DRAFT April 10, 2005 7:24 pm, 4359471 B.fm Applied Biosystems 3730/3730xl DNA Analyzer Quick Reference Card This quick reference card supplements the Applied Biosystems 3730/3730xl DNA Analyzers Getting Started Guide (PN 4354976). For safety guidelines, refer to the 3730/3730xl DNA Analyzers Getting Started Guide. IMPORTANT! Refer to the Material Safety Data Sheets (MSDSs) for chemicals listed in bold type for information. Wear gloves any time you handle the capillary array, septa, buffer reservoirs, polymer bottles, polymer blocks, interconnect tubing, and bottle cap tubing. Starting the Applied Biosystems 3730/ 3730xl System Do not rename the computer after the Applied Biosystems 3730/3730xl DNA Analyzer Data Collection Software has been installed. Doing so may cause the 3730/3730xl Data Collection software to malfunction. IMPORTANT! Be sure to start the computer workstation before starting the Applied Biosystems 3730/3730xl DNA Analyzers. Step 1: Start the computer workstation 1A. Power on the monitor. 1B. Power on the computer. The Begin Logon dialog box opens. 1C. Enter the user name and password (there is no default password) for the Data Collection Software logon. Step 2: Start the 3730/3730xl Instrument Wear gloves any time you handle the capillary array, septa, buffer reservoirs, polymer bottle, polymer block, interconnect tubing, and bottle cap tubing. 2A. Ensure that the computer is powered on. 2B. On the instrument, ensure that the: • Oven door is closed • Instrument door is closed • Stacker drawer is closed • Buffer, water, and waste trays are loaded. 2C. Turn on the instrument. Step 3: Prerun Setup 3A. Attach a clean, dry lower polymer block to the instrument. 3B. Install the capillary array using the Install Capillary Array wizard. IMPORTANT! When analyzing with KB ™ basecaller in Sequencing Analysis software, use the Capillary Array wizard to input the applicable capillary length information. 3C. Install the polymer bottle. See the Change Polymer wizard. 3D. Prepare the 1✕ running buffer . 3E. Fill the cathode buffer , water, and waste reservoirs with 80 mL of the appropriate liquid. 3F. Fill the clean, dry anode buffer reservoir with 67 mL of 1✕ running buffer . IMPORTANT! The meniscus should line up just under the red fill line before you install the anode buffer reservoir on the instrument (see figure below). Note: If the anode buffer jar buffer overflows as polymer is added, discard and then replace with fresh 1X running buffer. The anode buffer jar could overflow during bubble clearing. Polymer Blocks Assemble the lower polymer block as shown below: GR2209 Meniscus should be just under the fill line Anode buffer jar Pump block Polymer block interconnect tubing assembly Lower polymer block Check valve Polymer bottle cap assembly Polymer bottle Buffer jar Anode electrode Buffer pin valve Applied Biosystems 3730/3730xl DNA Analyzer
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Applied Biosystems 3730/3730xl DNA Analyzer
Applied Biosystems 3730/3730xl DNA Analyzer Quick Reference Card
This quick reference card supplements the Applied Biosystems 3730/3730xl DNA Analyzers Getting Started Guide (PN 4354976). For safety guidelines, refer to the 3730/3730xl DNA Analyzers Getting Started Guide.
IMPORTANT! Refer to the Material Safety Data Sheets (MSDSs) for chemicals listed in bold type for information. Wear gloves any time you handle the capillary array, septa, buffer reservoirs, polymer bottles, polymer blocks, interconnect tubing, and bottle cap tubing.
Starting the Applied Biosystems 3730/3730xl System
Do not rename the computer after the Applied Biosystems 3730/3730xl DNA Analyzer Data Collection Software has been installed. Doing so may cause the 3730/3730xl Data Collection software to malfunction.
IMPORTANT! Be sure to start the computer workstation before starting the Applied Biosystems 3730/3730xl DNA Analyzers.
Step 1: Start the computer workstation
1A. Power on the monitor.
1B. Power on the computer. The Begin Logon dialog box opens.
1C. Enter the user name and password (there is no default password) for the Data Collection Software logon.
