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abi PRISM 377 User Manual

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Summary of Contents for abi PRISM 377

  • Page 1 (217) 352-9330 | Click HERE Find the Thermo / Applied Biosystems Prism 377 at our website:...
  • Page 2 ABI P ® 377 DNA Sequencer RISM 96-Lane Upgrade User’s Manual Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 3 U.S. and certain other countries. ABI, AFLP Plant Mapping, AmpF l STR, AmpF l STR Profiler, AmpF l STR 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.

  • Page 4: Table Of Contents

    Contents 1 Introduction ....... 1-1 Overview ........... . 1-1 Upgrade Overview .
  • Page 5 C Part Numbers......C-1 ABI P 377 DNA Sequencer Parts ......C-1...

  • Page 6: Introduction

    This manual describes the enhancements to the ABI P 377 DNA RISM Sequencer included in the 96-lane upgrade. Manual Be sure to place this manual in your ABI P 377 DNA Sequencer RISM User’s Manual . Technical Support For technical support contact information refer to the ABI P RISM DNA Sequencer User’s Manual .

  • Page 7: Upgrade Overview

    Upgrade Overview Product Overview ® The ABI P 377 DNA Sequencer 96-lane Upgrade Kit enhances RISM the capabilities of the 377 DNA sequencer to support up to 96 lanes for both Sequencing and GeneScan applications. Key Features The following list provides an overview of the key features of the 96-lane upgrade.

  • Page 8: Important Upgrade Notes

    Important Upgrade Notes Matrices To ensure data quality, we strongly recommend rerunning matrices at installation and semiannually for applications where matrices may be critical for optimal signal-to-noise ratio (e.g., heterozygote detection and any GeneScan application). Combs The 96-lane run mode only supports the use of a shark’s-tooth comb. Clamps The 96-lane plates and casting combs require 10–12 lbs.

  • Page 9: Kit Configurations

    Kit Configurations Kit Configurations The following table lists the components and quantity of components ® included in ABI P 377 DNA Sequencer 96-lane upgrade kits. Table RISM Kit Contents Component Part No. 377-96- 377-96- 377-96- 377-96- 377-96- 377-96- (Quantity) (P/N)

  • Page 10: Gels

    Gels Overview In This Chapter The following topics are covered in this chapter. Topic See Page Preparing Gels Setting Run Conditions Loading Gels Gels 2-1 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 11: Preparing Gels

    Preparing Gels Pouring Gels To pour gels for use on the ABI P 377 96-lane DNA sequencer: RISM Step Action Cast the gels as instructed in the ABI P 377 DNA Sequencer RISM User’s Manual. Use 0.2-mm spacers (P/N 401837) and a 0.4-mm 96-lane casting comb (P/N 4305385) with the new stepped front plate (P/N 4305384).
  • Page 12 Preparing a Gel To prepare a gel for a run: Step Action Let the gel polymerize for at least two hours. Remove the clamps from the gel. Leave the casting comb in place until you are ready to insert the comb. Rinse the plate thoroughly with dH O and let dry.
  • Page 13 Place the gel and the cassette in the 377 instrument. Note For instructions on setting up the 377 instrument for a run refer to the ABI P 377 DNA Sequencer User’s Manual. RISM 2-4 Gels Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 14: Setting Run Conditions

    Setting Run To set gel run conditions: Conditions Step Action Open the 377-96 Collection software. Prepare a sample sheet as described in the ABI P 377 DNA RISM Sequencer User’s Manual. IMPORTANT Preparing a sample sheet prior to the run is required for optimal tracker operation.
  • Page 15 The tracker will not function unless the matrix file was selected before starting the run. Select the proper sample sheet. Perform the plate check, prerun, and run procedures as instructed in the ABI P 377 DNA Sequencer User’s Manual. RISM 2-6 Gels...

  • Page 16: Loading Gels

    Loading Gels Loader Options The following loaders can be used to load a 96-lane gel. Fixed-pitch, 10.8-mm loader and a plate rack holding micro-amp tubes spaced 10.8 mm apart P-10 microliter pipet with a flat loading tip Single-barrel syringe with 0.2-mm or 0.3-mm needles Two-pitch, eight-channel loader Note For reasons of loading speed and accuracy, Applied Biosystems highly...
  • Page 17 Suggested The following table lists the suggested load volumes and sample resuspension volumes for sequencing. Sequencing Load Volumes Resuspension Loading Vol. No. of Wells Vol. (µL) (µL) 24/36 6–9 2–4 1.0–1.5 2–4 1.0–1.5 2–4 1.0–1.5 a. 5:1 Deionized formamide to 50 mg blue dextran/mL in 25 mM EDTA b.
  • Page 18 Suggested Load The following schematic depicts a microtiter plate showing the suggested load mapping for an eight-channel loader. Mapping 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.
  • Page 19 Suggested Loading Follow the loading procedure to load the odd lanes first, electrophorese for 2 min, then load the even lanes. Sequence IMPORTANT If any wells leak, flush the contaminated lanes then follow the table below. If you are running... Then...
  • Page 20 Step Action Electrophorese for 2 min. Repeat steps 2–7 to load the even lanes. End the prerun and begin the run. Gels 2-11 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: Software And Firmware

