Bioruptor NGS User manual

USER MANUAL
Version 1.5
Bioruptor® NGS
Cat. No. UCD-600
Bioruptor®
Sonication System

Guarantee
Limited one year global warranty
Diagenode guarantees all products from any manufacturing defects as we rigorously test all products to meet strict
quality standards. Diagenode warrants that all standard components of its instruments will be free of defects in materials
and workmanship for a period of one (1) year from the date that the warranty period begins, unless the original quotation
or accompanying documentation states a different warranty period. All warranty periods begin on the date of delivery
and apply only to the first purchaser of the product. If a manufacturing defect arises and a valid claim is received within
the warranty period, Diagenode, at its discretion, will repair or replace the product in accordance with the warranty
terms and conditions stated herein. In case of repair or replacement of a product under warranty, Diagenode will cover
the expenses to return the repaired or replacement product.
This warranty covers only manufacturing defects and does not cover any damage caused by misuse, lack of compliance
to recommendations stated in the manual, neglect, accidents, abrasion, or exposure to extreme temperatures, chemical
solvents, or acids. We strongly recommend that maintenance or repairs of Diagenode’s products are performed by our
approved Diagenode service center. Improper or incorrectly performed maintenance or repairs will void the warranty.
Technical Assistance & Ordering Information
Diagenode s.a. BELGIUM | EUROPE
Avenue de l’hôpital,1
Tour GIGA, 3rd Floor
4000 Liège - Belgium
Tel: [phone]
Fax: [phone]
[e-mail]
[e-mail]
Diagenode Inc. USA | NORTH AMERICA
400 Morris Avenue, Suite #101
Denville, NJ 07834 - USA
Tel: [phone]
Fax: [phone]
[e-mail]
[e-mail]
For a complete listing of Diagenode’s international distributors, visit:
http://www.diagenode.com/en/support/distributors.php
For the rest of the world, please contact Diagenode s.a.

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DIAGENODE BIORUPTOR® NGS USER MANUAL
Diagenode Inc. North America / Phone: [phone] // Fax: [phone] // Mail: [e-mail]
Critical Steps for Maintenance and Efficient Shearing ....................................4
Introduction .........................................................................5
Bioruptor® Technical Specifications ....................................................6
Getting to Know Your Bioruptor® NGS System ............................................7
Bioruptor® Components Overview ...................................................7
Bioruptor® Water Cooler ...........................................................7
Connector kit for Water Cooler ......................................................8
Water bath ......................................................................8
Motorized lid .....................................................................9
Metallic Soundproof Box ...........................................................9
Tube holders .....................................................................9
Equipment Installation ..............................................................10
Installation overview .............................................................10
Installing the Bioruptor® NGS System with Water Cooler ...............................11
Controlling the Sonication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Tube Holders and tubes ..............................................................15
Standard protocol for DNA Shearing ...................................................15
Operating Conditions .............................................................15
Important comments about DNA shearing ...........................................16
Bioruptor® Packing Instructions ......................................................18
Related Products ...................................................................19
DNA Methylation Kits .............................................................19
Antibodies ......................................................................19
Ordering Information ........................................................Back Cover
Contents

PAGE 4 DIAGENODE BIORUPTOR® NGS USER MANUAL
Europe Diagenode sa / CHU - Tour GIGA - B34 - 3e étage // Avenue de l’Hôpital, 1 // 4000 Liège (Sart Tilman) // Belgium // Phone: [phone] // Mail: [e-mail]
Critical Steps for Maintenance and
Efficient Shearing
General warnings
• DO NOT turn on the instrument without water.
• DO NOT tilt the water bath. To change the water, use either the plastic pump or a beaker.
Water bath levels
• The water bath must be filled with distilled water to the fill line. Fill line replacement stickers can be obtained by
contacting Diagenode.
• Change water at least once per week.
Water bath temperature
• Optimal temperature for sonication is 4°C. Sample temperature should not exceed 10°C.
• The Diagenode Water Cooler (Cat. No. BioAcc-Cool) has to be used in combination with the Connector kit for Water
Cooler (Bioruptor® Plus & NGS) (Cat. No. VB-100-0001) to guarantee the automatic temperature control of the water
bath during the entire sonication process.
Magnetic Ultrasound Emitter Maintenance
• The ultrasound waves are created from a series of magnets that are attached to the water tank. This system is very
sensitive to the heat generated during a run.
• Do not exceed 2 hours of total sonication per run. It is critical that the machine is allowed to cool at least 20 minutes
between runs. Damage resulting from non compliance to manual instructions will void the warranty and shorten the
lifespan of the machine.
• Ultrasound Emitters can be damaged by tilting or jarring the machine. Exercise care if moving water tank.
Validated tubes for the Bioruptor® NGS
• DNA shearing: Bioruptor® NGS 0.65 ml Microtubes for DNA Shearing (Cat.No. WA-005-0500).
Fitting 0.65 ml tubes in the tube holder
1. Place the tubes on the corresponding tube holder (0.5/0.65 ml tube holder – Cat. No. UCD-pack 0.5). Never leave
empty spaces in the tube holder. Fill the empty spaces with tubes containing the same volume of water. Screw the lid
on the tube holder without over-tightening the lid.
2. Carefully place the tube holder on the holding plate.
3. During sonication, samples must remain at the bottom of the tube. If needed, briefly centrifuge samples during
sonication after pausing the run.
Bioruptor

