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

DRAFTApril 10, 2005 7:24 pm, 4359471 B.fm

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

DRAFTApril 10, 2005 7:24 pm, 4359471 B.fm

Page 2

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

DRAFTApril 10, 2005 7:24 pm, 4359471 B.fm

Page 3

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.

Check for and remove all bubbles from the:

• Lower polymer block• Interconnecting tubing• Polymer cap tubing• Polymer block channels

Check the loading-end header to ensure that the capillary tips are not crushed or damaged.

Check the lower polymer block to ensure that it fits securely on the instrument.

Check for leaks around all fittings on the pump and lower polymer blocks.

Task Frequency

Clean the:

• Water, waste, and buffer reservoirs with warm water and a thorough distilled/deionized water rinse

• Complete polymer path including the pump and lower polymer blocks

Weekly or when the polymer is changed

Flush the polymer delivery pump water trap. Weekly

Replace the polymer in the bottle, pump block, and capillary array.

Weekly or as needed

Restart the computer and instrument.

Check the storage conditions of the used arrays.

Weekly

Check database space and hard disk space.

Task Frequency

Clean the:

• Drip tray• Instrument surfaces

As needed

Change the array.

Remove any dried polymer from the capillary tips. Use a lint-free wipe moistened with deionized water.

Defragment the computer hard drive. As needed or monthly

DRAFTApril 10, 2005 7:24 pm, 4359471 B.fm

Page 4

48-Capillaries Load Map

96-Well Plate Load Map

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DRAFTApril 10, 2005 7:24 pm, 4359471 B.fm

Page 5

96-capillaries Load Map

96-Well Plate Load Map

384-Well Plate Load Map

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DRAFTwww.appliedbiosystems.com

© Copyright 2005, Applied Biosystems. All rights reserved.

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.

04/2005

Part Number 4359471 Rev. B

April 10, 2005 7:24 pm, 4359471 B.fm