    Software and Firmware Overview In This Chapter The following topics are covered in this chapter. Topic See Page Software Firmware Software and Firmware 3-1 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 23: Software

    The CCD pixel position value may become corrupted as the result of a power surge or power failure. If this occurs, you must enter the correct value before starting the run. For details, refer to the ABI P RISM DNA Sequencer User’s Manual.
  • Page 24 Module Files There are many choices available among the module files provided in the ABI P 377-96 upgrade. Because you may not use all of the RISM module files, move those you do not intend to use from the Modules folder into the Unused Modules folder.
  • Page 25 377-96 and Chiller Module Files (continued) 377-96 Modules Chiller Modules GS Run 36C-1200 GS Run 36C-1200 CHILLER GS Run 36C-2400 GS Run 36C-2400 CHILLER GS Run 36D-1200 GS Run 36D-2400 GS Run 36D-2400 CHILLER GS Run 36F-1200 GS Run 36F-1200 CHILLER GS Run 36F-2400 GS Run 36F-2400 CHILLER Plate Check A...

  • Page 26: Firmware

    Firmware Collection The 96-Lane Scan mode uses 480 collection channels per scan, up from 388 in an XL Scan mode. This provides a 5x oversampling for Channels analysis. Increased Position-Based Due to the increased demand for positional accuracy of the detection optics, a new integration scheme is used.
  • Page 27 Press the reset button on the back of the 377 instrument. Immediately press the reset button again. After a total reset, a new copy of the firmware will be downloaded to the instrument when you relaunch the ABI P 377-96 Collection RISM software.

  • Page 28: Troubleshooting

    Glass Plates Troubleshooting For more information on troubleshooting, refer to the following manuals: References GeneScan Reference Guide ABI P 377 DNA Sequencer User’s Manual RISM Troubleshooting 4-1 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 29: Troubleshooting

    Troubleshooting Gels Problem Possible Cause Solution Leaking wells Loose combs Sequencing: Electrophorese immediately, then after each three loads with the eight-channel loader. GeneScan: Leaking wells are not tolerated in GeneScan applications. If a well leaks, it is best to run another gel.
  • Page 30 Thermistors Problem Possible Cause Solution Error: “Thermistor One or more Schedule a service call Failure” thermistors are bad to replace the thermistors. Continue to use the instrument as usual. Error: “Temperature Ambient temperature is Turn on the pump below thermistor limit.” too low (<...
  • Page 31 Problem Possible Cause Solution Signal too weak Multiple Increase the CCD gain to four: Open 377-96 Collection. In the Run window select the Run module. Double-click the small document icon next to the Run Module pulldown menu. Change the CCD gain to four.
  • Page 32 Message Possible Cause Solution Flow Detected With Pump Off Either: If an external cooling device is –External Cooling In Use! in use: The wrong module is being Check the modules used for a run where an selected on the run sheet. external cooling device is Use Chiller modules.
  • Page 33 Glass Plates Applied Biosystems does not support the use of third party plates or combs on the 377 instrument. We have been 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.

  • Page 34: A Filter Set/Dye Combinations

    Filter Set/Dye Combinations Virtual Filter Set Dyes Chemistry GeneScan: R110, R6G, TAMRA, ROX [F} dNTP Sequencing: JOE (A), 5-FAM (C), TAMRA Dye primer (G), ROX (T) R6G (A), ROX (T), R110 (G), Dye terminator TAMRA (C) GeneScan: 6-FAM,TET, HEX, TAMRA Linkage Mapping Set V.
  • Page 35 A-2 Filter Set/Dye Combinations Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...

  • Page 36: B Two-Pitch, Eight-Channel Loader Suppliers

    Two-Pitch, Eight- Channel Loader Suppliers Supplier Information Tables Introduction For your convenience, the following tables provide information on suppliers of two-pitch, eight-channel loaders. IMPORTANT Contact the companies listed for availability, pricing, and technical information regarding these products. Suppliers Inside the U.S. Supplier Supplier Headquarters Product...
  • Page 37 Supplier Supplier Headquarters Product Part No. World Precision Sarasota International Trade Center Loader Gel Mate 96 Instruments, Inc. 175 Sarasota Center Blvd. Sarasota, FL 34240-9258 Needle, 0.25-mm 67124 (10) Voice: (941) 371-1003 Fax: (941) 377-5428 World Wide Web: http://www.wpiinc.com Outside U.S. offices are listed on the following page.
  • Page 38 Supplier Supplier Contact Geographic Areas Served World Precision Liegnitzer Str. 15 Austria Instruments, Inc. D-10999 Berlin, Germany Bulgaria Germany Voice: 49 (0) 30-6188845 Czechoslovakia Fax: 49 (0) 30-6188670 Germany E-mail: wpi@wpi.sireco.de Greece Holland (Netherlands) Hungary Italy Poland Rumania Russia Switzerland Yugoslavia World Precision 1-4-2-702 Naka-Meguro, Meguro...
  • Page 39 Supplier Supplier Contact Geographic Areas Served World Precision Sarasota International Trade Center Areas not listed above Instruments, Inc. 175 Sarasota Center Blvd. Other world-wide Sarasota, FL 34240-9258 areas Voice: (941) 371-1003 Fax: (941) 377-5428 E-mail wpi@wpiinc.com B-4 Two-Pitch, Eight-Channel Loader Suppliers Artisan Technology Group - Quality Instrumentation ...