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DIAGENODE BIORUPTOR® NGS USER MANUAL
Diagenode Inc. North America / Phone: [phone] // Fax: [phone] // Mail: [e-mail]
Introduction
Diagenode’s Bioruptor® NGS uses a gentle method of sonication to retain the integrity of DNA. The Bioruptor® Sonication
System uses a water bath to generate indirect sonication waves, which emanate from an ultrasound element below the water
tank. Because the system is gentler than other sonicators, the Bioruptor® produces better and more consistent results than
with harsher sonication methods. Up to 12 closed tubes can be sonicated in parallel and the continuous rotation of tubes
allows even distribution of the energy for efficient sonication. The Bioruptor® enables automation of sonication, guaranteeing
higher reproducibility of results.
The effect of ultrasound on biological samples.
The Bioruptor® sonication system uses ultrasound to create focused
mechanical stress to shear DNA. Ultrasound waves pass through
the sample expanding and contracting the liquid. During expansion,
negative pressures pull the molecules away from one another to form a
cavity or bubble. This process is called cavitation. The bubble continues
to absorb energy until it can no longer sustain itself and implodes. This
produces intense focused shearing forces, that disperse and break
biomolecules. The fragmentation of DNA takes place as a consequence
of this mechanical stress or shear.
With the Bioruptor®, the entire volume of water present in the water
bath is exposed to ultrasound, allowing all the samples to be efficiently sonicated in parallel (Figure 1).
Use of Bioruptor® by pregnant women
Exposure to 30-60 kHz sound waves has not been shown to be harmful to human health. However, we would recommend
avoiding unnecessary exposure. Diagenode recommends that pregnant women should not be exposed to 30-60 kHz wave
lengths for a long period of time.
Fig 1. Propagation in 0.65 ml tubes
Ultrasound
Transducer

PAGE 6 DIAGENODE BIORUPTOR® NGS USER MANUAL
Europe Diagenode sa / CHU - Tour GIGA - B34 - 3e étage // Avenue de l’Hôpital, 1 // 4000 Liège (Sart Tilman) // Belgium // Phone: [phone] // Mail: [e-mail]
Bioruptor® Technical Specifications
Bioruptor® NGS
Power Supply 100-230V, 50/60Hz, 2.1A (EU) / 4.2A (US)
Ultrasonic wave frequency 30-60 kHz
Ultrasonic wave output power 25-210 W
Transformer 220/100V dimensions Internal
Control unit dimensions 350(W) x 260(D) x 165(H) mm
Sonication unit dimensions (water bath) 175(W) x 160(D) x 280(H) mm
Soundproof box dimensions 350(W) x 350(D) x 500(H) mm
Water bath volume 750 ml
Timer Digital
Possibility to control water flow via connector kit for water cooler Yes
Tube holder Available for 0.65 ml tubes
Total weight 30 kg
Number of samples to be processed simultaneously 0.65 ml tubes – 12

PAGE 7
DIAGENODE BIORUPTOR® NGS USER MANUAL
Diagenode Inc. North America / Phone: [phone] // Fax: [phone] // Mail: [e-mail]
Getting to Know Your Bioruptor®
NGS System
Bioruptor® Components Overview
Power Cable (EU) Power Cable (US) Control Unit Cable
Control Unit Water bath Motorized lid Soundproof box
Tube holder
Bioruptor® Water Cooler
To learn more, please visit www.diagenode.com