Step 2: Start the 3730/3730xl Instrument
Wear gloves any time you handle the capillary array, septa, buffer reservoirs, polymer bottle, polymer block, interconnect tubing, and bottle cap tubing.
2A. Ensure that the computer is powered on.
2B. On the instrument, ensure that the:
• Oven door is closed
• Instrument door is closed
• Stacker drawer is closed
• Buffer, water, and waste trays are loaded.
2C. Turn on the instrument.
Step 3: Prerun Setup
3A. Attach a clean, dry lower polymer block to the instrument.
3B. Install the capillary array using the Install Capillary Array wizard.
IMPORTANT! When analyzing with KB™ basecaller in Sequencing Analysis software, use the Capillary Array wizard to input the applicable capillary length information.
3C. Install the polymer bottle. See the Change Polymer wizard.
3D. Prepare the 1✕ running buffer.
3E. Fill the cathode buffer, water, and waste reservoirs with 80 mL of the appropriate liquid.
3F. Fill the clean, dry anode buffer reservoir with 67 mL of 1✕ running buffer.
IMPORTANT! The meniscus should line up just under the red fill line before you install the anode buffer reservoir on the instrument (see figure below).
Note: If the anode buffer jar buffer overflows as polymer is added, discard and then replace with fresh 1X running buffer. The anode buffer jar could overflow during bubble clearing.
Polymer BlocksAssemble the lower polymer block as shown below:
GR
2209
Meniscus should be just under the fill line
Anode buffer jar
Pump block
Polymer block interconnect tubing assembly
Lower polymer block
Check valve
Polymer bottle cap assembly
Polymer bottle
Buffer jar
Anode electrode
Buffer pin valve
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Checking for BubblesBubbles can collect where the channels join. The following figure illustrates where bubbles may collect.
Removing Air Bubbles from the Polymer Block
To remove air bubbles, select Wizards > Bubble Remove Wizard, then follow the instructions in the wizard.
Supported Dye SetsApplied Biosystems 3730/3730xl Data Collection Software v3.0 supports:
Suggested Loading Volumes
CHEMICAL HAZARD. Formamide causes eye, skin, and respiratory tract irritation. It is a possible reproductive and birth defect hazard. Read the MSDS, and follow the handling instructions. Wear appropriate protective eyewear, clothing, and gloves.
Prepare the formamide:size-standard mix. For loading a:
• 96-well plate, use 10 µL per well (minimum volume).
• 384-well plate, use 5 µL per well (minimum volume).
Sealing Plates with Heat Seal Film
384-Well Plate Assembly Using a Heat-Sealed Plate
Sealing Plates with Septa
Septa-Based Plate Assembly
Application Chemistry Dye Set Chemistry File
Fragment Analysis
ABI PRISM® Linkage Mapping Set v2.5
G5 Matrix Standard
G5-RCT
Sequencing BigDye® Terminator v1.1
E-BigDyeV1 Sequencing Standard
BigDye® Terminator v3.1
Z-BigDyeV3
SNPlex™ SNPlex Chemistry
S Matrix Standard
Watch for bubbles:• At the array ferrule tip
• In all tubing
• In the elbow (internal channel) of the lower block
GR
2196
Plate retainer
Heat seal film
Heat-sealed sample plate
Gray plate base
GR
2199
Assembled components
GR
2194
Black plate base
Sample plate
Plate septum
Plate retainer
Align the septum holes with the plate sample holes
Align the notched corners
Plate septum
Sample plate
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Run Modules
Flushing and Filling the Water TrapFlush the polymer delivery pump water trap at least once per week to wash out any diluted polymer that may have passed through the water trap seals. Some air bubbles in the water trap are acceptable and do not affect performance. Leave the trap filled with either distilled or deionized water.
Note: The figure below shows a beaker being used to catch the trap’s flushed waste fluid.
To flush the water seal trap:
1. Fill the supplied 20-mL, all-plastic Luer lock syringe (PN 4324463) with distilled or deionized water. Expel any bubbles from the syringe.
Note: Do not use a syringe smaller than 20 mL. Doing so may generate excessive pressure within the trap.
