Applied Biosystems Prism 377 with XL Upgrade User Manual
Contents
1. This message may appear when you open data collection and start a plate check a pre run or a run if one of the thermisters is not functioning If this message appears schedule a service call to troubleshoot the thermister and continue to operate the instrument as usual Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com CCD Pixel Position Value CCD Pixel Position The instrument is shipped with the correct CCD pixel position value in Overview 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 y Could not complete your request because the CCD pixel position is incorrect The CCD pixel position value may become corrupted as the result of a power surge or failure If this occurs you must find the correct value and enter it as described in the following procedures before starting a run Locating the CCD The correct CCD pixel position value is written on a white label on the Pixel Position CCD camera It is visible from the front through the opening below the Label rear heat transfer plate as shown below Rear heat transfer plate CCD camera with pixel position label visible here l L Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Note The followi2. A rtisan Artisan Technology Group is your source for quality TecmoogyGroup new and certified used pre owned equipment FAST SHIPPING AND SERVICE CENTER REPAIRS WE BUY USED EQUIPMENT DELIVERY Experienced engineers and technicians on staff Sell your excess underutilized and idle used equipment TENS OF THOUSANDS OF at our full service in house repair center We also offer credit for buy backs and trade ins IN STOCK ITEMS www artisantg com WeBuyEquipment EQUIPMENT DEMOS HUNDREDS OF Instra e REMOTE INSPECTION LOOKING FOR MORE INFORMATION MANUFACTURERS Remotely inspect equipment before purchasing with Visit us on the web at www artisantg com 7 for more our interactive website at www instraview com 7 information on price quotations drivers technical LEASING MONTHLY specifications manuals and documentation RENTALS ITAR CERTIFIED ib SS aed Contact us 888 88 SOURCE sales artisantg com www artisantg com ABI PRISM 377 DNA Sequencer XL Upgrade User s Manual Applied E Biosystems Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Copyright 2000 Applied Biosystems For Research Use Only Not for use in diagnostic procedures ABI PRISM and its Design Applied Biosystems Aquapore AmpliCover Anitron Biobytes Brownlee FastPhoramidite GeneScan Genotyper HLP INHERIT Masterpiece MicroAmp MicroCoat MPLC NEWGUARD ONESTEP OPC P
3. Guaranteed 888 88 SOURCE www artisantg com Index 18 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com rtisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 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 Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free 1 800 345 5224 Fax 1 650 638 5884 Technical Support For technical support Toll Free 1 800 831 6844 ext 23 Fax 1 650 638 5891 www appliedbiosystems com LI AR Applied sw Biosystems 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 904412C Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com A rtisan Artisan Technology Group is your source for quality TecmoogyGroup new and certified used pre owned equipment FAST SHIPPING AND SERVICE CENTER REPAIRS WE BUY USED EQUIPMENT DELIVERY Expe
4. quit and then relaunch the data collection software Quit application and relaunch for this action to take effect Check the CCD pixel position value as follows a Open the Window menu and select Manual Control b Open the Fxn Name menu and select CCD Pixel Position Value The value is displayed in the Value box If it matches the value on the instrument it is OK If it does not match correct the value Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Index C Calibration file creatinga 11 transferring 12 Calibration File Make 11 Calibration File Send 12 CCD pixel position value 9 checking 10 entering in Calibration file 10 finding the 9 collection software 7 combs 1 F firmware 15 G GeneScan Analysis software 7 GeneScan load volumes 4 I integration scheme 15 L load volumes 3 for best resolution 3 GeneScan 4 sequencing 3 loading samples square tooth comb 6 M module files 13 P position based integration scheme 15 preference file 7 R resetting the instrument 15 resolution loading volumes for best 3 Run modes 5 Run windows 7 S Sequence Analysis software 7 sequencing load volumes 3 serial number entering in Calibration file 11 silanizing agent applying 6 small volumes loading 3 T temperature error 8 total reset performinga 15 Index 17 Artisan Technology Group Quality Instrumentation