PAGE 8 DIAGENODE BIORUPTOR® NGS USER MANUAL
Europe Diagenode sa / CHU - Tour GIGA - B34 - 3e étage // Avenue de l’Hôpital, 1 // 4000 Liège (Sart Tilman) // Belgium // Phone: [phone] // Mail: [e-mail]
Connector kit for Water Cooler
To learn more, please visit www.diagenode.com
Water bath
The water bath is a critical component of the instrument. The generators below the tank
produce ultrasonic waves which are then transferred through water. The water bath
requires special handling and care as described below.
Handling
The water bath must remain upright at all times, especially when moved. Tilting the water
bath or handling roughly may damage the ultrasound emitter component, resulting in a
substantial drop in sonication efficiency. If transportation of the apparatus is required after
initial set-up, it is imperative to keep the tank at a right angle to the ground during the
transport at all times.
Water level and quality
The level of the water has been optimized and should always reach the red line (sticker on the wall of the tank). Distilled
water should be used to fill the tank. Replacement stickers can be obtained from Diagenode.
Water temperature
The water in the water bath must be kept at 4°C. Ultrasonic waves produced by the Bioruptor® generate heat. Drop
off in sonication efficiency will occur above 10°C. To ensure preservation of the samples and to prevent damage to the
instrument, it is necessary to start the sonication process with cold water and to keep it at 4°C during the sonication
process.
Solenoid valve with
connector cable
Plastic connector for
motorized lid
Male nozzle connector Tubing
Open-end wrench N° 14 Open-end wrench N°17 Plumbing Teflon Spare Tubing

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DIAGENODE BIORUPTOR® NGS USER MANUAL
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Automatic temperature control
The Bioruptor® Water Cooler (Cat. No. BioAcc-Cool) has to be used in combination with the Connector kit for Water
Cooler (Bioruptor® Plus & NGS) (Cat. No. VB-100-0001) to guarantee the automatic temperature control of the water
bath during the entire sonication process (Figure 2). The cooling system features two pumps and produces a regular
water flow to maintain a constant water level in the tank. The regulating valve (Connector kit for Water Cooler) ensures
that water will only be replaced during the off cycle to avoid any interference between water flow and the sonication
process.
Note: You may permanently install the Bioruptor® in a cold room, though this is not sufficient to avoid the temperature
increase during sonication.
Motorized Lid
The motorized lid, along with the gear plate accessory, keeps the sample tubes in constant
rotation and ensures optimal position in the water bath during sonication. When in motion, do
not hamper the rotation of the blue gear plate. Avoid the immersion of the motor into the water.
Do not heat the blue plastic as it will warp.
Metallic Soundproof Box
This metallic soundproof box absorbs very efficiently the noise generated by the ultrasonic
waterbath.
Tube Holders
The 0.5/0.65 ml tube holder allows for simultaneous sonication of up to 12 DNA samples. The
optimal volume for DNA shearing is 100 µl and Bioruptor® NGS 0.65 ml Microtubes for DNA
Shearing (Cat. No. WA-005-0500) are recommended for processing your samples.
Bioruptor® Water Cooler Water bath Control Unit
Connector kit for Water Cooler
Bioruptor® NGS
Fig 2. Setup of the Bioruptor® NGS System including Bioruptor® Water Cooler and Connector kit for Water cooler.

