverse Transcriptase RNA PCR Kit with F dUTP Set N808 0223 GeneAmp PCR Reagent Kit with AmpliTaq DNA Polymerase with F dCTP Set N808 0224 GeneAmp PCR Core Reagents with F dCTP Set N808 0225 GeneAmp Thermostable rTth Reverse Transcriptase RNA PCR Kit with F dCTP Set P N Item Quantity 401527 6 FAM Phosphoramidite ...

Page 44: ...EX and ROX dyes in the Fluorescent Amidite Matrix Standards Kit P N Kit 402246 Kit A PCR reagents Contains six fluorescent labeled PCR primer pairs labeled with HEX TET FAM two control DNAs CEPH 1347 02 and 1347 10 and a ready made mix of PCR reagents containing AmpliTaq Gold DNA Polymerase GeneAmp PCR Buffer II dNTPs and magnesium chloride Also includes GeneScan 350 Internal Lane Size Standard an...

Page 45: ...5 6 403100 403129 11 7 8 403101 403130 12 7 8 403102 403131 13 9 10 11 403103 403132 14 9 10 11 403104 403133 15 9 10 11 403105 403134 16 9 10 11 403106 403135 17 12 13 403107 403136 18 12 13 403108 403137 19 12 13 403109 403138 20 14 403110 403139 21 15 16 403111 403140 22 15 16 403112 403141 23 17 18 403113 403142 24 17 18 403114 403143 25 19 20 21 22 403115 403144 26 19 20 21 22 403116 403145 2...

Page 46: ... Mapping Set Version 2 Must be ordered through Applied Biosystems Custom Oligonucleotide Synthesis Service specify locus name 3000 pmol 403061 True Allele PCR Premix 18 mL enough for 2000 rxns 403062 Control DNA CEPH 1347 02 180 µL enough for 150 rxns Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 47: ...action Kits with AmpliTaq DNA Polymerase FS P N Kit Reactions 403044 Ready Reaction 100 403045 Ready Reaction 1000 4303143 Ready Reaction 5000 P N Primer Reactions 403051 21 M13 100 403049 21 M13 5000 403052 M13 Reverse 100 403050 M13 Reverse 5000 P N Kit Reactions 4303573 Ready Reaction 24 4303149 Ready Reaction 100 4303150 Ready Reaction 1000 4303151 Ready Reaction 5000 P N Primer Reactions 4021...

Page 48: ... all necessary reagents in one stable premix The Core Kit configuration contains all essential reagents packaged in separate tubes P N Primer Reactions 402071 21 M13 100 402072 M13 Reverse 100 402073 21 M13 M13 Reverse 100 402125 Kit reagents only primerless 100 402126 T7 100 402127 T3 100 402128 SP6 100 402129 T7 SP6 100 402130 T3 T7 100 402799 SK 100 402798 KS 100 402797 SK KS 100 P N Kit Reacti...

Page 49: ...s 4 x 50 5 ATT TAG GTG ACA CTA TAG 3 402787 SK Dye Primers 4 x 50 5 CGG CCG CTC TAG AAC TAG TGG ATC 3 402786 KS Dye Primers 4 x 50 5 CCT CGA GGT CGA CGG TAT CG 3 403013 PI Dye Primers 4 x 50 5 CAG GAC ATT GGA TGC TGA GAA TTC G 3 403014 PI Dye Primers 4 x 50 5 CAG GAG CCG TCT ATC CTG CTT GC 3 P N Standard 403047 dRhodamine Matrix Standards Kit 401114 Dye Primer Matrix Standards Kit 401071 Dye Termi...

Page 50: ...4 ABI PRISM Dye Primer Cycle Sequencing Core Kit Protocol 402078 ABI PRISM Dye Terminator Cycle Sequencing Ready Reaction Kit Protocol 402116 ABI PRISM Dye Terminator Cycle Sequencing Core Kit Protocol 403041 ABI PRISM dRhodamine Terminator Cycle Sequencing Ready Reaction Kit Protocol 403057 ABI PRISM BigDye Primer Cycle Sequencing Ready Reaction Kit Protocol 4303237 ABI PRISM BigDye Terminator Cy...

Page 51: ...stems com techsupport for updated information 903433 ABI PRISM 377 DNA Sequencer User s Manual 902376 373 DNA Sequencing System User s Manual 904435 GeneScan Analysis Software User s Manual 902842 GeneScan 672 Software User s Manual 4303188 GeneScan Reference Guide Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 52: ...Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ...

Page 53: ...rive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free 1 800 345 5224 Fax 1 650 638 5884 www appliedbiosystems com PE Corporation is committed to providing the world s leading technology and information for life scientists PE Corporation consists of the Applied Biosystems and Celera Genomics businesses Printed in the USA 09 2000 Part Number 4305423B Technical Support For technical support To...

Page 54: ...quipment Have surplus equipment taking up shelf space We ll give it a new home Learn more Visit us at artisantg com for more info on price quotes drivers technical specifications manuals and documentation Artisan Scientific Corporation dba Artisan Technology Group is not an affiliate representative or authorized distributor for any manufacturer listed herein We re here to make your life easier How...

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