5. 15 Position Based Integration Scheme 15 Resetting the Instrument 00 0 0 eee ee eee ee 15 Performing a Total Reset 00 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com ABI PRISM 377 XL Upgrade Overview About This This manual describes the ABI PRISM9 377 DNA Sequencer Manual enhancements included in the XL upgrade Be sure to place this manual in your ABI PRISM 377 DNA Sequencer User s Manual Upgrade Overview With the XL upgrade the primary enhancement to the ABI PRISM 377 DNA Sequencer is the increase in the number of samples that can be analyzed simultaneously This increased throughput was made possible by re engineering the instrument and software to acquire more data as the laser scans across the gel XL Specific Combs This upgrade also includes new combs specifically designed for upgraded instruments These combs are 48 and 64 well shark s tooth and 50 and 66 well square tooth combs Other ABI PRISM 377 combs may be used Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Safety Information Site Preparation and Safety Guide Ergonomic Hazard The ABI PRISM 377 Site Preparation and Safety Guide includes important safety information that should be read by all users before they operate the instrument Topics covered in the guide include Anexplanation of the safety labels affixed t
6. The ABI PRISM 377 DNA Sequencing GeneScan Chemistry Guide P N 4303188 The Automated DNA Sequencing Chemistry Guide P N 4305080 Loading the small volumes required by the ABI PRISM 377 XL upgrade is easier if you use a gel loading syringe such as a multiplexed loader of four or eight syringes arrayed to match the XL upgrade well spacing An alternative is an adjustable volume pipet with 0 17 mm gel loading tips Volumes below 1 0 uL may be difficult to load with a pipet For best resolution loading volumes should be smaller when using the 12 cm separation distance Loading volumes of 0 5 uL are acceptable You may find it possible and advantageous to use even smaller volumes Use the following table to determine resuspension and loading volumes for sequencing based on the comb configuration used Comb Configuration No of Wells 24 36 Wells 48 Wells 64 Wells Resuspension vol uL 6 9 2 4 2 4 Loading vol uL 1 5 0 5 1 0 0 5 1 0 a 5 1 Deionized formamide to 50 mg blue dextran mL 25 mM EDTA WARNING CHEMICAL HAZARD Formamide is a known teratogen It can cause birth defects Wash thoroughly after handling formamide Wear appropriate protective eyewear clothing and gloves Obtain a copy of the MSDS from the manufacturer Wash thoroughly after handling formamide Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Loading Volumes Use the fol
7. with SAGelTracker Preference File Define default values in the new software following the procedures described under Setting Preferences in the AB PRISM 377 DNA Sequencer User Manual The default values you define for Sequencing or GeneScan run modules and sample sheets are maintained in the Preference file Sequencing and The Sequencing and GeneScan Run windows now include the Run GeneScan Run Mode pulldown menu as shown below You can now choose either Full Windows Scan standard with the ABI PRISM 377 or XL Scan with the upgrade See Lanes Combs and Run Modes Table on page 5 a Run 10 6 96 2 28 PM er E DE Plate Check Module Plate Check vj PreRun Module Seq PR 36 24 w Run Module Seq Run 364 2 v Collect time hours Sample Sheet none v DO Well to Read distance cm Instrument File Instrument File E v Operator iE imti Lanesf 48 v Run Run Mode LEES Mode pulldown Sample File Name menu Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Error Alert The following error message has been added to alert you of a possible Message problem with the heat transfer plate thermisters E 2 Error Alert Error Alert from Instrument Temperature below thermistor limit