PAGE 10 DIAGENODE BIORUPTOR® NGS USER MANUAL
Europe Diagenode sa / CHU - Tour GIGA - B34 - 3e étage // Avenue de l’Hôpital, 1 // 4000 Liège (Sart Tilman) // Belgium // Phone: [phone] // Mail: [e-mail]
Equipment Installation
The following pages contain information on installing your particular Bioruptor® NGS model. This equipment must only
be installed by personnel after reading this section. Consider all hazards even though no particular hazards have been
identified during installation. Before starting installation work, turn the main switch off (beyond power connection) and
secure the unit against being re-energized. No special tools are required. Three (3) square meters are needed to set-up
the Bioruptor®.
Devices are designed to be safe under the following conditions:
Installation overview
• Indoor use
• Altitude up to 2,000 meters
• Operating external temperature 0°C to 25°C
• Maximum relative humidity 80%
• Transient overvoltage typically present on the
MAINS supply
• Degree of protection: IP20
• Power plug must be grounded
• POLLUTION DEGREE 2 (Normally only non-conductive
pollution occurs. However, occasionally a temporary
conductivity caused by condensation is expected)
• Never install this equipment in a place where
environmental conditions and warnings mentioned
above are infringed
0.5/0.65 ml
tube holder
Water
Connector kit for
Bioruptor® Water Cooler
Water bath
Motorized lid
Metallic soundproof box
Bioruptor® Water Cooler
Power button
Stop button
Output selector switch
Start button
Power cord Power cord
Level meter
Digital timer
Fig 4. Schematic installation overview of the Bioruptor® NGS System in combination with the Bioruptor® Water Cooler
and the Connector kit.

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DIAGENODE BIORUPTOR® NGS USER MANUAL
Diagenode Inc. North America / Phone: [phone] // Fax: [phone] // Mail: [e-mail]
Installing the Bioruptor® NGS System with Water Cooler
1. Open the boxes and unpack all components.
3. Remove the rubber cap (upper left hole marked machine cable) from the
back of the soundproof box and feed the control unit cable through the
hole.
2. Place water bath in front
of the soundproof box.
4. Plug the control unit cable into the water bath. Make
sure the red arrow on the plug is pointing up.
5. Place the 2 black plastic connectors on the motorized lid. Both connectors can be placed into one or the other hole of
the motorized lid.
Screw the plastic nut over the motorized lid. The short red and blue pieces of tubing have to be inserted in the plastic
connectors.
IMPORTANT NOTE:
If you need to cut a part of the tubing, always use the provided Cutting Device. Never use
scissors because pieces of tubing with bad cuts generate leaks at junctions. Only properly
cut tubes can be inserted in the connectors.
The length determines the water level in the sonication bath. After installation, if the water
level is not correct, use the spare tubing and cut it at the right length (The suction pipe (red
pipe) must be set at the same level as the water level sticker is).

PAGE 12 DIAGENODE BIORUPTOR® NGS USER MANUAL
Europe Diagenode sa / CHU - Tour GIGA - B34 - 3e étage // Avenue de l’Hôpital, 1 // 4000 Liège (Sart Tilman) // Belgium // Phone: [phone] // Mail: [e-mail]
9. Connect the Bioruptor® water bath to the Water Cooler
with the red and blue tubes by inserting them in the
appropriate connectors. (Optional: Cut the length you
need for the output and input flow. Make sure there is
enough slack.) The red and blue tubes must go through
the soundproof box holes before being connected to the
motorized lid (see picture).
10. Place the water bath into the soundproof box.
a b
7. Unpack the Water Cooler and remove the black protection rubber which connects inlet and outlet.
8. Place the solenoid valve and the male nozzle connector on the outlet and inlet as shown in the picture. Use an open-
end wrench N° 14 to install the male nozzle connector and N°17 to install the solenoid valve. Seal each thread by
adding Plumbing Teflon (Note: Red connectors and red tubing will ensure the waterflow from the water bath to the
Water Cooler. Blue connector and blue tubing will ensure the waterflow from the Water Cooler to the water bath).
Bioruptor® Water Cooler & Connector kit
Location Requirements: The Water Cooler must be located underneath the Bioruptor® water bath.
Male nozzle
connector Solenoid valve
6. Place the motorized lid (a) on the top of the water bath
and connect it (b).

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DIAGENODE BIORUPTOR® NGS USER MANUAL
Diagenode Inc. North America / Phone: [phone] // Fax: [phone] // Mail: [e-mail]
17. Plug the power cable into the back side of the Bioruptor® Water Cooler. Fill the tank of the circulator with 4.5 litres
of water. Distilled water should be used in order to minimize the proliferation of bacteria.
18. Press first the power button on the back side of the Bioruptor® Water Cooler. Then press power button on the front
side of the device. Temperature can be set by pushing and turning the knob on the first side of the device.
Note: See Bioruptor® Water Cooler manual for additional information.
Now you are ready to start !
12. Plug the control unit cable into the control unit. Make
sure the red arrow on the plug is pointing up.
13. Plug the power cable into the control unit.
14. Plug the solenoid valve cable into the control unit.
15. Plug the power cable into the outlet and switch on the
power switch on the back of the control unit.
11. Place the control unit on the top of the soundproof
box.
16. Fill the water bath up to the red fill line with distilled
water.