  • Page 40: C Part Numbers

    Part Numbers ABI P 377 DNA Sequencer Parts RISM Plates and Spacers Item 401878 48-cm Glass plates/spacers kit includes two sets of 48-cm well-to-read glass plates and gel spacers 401876 36-cm Glass plates/spacers kit: includes two sets of 36-cm well-to-read glass plates and gel spacers...
  • Page 41 Cassette, Buffer Item Chambers, Heat Plate, and Clamps 603627 Gel cassette 603947 Top and bottom gel pouring fixtures 401969 Top 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...

  • Page 42: Abi Prism Dna Fragment Analysis Kits And Reagents

    ABI P DNA Fragment Analysis Kits and Reagents RISM Internal-Lane Size GeneScan-350, 500, and 400HD contain enough material for 800 lanes. GeneScan-1000 and 2500 contain enough material for 400 Standards lanes. GeneScan-500XL contains enough material for 1600 lanes. Loading buffer is included.
  • Page 43 Fluorescent dNTP Each kit listed below includes a GeneAmp ® kit as specified (100 reactions) along with an [F]dNTP set that contains 30 µL each of PCR Kits [R110]dNTP (3 nmol), [R6G]dNTP (3 nmol), and [TAMRA]dNTP (12 nmol). N808-0220 GeneAmp PCR Reagent Kit with AmpliTaq ®...
  • Page 44 Matrix Standard Sets 401114 Dye Primer Matrix Standards Kit (Filter Set A) for NHS-ester labeling Contains one tube each of 5-FAM-, JOE-, TAMRA-, and ROX- labeled DNA 402792 [F]dNTP matrix standards Contains one tube each of R110-, R6G-, TAMRA-, and ROX- labeled DNA 401546 Fluorescent Amidite Matrix Standards Kit (Filter Set C) for...
  • Page 45 ABI P RISM 50-Rxn Kits 300-Rxn Kits Panel Chromosome Linkage Mapping Set Version 2 403089 403118 Complete Set 1–22, X 403090 403119 403091 403120 403092 403121 403093 403122 403094 403123 403095 403124 403096 403125 403097 403126 403998 403127 403099 403128...
  • Page 46 ABI P RISM Quantity Linkage Mapping Set Version 2 450096 Individual Primer Pairs from the ABI P ™ 3000 pmol RISM Linkage Mapping Set Version 2 (continued) Must be ordered through Applied Biosystems Custom Oligonucleotide Synthesis Service (specify locus name)

  • Page 47: Abi Prism Dna Sequencing Kits And Reagents

    ABI P DNA Sequencing Kits and Reagents RISM dRhodamine Reactions Terminator Cycle Sequencing Kits 403044 Ready Reaction with AmpliTaq ® 403045 Ready Reaction 1000 DNA Polymerase, 4303143 Ready Reaction 5000 BigDye Primer ™ Primer Reactions Cycle Sequencing Ready Reaction 403051 –21 M13...
  • Page 48 Dye Primer Cycle Core Kit configurations contain all essential reagents packaged in separate tubes. Each kit sequences both single-stranded and double- Sequencing Core stranded templates. Kits with AmpliTaq DNA Primer Reactions Polymerase, FS 402071 –21 M13 402072 M13 Reverse 402073 –21 M13/M13 Reverse 402125 Kit reagents only (primerless)
  • Page 49 Dye Primers Kits include 20 pmol of FAM- and JOE-labeled primer, 40 pmol of TAMRA- and ROX-labeled primer, and a control template in quantity enough for 50 ss- or ds-DNA sequencing reactions. Primers 401131 –21 M13 Dye Primers (4 x 50), 5´ TGT AAA ACG ACG GCC AGT 3´...
  • Page 50 HLA-DRB Sequencing-Based Typing Starter Kit 403085 MicroSeq 16S rRNA Gene Kit 4003015 Primer Island Transposition Kit Reagent Kit Protocol Protocols 402113 ABI P Dye Primer Cycle Sequencing Ready Reaction Kit RISM Protocol 402114 ABI P Dye Primer Cycle Sequencing Core Kit Protocol RISM 402078...

  • Page 51: User's Manuals

    User’s Manuals 903433 ABI P ® 377 DNA Sequencer User’s Manual RISM 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 Part Number Updates Part numbers are subject to change. Consult the Applied Biosystems World Wide Web site (www.appliedbiosystems.com/techsupport) for...
  • Page 52 Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com...
  • Page 53 Worldwide Sales Offices Applied Biosystems vast distribution and service network, composed of highly trained support and applications personnel, reaches into 150 countries on six continents. For international office locations, please call our local office or refer to our web site at www.appliedbiosystems.com.

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