8. CR MATE Phosphalink POLYPORE Precipitette ProBlott PROCISE ProFocus ProSort ProSpin SeqEd Sequence Navigator SPHERIS SPHERI10 StockMarks Stretch Synergy SynthAssist and VeloSep are registered trademarks of PE Corporation or its subsidiaries in the U S and certain other countries ABI AutoAssembler BaseSprinter BigDye CATALYST GeneAssist LV40 MatchMaker PDQ POP POP 4 POP 6 Primer Express and ProSorb are trademarks of PE Corporation or its subsidiaries in the U S and certain other countries AmpErase AmpliTaq AmpliTaq Gold EnviroAmp GeneAmp and TaqMan are registered trademarks of Roche Molecular Systems Inc Centricon is a registered trademark of W R Grace and Co Centri Sep is a trademark of Princeton Separations Inc Long Ranger is a trademark of The FMC Corporation AppleScript Power Macintosh and Macintosh are registered trademarks of Apple Inc pGEM is a registered trademark of Promega Corporation All other trademarks are the sole property of their respective owners Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Contents ABI PRISM 377 XL Upgrade Overview 0 0 00 ce eee ee ee 1 About This Manual LL 1 Upgr de Overview w2 biseei minkeb bed ho rtd done hee here tow 1 safety Information seoce chee i A 2 Site Preparation and Safety Guide lille esee 2 Ergonomic Hazard 0 eee eee 2 Loading Volume s
9. S PR 124 1200 CHILLER GS PR 124 2400 GS PR 124 2400 CHILLER GS PR 12C 1200 GS PR 12C 1200 CHILLER GS PR 12C 2400 GS PR 12C 2400 CHILLER GS PR 12D 1200 GS PR 12D 1200 CHILLER GS PR 12D 2400 GS PR 12D 2400 CHILLER GS PR 12F 1200 GS PR 12F 1200 CHILLER GS PR 12F 2400 GS PR 12F 2400 CHILLER GS PR 364 1200 GS PR 364 1200 CHILLER GS PR 364 2400 GS PR 364 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 36F 1200 GS PR 36F 1200 CHILLER GS PR 36F 2400 GS PR 36F 2400 CHILLER GS Run 12A 1200 GS Run 12A 1200 CHILLER GS Run 12A 2400 GS Run 12A 2400 CHILLER GS Run 12C 1200 GS Run 12C 1200 CHILLER GS Run 12C 2400 GS Run 12C 2400 CHILLER GS Run 12D 1200 GS Run 12D 1200 CHILLER GS Run 12D 2400 GS Run 12D 2400 CHILLER GS Run 12F 1200 GS Run 12F 1200 CHILLER GS Run 12F 2400 GS Run 12F 2400 CHILLER GS Run 2140V A CHILLER GS Run 2140V C CHILLER 13 14 2 5 Collection Module Files continued 377XL Modules Chiller Modules GS Run 2140V D CHILLER GS Run 2140V F CHILLER GS Run 36A 1200 GS Run 36A 1200 CHILLER GS Run 36A 2400 GS Run 36A 2400 CHILLER GS Run 36C 1200 GS Run 36C 1200 CHILLER GS Ru
10. Silanizing Agent Purpose for Preparing Gels When using a square tooth comb silate the unnotched glass plate in the well area to facilitate loading samples Use a silanizing agent such as methacryloxypropyltrimethoxysilane Sigma P N M6514 to bind the gel to the glass Procedure Perform the following procedure every time a new gel is poured WARNING CHEMICAL HAZARD Silanizing agents are irritating to the eyes respiratory system and skin Always work in a fume hood Obtain a copy of the MSDS from the manufacturer Wear appropriate protective eyewear clothing and gloves To apply a silanizing agent and remove a gel after a run Step Action 1 Wash the unnotched glass plate in detergent and distilled water Rinse well in distilled water then air dry 2 Apply a small amount of silanizing agent to a cotton swab and spread it across the top 3 5 cm of the unnotched glass plate 3 Allow the agent to dry thoroughly Assemble the plates for the run as usual 5 Remove the gel from the silated area with 0 1 N HCI or 0 1 N NaOH or scrape off gently Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Software Collection The current collection software is version 2 5 Software GeneScan Analysis The current GeneScan Analysis software is version 3 1 with GSGelTracker Sequence Analysis The current Sequence Analysis software is version 3 3
11. e the ABI 377XL Calibration file and store the CCD pixel position value and instrument serial number in it When created the file is named ABI 377XL Calibration and is placed in the Preferences folder inside the System folder To read edit or print the Calibration file use the SimpleText application Creating a Calibration File To create a Calibration file with Calibration File Make Step Action 1 Turn on power to the instrument Select Manual Control from the Window menu Open the Fxn Name pulldown menu Select Calibration File Make c1 B Click Execute Entering the Serial To enter the instrument serial number in the calibration file Number Step Action 1 Make a note of the serial number from the back of the instrument 2 Open the System Folder and the Preferences Folder inside the System Folder Open the ABI 377XL Calibration file Using SimpleText type the instrument serial number or name up to eight characters by replacing the question marks ABI 377HL Calibrations SSE 77777777 Instrument Serial Number 00206 CCD X Skip Select Save from the File menu Close the ABI 377XL Calibration File window Quit the SimpleText program 11 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using Calibration IMPORTANT You must have the correct CCD p