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Europe Diagenode sa / CHU - Tour GIGA - B34 - 3e étage // Avenue de l’Hôpital, 1 // 4000 Liège (Sart Tilman) // Belgium // Phone: [phone] // Mail: [e-mail]
Controlling the Sonication
Switch on power switch (front side of control unit).
CYCLE NUMBER, TIME ON, TIME OFF and SONICATION INTENSITY are the parameters controlling the sonication. First
press + or - depending on the value to be modified. The five flashing black squares move up or down. Once you have
selected the parameter to be modified, press OK again. The five flashing black squares disappear and 2 digits start
flashing. The digits can be changed by pressing + or -. To select and save the correct number, press OK to confirm or
ESC to escape without saving the change.
Digital Timer
After the introductory message, the control screen shows the main sonication parameters in the first two lines (CYCLE
Number, Time) and summary of actions in the last line (see example below).
Buttons and their functions
Button A: Pause / restart after pausing
Button B: Press and hold this button during sonication to display T1 (total on time per cycle) and T2 (total off time per cycle).
ESC: Cancels previous selection
OK: Validate selection
- : Decrease selected parameter/move down
+ : Increase selected parameter/move up
Once all parameters are selected and confirmed, press START.
Once the run is started, “BIORUPTOR RUNNING” is displayed on the control screen.
Intensity Setting Button:
Adjusts intensity of the
generated ultrasonic waves
Start Button:
Begins sonication
Stop Button:
Cancels sonication
Power Switch: Turns
Bioruptor® on and off
Intensity Level Meter:
Visualizes the power
delivered by the control unit
to the water bath (relative
scale)
Digital Timer:
Allows the user to easily program
the sonication of samples (ON/OFF
pulse time & total time). See use of
digital timer in next section below.
BIORUPTOR RUNNING
*****************
CYCLE Num : 04/10
The display shows cycle 4 of 10. Bioruptor® NGS will sonicate as shown.
CYCLE Num : 10
Time ON : 30sec
Time OFF : 30sec
Press OK = Modify
ON
OFF
TIME
ON
TIME
OFF
CYCLE
START
Cycle number reached
(4 cycles in this example)
IMPORTANT NOTE: Minimum time of the off cycle: 30 seconds.

PAGE 15
DIAGENODE BIORUPTOR® NGS USER MANUAL
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Tube holders & tubes
For DNA shearing we highly recommend to use the tube holder for 0.5/0.65 ml tubes (Cat. No. UCD-pack 0.5)
and the corresponding Bioruptor
®
NGS 0.65 ml Microtubes for DNA Shearing (Cat. No. WA-005-0500).
To use the tube holder, remove the lower part by turning counterclockwise. Then place microtubes in the unit. Attach the
lower part to the upper part of the adaptor. To guarantee homogeneity of DNA shearing, the tube holders should always
be completely filled with tubes. Never leave empty spaces in the tube holder. Fill the empty spaces with tubes containing
the same volume of distilled water.
0.5/0.65 ml tube holder
(Cat. No. UCD-pack 0.5)
Bioruptor® NGS 0.65 ml Microtubes for DNA Shearing
(Cat. No. WA-005-0500)

