Agilent Technologies DNA 7500 Manual

Agilent Technologies

Agilent

DNA 7500 and

DNA 12000

Kit Guide

Notices

2016

No part of this manual may be reproduced

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United States and international copyright

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Manual Part Number

G2938-90024 Rev. C

Edition

12/2016

Printed in Germany

Agilent Technologies

Hewlett-Packard-Strasse 8

76337 Waldbronn

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For Research Use Only

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Contents

1 Agilent DNA 7500 and DNA 12000 Kit 4

2 Equipment Required for a DNA 7500 and DNA 12000 Assay 6

3 Setting up the Assay Equipment and Bioanalyzer 7

Setting up the Chip Priming Station 8

Setting up the Bioanalyzer 9

Vortex Mixer 9

Starting the 2100 Expert Software 10

4 Essential Measurement Practices 11

5 Agilent DNA 7500 and DNA 12000 Assay Protocol 12

Preparing the Gel-Dye Mix 12

Loading the Gel-Dye Mix 14

Loading the Marker 15

Loading the Ladder and the Samples 16

Inserting a Chip in the Agilent 2100 Bioanalyzer 17

Starting the Chip Run 18

Cleaning Electrodes after a Chip Run 20

6 Checking Your Agilent DNA 7500 and DNA 12000 Assay Results 21

DNA 7500 and DNA 12000 Ladder Well Results 21

DNA 7500 and DNA 12000 Sample Well Results 23

Agilent Technologies

Agilent DNA 7500 and DNA 12000 Kit 1

Agilent DNA 7500 Kit (reorder number 5067-1506) Agilent DNA 12000 Kit (reorder number 5067-1508)

DNA Chips DNA Chips

25 DNA Chips 25 DNA Chips

1 Electrode Cleaner 1 Electrode Cleaner

DNA 7500 Reagents (reorder number 5067-1507)&

Supplies

DNA 12000 Reagents (reorder number 6067-1509)&

Supplies

(yellow) DNA 7500 Ladder (yellow) DNA 12000 Ladder

(green) DNA 7500 Markers (2 vials) (green) DNA 12000 Markers (2 vials)

(blue) DNA Dye Concentrate

(1 vial) (blue) DNA Dye Concentrate

(1 vial)

(red) DNA Gel Matrix (3 vials) (red) DNA Gel Matrix (3 vials)

3 Spin Filters 3 Spin Filters

Syringe Kit Syringe Kit

1 Syringe 1 Syringe

“This product is provided under a license by Life Technologies Corporation to Agilent Technologies. The purchase of this

product conveys to the buyer the non-transferable right to use the purchased amount of the product and components of

the product only as described in accompanying product literature. The sale of this product is expressly conditioned on the

buyer not using the product or its components (1) in manufacturing; (2) to provide a service, information, or data to an un-

affiliated third party for payment; (3) for therapeutic, diagnostic or prophylactic purposes; (4) to resell, sell or otherwise

transfer this product or its components to any third party, or use for any use other than use in the subfields of research

and development, quality control, forensics, environmental analysis, biodefense or food safety testing. For information on

purchasing a license to this product for purposes other than described above contact Life Technologies Corporation,

Cell Analysis Business Unit, Business Development, 29851 Willow Creek Road, Eugene, OR 97402, Tel: (541) 465-8300.

Fax: (541) 335-0354.”

Agilent DNA 7500 and DNA 12000 Kit

Table 1 Physical Specifications

Type Specification

Analysis time 30 minutes

Samples per chip 12

Sample volume 1 µL

Kit stability 4 months (see box for storage temperatures)

Kit size 12 samples/chip = 300 samples/kit

Table 2 Analytical Specifications

Type Agilent DNA 7500 Agilent DNA 12000

Sizing range 100 – 7500 bp 100 – 12000 bp

Sizing resolution 100 – 1000 bp: 5 %

1000 – 7500 bp: 15 %

100 – 1000 bp: 5 %

100 – 12000 bp: 15 %

Sizing accuracy ± 10 % ± 15 %

Sizing reproducability 5 % CV 5 % CV

Quantitation

accuracy

Determined using the respective DNA ladder as sample

20 % 25 %

Quantitation

reproducibility

100 – 1000 bp: 10 % CV

1000 – 7500 bp: 5 % CV

100 – 1000 bp: 15 % CV

1000 – 12000 bp: 10 % CV

Quantitative range

0.5 – 50 ng/µl 0.5 – 50 ng/µl

Maximum salt 250 mM for KCl

15 mM for MgCl

250 mM NaCl

250 mM for KCl

15 mM for MgCl

250 mM NaCl

Agilent Technologies

Equipment Required for a DNA 7500 and

DNA 12000 Assay 2

Equipment Supplied with the Agilent 2100 Bioanalyzer

•Chip priming station (reorder number 5065-4401)

•IKA vortex mixer

Additional Material Required (Not Supplied)

•Pipettes (10 μl, 100 μl and 1000 μl) with compatible tips

•Microcentrifuge tubes:

•0.5 ml for sample preparation

•1.5 ml for gel-dye mix preparation

•Microcentrifuge

Check the Agilent Lab-on-a-Chip webpage for details on assays:

www.agilent.com/chem/labonachip.

Agilent Technologies

Setting up the Assay Equipment and

Bioanalyzer 3

Before beginning the chip preparation protocol, ensure that the chip priming

station and the bioanalyzer are set up and ready to use.

You have to

•replace the syringe at the chip priming station with each new kit

•adjust the base plate of the chip priming station

•adjust the syringe clip at the chip priming station

•set up the vortex mixer

•finally, make sure that you start the software before you load the chip.

NOTE

The DNA 7500 and DNA 12000 assay is a high sensitivity assay. Please read this guide

carefully and follow all instructions to guarantee satisfactory results.

Setting up the Assay Equipment and Bioanalyzer

Setting up the Chip Priming Station

1Replace the syringe:

aUnscrew the old syringe from the lid of the chip

priming station.

bRelease the old syringe from the clip. Discard the old

syringe.

cRemove the plastic cap of the new syringe and insert it

into the clip.

dSlide it into the hole of the luer lock adapter and screw

it tightly to the chip priming station.

2Adjust the base plate:

aOpen the chip priming station by pulling the latch.

bUsing a screwdriver, open the screw at the underside

of the base plate.

cLift the base plate and insert it again in position C.

Retighten the screw.

3Adjust the syringe clip:

aRelease the lever of the clip and slide it up to the top

position.

NOTE

Replace the syringe with each new reagent kit.

Setting up the Assay Equipment and Bioanalyzer

Setting up the Bioanalyzer

1Open the lid of the bioanalyzer and make sure that the electrode cartridge is

inserted in the instrument. If not, open the latch and insert the electrode

cartridge.

Figure 1 Electrode cartridge inserted in the instrument (graphic shows an

example).

2Remove any remaining chip.

Vortex Mixer

IKA - Model MS3

1To set up the vortex mixer, adjust the

speed knob to 2400 rpm.

Setting up the Assay Equipment and Bioanalyzer

Starting the 2100 Expert Software

To start the software:

1Go to your desktop and double-click the following icon.

The screen of the software appears in the Instrument context. The icon in the

upper part of the screen represents the current instrument-PC

communication status:

2If more than one instrument is connected to your PC, select the instrument

you want to use in the tree view.

Lid closed, no chip or chip

empty

Lid open

Dimmed icon: no

communication

Lid closed, chip inserted,

DNA or demo assay

selected

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