Applied Biosystems
3130 and 3130xl Quick Reference Card Rev A Nov 2004
Quick Reference Card
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Applied Biosystems 3130/3130xl Genetic Analyzers
Applied Biosystems 3130/3130xl Genetic Analyzers Quick Reference Card
Default Plate Mapping Note: Multiple injections (Instrument Protocol 2 and higher) are run before moving to the next set of wells.
For the 3130xl Instrument 96-Well Plates
Run 1
Run 2
Run 3
Run 4
A full 96-well plate requires 6 runs to inject all the samples once.
This quick reference card supplements the Applied Biosystems 3130/3130xl Genetic Analyzers Getting Started Guide (P/N 4352715) and the Applied Biosystems 3130/3130xl Maintenance, Troubleshooting, and Reference Guide (P/N 4352716). Refer to the guides about performing the specified tasks and for important safety information.
Instrument Maintenance Schedule
Elements of Data Collection Software v3.0
IMPORTANT! Refer to the Material Safety Data Sheets (MSDSs) for chemicals listed in bold for safety information. Wear gloves any time you handle the polymer bottle, capillary array, septa, or buffer reservoirs.
See the Getting Started Guide, unless noted otherwise
pages 70, 98,115 Tasks
384-Well Plates
Run 1
Run 2
Run 3
Run 4
A full 384-well plate requires 24 runs to inject all the samples once.
Ensure that the: • • •
Reservoir septa are firmly seated and flat. Holes in the plate retainer align with the holes in the septa. Plate assembly sits snugly on the plate deck.
Replenish the water and 1✕ running buffer reservoirs on the 3130/3130xl instrument. Remove bubbles in the polymer system.
Frequency Before each batch of runs
See the maintenance guide. pages 77, 102, 123 page 35
Daily or before each batch of runs
See the maintenance guide. page 145 page 145
Check the loading-end header to ensure the capillary tips are not crushed or damaged.
For the 3130 Instrument 96-Well Plates
Run 1
Run 2
Run 3
Run 4
Check the polymer block to ensure it fits securely on the 3130/3130xl instrument.
A full 96-well plate requires 24 runs to inject all the samples once.
pages 35, 55
Check the level of polymer in the polymer supply bottle to ensure enough is available for all scheduled runs.
page 145 Daily
page 145 page 145
Clean the 3130/3130xl instrument surfaces.
page 145
Check for dried polymer around the polymer block and clean as necessary.
page 145
Check for leaks around all fittings on the pump and lower polymer blocks. Clean the water and buffer reservoirs.
page 139 Weekly page 141
Clean the pump and lower polymer blocks.
384-Well Plates
Run 2
Run 1
Run 3
Run 4
pages 42, 142 Check the storage conditions of the used arrays. pages 22
A full 384-well plate requires 96 runs to inject all the samples once.
Check database space and hard disk space. Restart the computer and instrument. Select Replenish Polymer or Change Polymer Type Wizard to replace polymer older than one week, in the upper polymer block and capillary array. Defragment the computer hard drive.
Weekly or as needed
page 129 pages 40, 137 page 138 page 143
Monthly
page 144 page 43 See the maintenance guide.
© Copyright 2004, Applied Biosystems. All rights reserved. For Research Use Only. Not for use in diagnostic procedures. The Applied Biosystems 3130 and 3130xl Genetic Analyzers include patented technology licensed from Hitachi, Ltd. as part of a strategic partnership between Applied Biosystems and Hitachi, Ltd., as well as patented technology of Applied Biosystems. Applied Biosystems, GeneMapper, and SeqScape are registered trademarks and AB (Design) and Applera are trademarks of Applera Corporation or its subsidiaries in the U.S. and/or certain other countries. All other trademarks are the sole property of their respective owners. 11/2004
www.appliedbiosystems.com
DRAFT November 4, 2004 9:59 am, 4362825A.fm
Part Number 4362825 Rev. A
DRAFT November 4, 2004 9:59 am, 4362825A.fm
See Chapter 1
Preparing the Instrument
Applied Biosystems 3130/3130xl Genetic Analyzers Quick Reference Card
1
Power on computer and log on.
2
Power on 3130/3130xl instrument; wait for solid green light.
3
Start 3130/3130xl Data Collection Software.
4
Select Start > Programs > Applied Biosystems > Data Collection > Run 3130 Data Collection v3.0 or Run 3130xl Data Collection v3.0.
Array installed?
Wait for service console to start all four application services (green squares).
YES Select Install Array Wizard
See Chpt. 4 (DNA Sequencing), Chpt. 5 (SeqScape Software), and Chpt. 6 (Fragment Analysis) See Chapter 2 (Spatial) and Chapter 3 (Spectral)
NO: Click REJECT
Click:
1
Spatial calibration done?
GA Instruments ga3130 or ga3130xl <Instrument Name> Spatial Run Scheduler
NO
Select spatial protocol.
Click Start .
Does data pass?
Review data.
YES: Click ACCEPT
YES
Click:
2
Spectral calibration for dye set and array length done?
GA Instruments ga3130 or ga3130xl Protocol Manager
NO
Click NEW , complete Instrument Protocol dialog box for spectral type.
NO Click Plate Manager, then click NEW . Complete and save plate record for spectral calibration application.
Prepare and mount plate on autosampler.
Click
<Instrument Name> Run Scheduler
Click FIND ALL , select the plate, link plate and start run.
Click Spectral Viewer to review data.
Click:
1
Instrument protocol created and saved?
GA Instruments ga3130 or ga3130xl Protocol Manager
NO
In the Instrument Protocols section, click NEW .
Complete: • Name • Type • Run Module • Dye set
In the Analysis Protocols section, click NEW .
Complete each tab: • General • Basecalling • Mixed Bases • Clear Range • Filter Settings (SeqScape only)
Click OK to save.
Complete each tab: • General • Analysis • Destination • Naming • Automated Processing (GeneMapper only)
Click OK to save.
Click OK to save.
YES
Click:
2
Analysis protocol created and saved? Sequencing only
GA Instruments ga3130 or ga3130xl Protocol Manager
NO
YES
Click:
3
Results Group created and saved?
NO
GA Instruments Results Group
In the Results Group section, click NEW .
YES
Click:
4
Create and save a plate record.
1
Prepare and assemble plate(s); mount on autosampler.
GA Instruments ga3130 or ga3130xl Plate Manager
Click NEW . Complete New Plate dialog box, then click OK .
Complete plate record.
Click OK to save.
Click:
2
Search and select plate record, then link plate.
3
Click , then click OK in Start Processing dialog box.
4
Start Autoanalysis Manager v3.0 for analysis using either SeqScape ® or GeneMapper ® Software.
5
Review data in appropriate analysis software.
Optional
Does data pass? YES
YES
®
See Chapter 7
Running the Instrument
Setting Up the 3130/3130xl Genetic Analyzer Data Colllection Software
Performing Spatial and Spectral Calibration
NO
GA Instruments ga3130 or ga3130xl <Instrument Name> Run Scheduler
Click FIND ALL or use Advanced to search plate record list.
View data during run using the Cap/Array viewer.
Select Start > Applied Biosystems > Autoanalysis Manager v3.0.
www.appliedbiosystems.com
Link the plate: a. Select plate record from list. b. Click plate position indicator.
Link additional plate, if applicable.