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Standard protocols for DNA shearing
Operating conditions
Sample volume: 100 µl
Tubes: Bioruptor® NGS 0.65 ml Microtubes for DNA Shearing (Cat. No. WA-005-0500)
Tube holder: 0.5/0.65 ml tube holder (Cat. No. UCD-pack 0.5) for 12 x 0.65 ml tubes
Sonication buffer: TE (10 mM Tris, 1mM EDTA, pH 7.5 - 8.0)
DNA concentration: 0.001-0.02 µg/µl (0.01 µg/µl recommended)
Samples are vortexed (10-15 sec) and centrifuged (10 sec) before shearing.
For optimal results samples should be stored on ice during 10-15 minutes prior to sonication.
Temperature: 4°C – Bioruptor® Water Cooler (Cat. No. BioAcc-Cool) & Single cycle valve for Water Cooler (Cat.
No. VB-100-0001)
Power setting: H position (High)
Sonication cycle & total sonication time: varies depending on desired DNA size (see table)
Note: Recommended protocols are subject to change without notice. Additional protocols are available on demand.
115 bp
135 bp
183 bp
200 bp
234 bp
319 bp
476 bp
696 bp
848 bp
1036 bp
1230 bp
Programmable DNA size distributions, excellent
reproducibility, and high dsDNA yields with
Bioruptor® NGS
Figure shows different DNA size distributions of
sheared genomic DNA produced by varying the
duration of sonication using power setting high (H).
The different curves depict a specific Bioruptor®
NGS run, optimized to produce specific mean sizes
and size ranges for Next-Generation sequencing.
All samples were analyzed on Bioanalyzer 2100
using DNA High Sensitivity chip.

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DIAGENODE BIORUPTOR® NGS USER MANUAL
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Target size Cycle condition
(On/Off cycle time) Cycle number
150 bp 30’’/30’’ 30
200 bp 30’’/30’’ 13
400 bp* 15’’/90’’ 7 - 8
1000 bp* 5’’/90’’ 7 - 8
* For longer fragments (400 up to 1000 bp), a short centrifugation step after half of the cycle numbers can significantly improve the results.
Protocols for other size ranges (incl. longer fragments up to 1300 bp) are available on request.
Important comments about DNA shearing
The Diagenode ACT (Adaptative Cavitation Transfer technology) process is highly reproducible. However, attention must
be paid to the following treatment attributes to ensure best results:
• Tubes: At present, the recommended tube vessels are the Diagenode’s Bioruptor® NGS 0.65 ml Microtubes for DNA
Shearing (Cat No. WA-005-0500). Pay attention not to damage the cap when closing the tubes since this could alter
sonication results.
• Sample volume: The recommended volume of the Diagenode’s Bioruptor® NGS 0.65 ml Microtubes for DNA Shearing
(Cat No. WA-005-0500) is 100 µl. When using lower volumes (e.g. ≤ 50 µl), less reproducible results may be observed
due to an alteration of the ultrasonic waves distribution in the sample fluid; thus, reducing the efficiency of sonication
which may result in broader size distribution or larger peaks.
• Sample concentration: Diagenode recommends using DNA concentration ranging between 1 and 20 ng/µl
(10 ng/µl recommended). Using larger concentration (e.g. 50-100 ng/µl) may result in broader peaks or variable peak
distribution.
• Sample preparation: Sample viscosity may have a major impact on sonication results. Careful resuspension of DNA
sample is strongly recommended before sonication processing. Multiple pipetting and gentle vortexing followed by a
short centrifugation to recover sample volume at the bottom of the tube is therefore strongly recommended. Storing
DNA samples on ice during 10-15 minutes before sonication has also been shown to improve reproducibility.
• DNA quality: DNA quality and quantity must be considered carefully since bad quality and quantity DNA may have
several impacts on sonication and next-gen sequencing downstream applications. First, DNA contamination (e.g.
from superfluous nucleic acids such as RNA, small nucleic acid fragments, excess proteins, or other contaminating
materials) may interfere with DNA measurement method leading to incorrect DNA quantitation thus. Also contaminating
RNA in genomic DNA preparation might generate a biased fragment distribution profile on microfluidics-based
platform (e.g. Agilent Bioanalyzer) or alter sonication effiency.
Therefore it is highly recommended to use only high quality DNA when sonicating DNA for Next-Gen sequencing library
preparation. The DNA sample to be processed should be highly pure, having an OD260/280 ratio of between 1.8 and
2.0, and should be as intact as possible. DNA extracted using standard techniques (e.g. Proteinase K digested, double
phenol/chloform extraction, ethanol precipitated, treatment with RNase-DNase free enzymatic digestion to remove
contaminant RNA) or commercial spin-column based kits are recommended.
• Water temperature: Propagation of ultrasound in a liquid unavoidably produces heat that can ultimately alter DNA
sample (e.g. by thermal denaturation). To ensure the best preservation of the sample, it is recommended to start the
sonication process with cold water in the water bath. During sonication, especially when doing long sonication runs,
the temperature must also be controlled. This is obtained by the automatic temperature control.
The protocol settings listed above are recommended guidelines and actual results may vary depending on the type and amount
of starting material, purity level, concentration and/or sample viscosity. It is highly recommended that a time course response
experiment be carried out (e.g. varying the time of “on” and “off” durations as well as the number of cycles) to determine the
appropriate treatment for your specific sample. Starting material with a smaller sample volume and a greater concentration
than the recommended range may require a different time course to ensure homogenous shearing results.

