Agilent Technologies DNA 7500 Manual

Agilent Technologies
Agilent
DNA 7500 and
DNA 12000
Kit Guide

Notices
© Agilent Technologies, Inc. 2000-2015,
2016
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Manual Part Number
G2938-90024 Rev. C
Edition
12/2016
Printed in Germany
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For Research Use Only
Not for use in diagnostic procedures

3
Contents
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

4
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
(1 vial) (blue) DNA Dye Concentrate
1
(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
1
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5
Agilent DNA 7500 and DNA 12000 Kit
1
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
1
1
Determined using the respective DNA ladder as sample
20 % 25 %
Quantitation
reproducibility
1
100 – 1000 bp: 10 % CV
1000 – 7500 bp: 5 % CV
100 – 1000 bp: 15 % CV
1000 – 12000 bp: 10 % CV
Quantitative range
1
0.5 – 50 ng/µl 0.5 – 50 ng/µl
Maximum salt 250 mM for KCl
15 mM for MgCl
2
250 mM NaCl
250 mM for KCl
15 mM for MgCl
2
250 mM NaCl

6
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.

7
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.

8
3 Setting up the Assay Equipment and Bioanalyzer
Setting up the Chip Priming Station
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.

9
Setting up the Assay Equipment and Bioanalyzer
3
Setting up the 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.

10
3 Setting up the Assay Equipment and Bioanalyzer
Starting the 2100 Expert Software
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