12. ixel position value in File Send instrument memory before using the Calibration File Make or Send functions 12 After creating a Calibration file use Calibration File Send from the Manual Control window to send the instrument s serial number or name and CCD pixel position value to the instrument These values will be displayed in the Collection Log window The serial number or name is transferred into all sample files created by the instrument It can be viewed in the annotative view of the sample file This is useful for identifying instruments particularly if you operate more than one instrument To transfer a Calibration file with Calibration File Send Step Action 1 Turn on power to the instrument Select Manual Control from the Window menu Open the Fxn Name pulldown Select Calibration File Send c1 B OIN Click Execute Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Module Files Unused Module Folder Collection 2 5 Module Files Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Move all of the module files that you do not intend to use from the Modules folder into the Unused Modules folder The following table lists the module files in Collection Software v 2 5 2 5 Collection Module Files 377XL Modules Chiller Modules GS PR 124 1200 G
13. lowing table to determine component and loading volumes for GeneScan for GeneScan based on the comb configuration used Comb Configuration No of Wells 24 34 Wells 50 Wells 66 Wells Deionized formamide 2 5 2 5 2 5 uL 50 mg Blue dextran mL 25 mM EDTA 0 5 0 5 0 5 P N 402055 uL Size standard uL 0 5 0 5 0 5 DNA pL 1 5 1 5 1 5 Loading vol uL 1 5 1 0 1 5 0 5 1 0 a If the peak heights fall below 50 fluorescent units increase the concentration by doubling the volume of the size standard in the cocktail Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Lanes Combs and Run Modes Lanes Combs and The number of lanes the types of combs used and the corresponding Run Modes Table run modes are shown in the following table Lanes Comba 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 Square tooth XL Scan 64 Shark s tooth XL Scan 66 Square tooth XL Scan a Well spacing for the XL combs is 9 mm on center to accommodate multichannel pipettes IMPORTANT For 48 50 64 and 66 lanes you must use XL Scan Run mode Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Silanizing Agent
14. mand for positional accuracy of the detection optics a new integration scheme is used Previously a given time was given to each channel before reading the CCD camera and switching to the next channel This release of firmware uses position based CCD integration where predetermined stage positions determine when to switch Reset the instrument under the following situations Reset the instrument when To reset perform a Resetting is necessary because new firmware version has been downloaded single reset Press the reset button once the running TPU code needs to be reinitialized IMPORTANT Failure to reset the instrument will cause a lockup the instrument does not respond to commands or it responds inappropriately total reset Follow the procedure that follows the firmware image may be corrupted Step Action 1 Using the eraser end of a pencil or similar object press the red reset button on the back of the instrument twice in rapid succession 2 Quit the data collection software 15 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com 16 Step Action Launch the data collection software The firmware is automatically downloaded to the instrument This will take 60 90 seconds Firmware Image Sending Firmware Image to Instrument In response to this prompt
15. n 36C 2400 GS Run 36C 2400 CHILLER GS Run 36D 1200 GS Run 36D 1200 CHILLER 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 GS Run 60W A CHILLER GS Run 60W C CHILLER GS Run 60W D CHILLER GS Run 60W F CHILLER Plate Check A Plate Check A CHILLER Plate Check C Plate Check C CHILLER Plate Check D Plate Check D CHILLER Plate Check E Plate Check E CHILLER Plate Check F Plate Check F CHILLER Seq PR 36A 1200 Seq PR 364 1200 CHILLER Seq PR 364 2400 Seq PR 36A 2400 CHILLER Seq PR 36E 1200 Seq PR 36E 1200 CHILLER Seq PR 36E 2400 Seq PR 36E 2400 CHILLER Seq PR 484 1200 Seq PR 484 1200 CHILLER Seq PR 48E 1200 Seq PR 48E 1200 CHILLER Seq Run 36A 1200 Seq Run 364 1200 CHILLER Seq Run 36A 2400 Seq Run 364 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 48E 1200 Seq Run 48E 1200 CHILLER a PR Prerun Seq Sequencing GS GeneScan Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Firmware Position Based Integration Scheme Resetting the Instrument Performing a Total To perform a total reset Reset Due to the increased de