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Europe Diagenode sa / CHU - Tour GIGA - B34 - 3e étage // Avenue de l’Hôpital, 1 // 4000 Liège (Sart Tilman) // Belgium // Phone: [phone] // Mail: [e-mail]
Note: The permanent installation of the Bioruptor® in a cold room is possible, although not sufficient to avoid the
temperature increase due to sonication.
• Automatic temperature control: A recirculating water cooler is used to guarantee the automatic temperature control
of the water bath during the whole sonication process. This water cooler (Cat No. BioAcc-cool) produces a regular
water flow with a constant water level in the tank. An additional regulating valve (Single cycle valve for Water Cooler,
Cat. No. VB-100-0001) ensures that water will only be replaced during the off cycle to avoid any interference the
between water flow and the sonication process.
• Sonication time: Minor adjustments in cycle number may be made to optimize results for various sample types and
concentrations. Cycle number listed above is a recommended guideline. Actual results may vary depending on the
amount and type of starting material, concentration, viscosity and/or plastic tubes. Diagenode recommends setting
up a time dose response experiment for determining appropriate cycle number. Larger length starting material (e.g.
total genomic DNA) and higher concentration may require a longer dose to ensure a homogeneous shearing result.
• Water bath: The sonication water bath is a critical component of the Bioruptor® sonication system.
1. Water purity: Contaminants such as algae and particules may alter the ultrasonic waves propagation,
resulting in broader size distribution or larger peaks. Bath water should be pure distilled water, changed
regularly.
2. Water bath maintenance: The water bath metal surface is fragile and requires a careful maintenance. Use
only soft sponge to remove traces. Never use scratch scrub sponge since this would alter the ultrasonic wave
emitter surface.
Supplementary Data:
Please note that there are three main sources of variation in both peak base-pair size and distribution:
1) The physical process of DNA fragmentation might not be entirely random in AT- or GC- rich regions.
2) The analytical process to determine fragment size has inherent variances (for example, gel electrophoresis and
microfluidics-based platform). Therefore, fragment distributions and peak values, even from technical replicates,
may not appear identical. If the sheared DNA sample will be resin or column purified or concentrated prior to analysis,
please remember to take out an aliquot for use as control prior to that step. Column purification and concentration of
the sheared DNA will generate a biased fragment distribution profile due to the inherent greater loss of the smaller
DNA fragments.
3) RNA contamination in genomic DNA preparation should be carefully removed using RNase-DNase free enzymatic
digestion since they might generate a biased fragment distribution profile on microfluidics-based platform (e.g.
Agilent Bioanalyzer) or alter sonication effiency.