2. Attach the syringe to the forward-facing Luer fitting at the top of the pump block. Hold the fitting with one hand while threading the syringe onto the fitting with the other hand.
3. Open the Luer fitting by grasping the body of the fitting and turning it and the attached syringe approximately one-half turn counterclockwise.
4. Open the exit fitting at the top left side of the pump block by turning it approximately one-half turn counterclockwise.
5. While holding an empty tube or beaker under the exit fitting, flush the trap at a flow rate of 5 mL per 30 sec by pushing steadily on the syringe plunger.
DO NOT USE EXCESSIVE FORCE when you push the syringe plunger. Excessive force may damage the trap seals. Take approximately 30 seconds to flush 5 mL of either distilled or deionized water through the trap.
Part Numbers for High-Use Items
Analysis TypeCapillary
Array Length (cm)
Run Module
Fragment analysis 36 GeneMapper36_POP7
50 GeneMapper50_POP7
Extra long-read DNA sequencing
50 XLRSeq50_POP7
Long DNA sequencing 50 LongSeq50_POP7
Fast-read DNA sequencing
50 FastSeq50_POP7
Standard-read DNA sequencing
36 StdSeq36_POP7
Rapid-read DNA sequencing
36 RapidSeq36_POP7
SNPlex 36 cm 36 HTSNP36_POP7_V3
SNPlex 50 cm 50 HTSNP50_POP7
Item Part No
3730 36-cm capillary array 4331247
3730 50-cm capillary array 4331250
3730xl 36-cm capillary array 4331244
3730xl 50-cm capillary array 4331246
3700/3730 BigDye Terminator v3.1 Sequencing Std
4336943
3700/3730 BigDye Terminator v1.1 Sequencing Std
4336799
Matrix Standard Set DS-33 4345833
HiDi™ formamide, 25 mL 4311320
POP™-7 (1 bottle of 25-mL) 4363929
POP™-7 (10 bottles of 25-mL each) 4363935
POP™-7 (30 bottles of 25-mL each) 4335611
Buffer (10✕) with EDTA, 500 mL 4335613
Buffer (10✕ with EDTA, 4 L 4318976
96-well sample plates w/bar code 4306737
96-well sample plates, no bar code N801-0560
96-well plate septa 4315933
96-well plate base (septa sealed) 4334873
96-well plate base (heat sealed) 4334875
96-well plate retainer (septa sealed) 4334869
96-well and 384-well plate retainer (heat sealed) 4334865
384-well sample plates with barcode 4309849
384-well plate septa 4315934
384-well plate base (septa-sealed) 4334874
384-well plate base (heat-sealed) 4334877
384-well plate retainer (septa-sealed) 4334868
Heat seal film, 3-mil 4337570
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Instrument Maintenance Schedule IMPORTANT! Refer to the Material Safety Data sheets (MSDSs) for chemicals listed in bold for safety information. Wear gloves any time you handle the capillary array, septa, buffer reservoirs, polymer bottles, polymer blocks, interconnect tubing, and bottle cap tubing.
Daily Maintenance
Weekly Maintenance
As Needed Maintenance
Task Frequency
Replace the appropriate liquid in the water, waste, and 1✕ running buffer reservoirs on the instrument.
IMPORTANT! Do not top off buffer/water/waste fluids after a run. Empty the reservoir fluids every 48 hours and then refill with fresh solutions for optimal performance.
Every 24 to 48 hours
Check for dried polymer around the polymer block and clean as necessary.
Daily, or before each batch of runs
Ensure adequate:
• Buffer and water levels in the cathode reservoirs
• Buffer level in the anode buffer jar• Polymer level in the bottle for scheduled
runs
Ensure that the:
• Plate assemblies are put together properly. The holes in the plate retainer must align with the holes in the septa; otherwise the capillary tips will be damaged.
• Reservoir plate assemblies are positioned on the plate deck properly. Plates should sit snugly on the deck. Never use warped plates.
For Research Use Only. Not for use in diagnostic procedures.
The Applied Biosystems 3730 and 3730xl DNA 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.
ABI PRISM, Applied Biosystems, BigDye, and GeneMapper are registered trademarks and AB (Design), Applera, Hi-Di, KB, and POP 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.