16. ng procedure requires the use of a flashlight To locate the CCD pixel position value on the label Step Action 1 Open the front door of the instrument 2 Shine a light through the opening below the rear heat transfer plate to view the white label on the CCD camera Record the value from the white label If you cannot find the label call technical support Entering the To enter the correct CCD pixel position value in the calibration file Action Turn power on to the instrument Select Manual Control from the Window menu Open the Fxn Name pulldown menu Select the CCD Pixel Position function The current pixel position value is displayed Compare the displayed value with the value on the white label If the pixel position is Then the same as the value on the Stop here white label different than the value on the a Select the text box and white label type the correct CCD pixel position value b Click Execute Correct CCD Pixel Position Value Step 1 2 3 4 5 10 Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Using Calibration IMPORTANT You must have the correct CCD pixel position value in File Make instrument memory before using the Calibration File Make or Send functions Use the Calibration File Make function from the Manual Control Window to creat
17. o the instrument Laser safety including hazards and safe operation requirements Chemical safety including a waste profile and Material Data Safety Sheets for the chemicals commonly used with the instrument We strongly recommend that this guide be kept readily available for reference at all times WARNING ERGONOMIC HAZARD Performing loading activities may increase the risk of developing cumulative trauma disorders repetitive motion or repetitive strain injuries which include but are not limited to tendonitis tenosynovitis epicondylitis strains and or sprains To reduce the risk of these disorders the following recommendations have been developed to decrease awkward posture repetitive motion excessive force static muscle loading and soft tissue contact Use an automated multi channel pipet loader Locate the instrument on a variable or predetermined height worktable or lab bench Use a stable stool or stepladder Install adequate lighting in the appropriate area to facilitate loading Ensure adequate front access to the instrument while performing loading activities Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Loading Volumes Loading References Tips on Loading Small Volumes Loading Volumes for Sequencing The new combs require smaller loading volumes For more information refer to The loading volume tables in this manual
18. rienced engineers and technicians on staff Sell your excess underutilized and idle used equipment TENS OF THOUSANDS OF at our full service in house repair center We also offer credit for buy backs and trade ins IN STOCK ITEMS www artisantg com WeBuyEquipment EQUIPMENT DEMOS HUNDREDS OF Instra e REMOTE INSPECTION LOOKING FOR MORE INFORMATION MANUFACTURERS Remotely inspect equipment before purchasing with Visit us on the web at www artisantg com 7 for more our interactive website at www instraview com 7 information on price quotations drivers technical LEASING MONTHLY specifications manuals and documentation RENTALS ITAR CERTIFIED ib SS aed Contact us 888 88 SOURCE sales artisantg com www artisantg com
19. sisien 3 Loading References 00 3 Tips on Loading Small Volumes 00 00 0000 00000 3 Loading Volumes for Sequencing 00 ee eee eee eee 3 Loading Volumes for GeneScan 0 0 0 eee eee eee ee 4 Lanes Combs and Run Modes 0 0 0 c eee eee eee eee eee 5 Lanes Combs and Run Modes Table 5 Slamzing Agent seere opos ERR cet Ue Reed bo dees aa des 6 Silanizing Agent for Preparing Gels nrn 6 Nini EE 7 Collection Software sess e RR E XE DR ERR ER RES 7 GeneScan Analysis si rtp Re ER ERR 7 Sequence Analysis isle ecl peer kp bo ben l rich 7 Preference Fil a4 iia eR bUERRREUERRURRRBUPEE e Racks 7 Sequencing and GeneScan Run Windows seseuss 7 FrrorAlert M ss ge coiro iad b e dS ede a Seed e ope ad 8 CCD Pixel Position Value 0 0 eee 9 CCD Pixel Position Overview 0 0 c eee eee eee eee 9 Locating the CCD Pixel Position Label 000 9 Entering the Correct CCD Pixel Position Value 10 Using Calibration File Make 11 i Artisan Technology Group Quality Instrumentation Guaranteed 888 88 SOURCE www artisantg com Entering the Serial Number LL 11 Using Calibration File Send 0 0 00 cee eee eee 12 Module Fl ss i verbe ROSE eee pr Re ER DP ROIG EQ 13 Unused Module Folder eese 13 Collection 2 5 Module Files eee 13 PirinWate eL RERLCPRERUPNS NEA eer tactis Bere RR E epus
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