PAGE 19
DIAGENODE BIORUPTOR® NGS USER MANUAL
Diagenode Inc. North America / Phone: [phone] // Fax: [phone] // Mail: [e-mail]
Related Products
Diagenode develops and sells premium products for Epigenetics research that provide industry-leading sensitivity and
consistency.
Diagenode offers a number of kits for Chromatin Immunoprecipitation (ChIP) and DNA methylation assays like Methylated
DNA immunoprecipitation (MeDIP), MethylCap (MBD) and Bisulfite conversion (MagBisulfite kit). The Bioruptor®, with
its powerful yet gentle ultrasound technology, allows for consistent shearing, a narrow size range of sheared DNA or
chromatin, and sample preservation, necessary for successful experiments.
Antibodies
Diagenode offers a large selection of optimized ChIP & ChIP-seq grade, as well as MeDIP & MeDIP-seq
grade antbodies that we have developed and characterized in-house.
For a complete listing of Diagenode’s antibodies, please visit www.diagenode.com for more information.
Chromatin Immunoprecipitation kits
Automated ChIP kits
Auto ChIP kit (1) Auto Histone ChIP-seq kit (1) Auto Transcription ChIP kit (1)
Features All DNA-protein interaction, saving
time, maximum reproducibility
Optimized for working with histone
antibodies in ChIP-seq experiments,
saving time, maximum reproducibility
Optimized for working with TF
anbosies, saving time, maximum
reproducibility
Optimized for All DNA-protein interactions Histones and histone modifications Transcription factors and co-factors
Downstream applications qPCR qPCR, sequencing, arrays (2) qPCR, sequencing, arrays (2)
Amount of cells/IP 1.000 - 1 million 1.000 - 10 million 1.000 - 10 million
Total Time of Assay 1 day 1 day 1 day
Handling time 30 min 30 min 30 min
Buffers and reagents
IP, DNA Isolation IP IP
Control antibodies
anti-IgG (rabbit) anti-IgG (rabbit) anti-IgG (rabbit)
DNA purification
DNA isolation buffer (DIB) - -
#rxns per kit
16 or 100 16 or 100 16 or 100
Cat. No.
AB-Auto01-A016
AB-Auto01-G016
AB-Auto01-A100
AB-Auto01-G100
AB-Auto02-A016
AB-Auto02-G016
AB-Auto02-A100
AB-Auto02-G100
AB-Auto03-A016
AB-Auto03-G016
AB-Auto03-A100
AB-Auto03-G100
(1) Validated on SX-8G IP-Star® and SX-8G IP-Star® Compact Automated Systems
(2) DNA purification has to be carried out with the IPure kit (Cat. No. AL-100-0100; not included in the kit).

PAGE 20 DIAGENODE BIORUPTOR® NGS USER MANUAL
Europe Diagenode sa / CHU - Tour GIGA - B34 - 3e étage // Avenue de l’Hôpital, 1 // 4000 Liège (Sart Tilman) // Belgium // Phone: [phone] // Mail: [e-mail]
Manual ChIP kits
LowCell# ChIP kit HighCell# ChIP kit Transcription ChIP
kit Histone ChIP kit OneDay ChIP kit
Features
Magnetic bead-based
protocol for all DNA-
protein interaction,
fast, increased DNA
yield
Magnetic bead-based
protocol Ideal to
recover large amount
of DNA (transcription
factors, ChIP-on-chip)
and to avoid biais due
to amplification steps
Standard protocol
with agarose beads
optimized for
transcription factors
Standard protocol
with agarose beads
optimized for histones
and their modifications
Protocol using agarose
beads quick and
ready-to-use on large
quantities of sheared
chromatin, fast.
Optimized for All DNA-protein
interactions
All DNA-protein
interactions
Transcription factors
and co-factors
Histones and
histone modifications All DNA-protein
interactions
Suitable for ChIP-
seq and ChIP-on-
chip
Yes (1) Yes (1) Yes Yes Yes
Amount of cells/IP 1.000 - 1 million 1 - 10 million 1 million 100.000 1.5 - 2 x 10e6
Total Time of Assay 1 day 1 day 3 days 3 days 1 day
Handling time 1.5 h 1.5 h 2h 2h 2h
Buffers and
reagents for
Cell lysis, chromatin
shearing, IP, DNA
purification
Cell lysis, chromatin
shearing, IP, DNA
purification
Cell lysis, chromatin
shearing, IP
Cell lysis, chromatin
shearing, IP IP, DNA purification
Control antibodies
anti-IgG (rabbit) anti-IgG anti H3 (K4me3) anti-TBP or RNA Pol
II (2) anti-IgG (rabbit)
Control PCR
primer pairs
human TSH2B / c-fos /
myoglobin exon 2
human TSH2B /
GAPDH promoter
BMX / c-fos / beta
actin / myoglobin
exon 2
GAPDH /
0,5 kb / idem -1
kb / c-fos / beta
actin / myoglobin
exon 2
-
DNA purification DNA isolation buffer DNA isolation buffer Not included Not included DNA purifying slurry
#rxns per kit 16 or 48 16 18 18 60 / 180
Cat. No.
kch-maglow-A16
kch-maglow-G16
kch-maglow-A48
kch-maglow-G48
kch-mahigh-A16
kch-mahigh-G16 kch-redTBP-012 kch-orgHIS-012 kch-oneDIP-060 kch-oneDIP-180
(1) DNA purification has to be carried out with the IPure kit (Cat. No. AL-100-0100; not included in the kit).
(2) Please mention your choice of antibody on your purchase order.