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PAGE 16 

DIAGENODE 

BIORUPTOR

®

 PLUS 

USER MANUAL

Europe Diagenode sa

 / CHU - Tour GIGA - B34 - 3e étage // Avenue de l’Hôpital, 1 // 4000 Liège (Sart Tilman) // Belgium // Phone: (+32) 4 364 20 50 // Mail: info

@

diagenode.com

O rings 

(for 10ml, 15ml, 50ml tube holders)

By removing the black knob, it is possible to replace the O-ring. The complete tube holder chip 
(including O-ring) can be sterilized in the autoclave. After more than 20 autoclave sterilizations 
the O-ring might need to be replaced (visit www.diagenode.com).

Holding Plates 

(included with any tube holder)

The holding plate for 10 ml and 15 ml tubes can accommodate up to 
6 tubes. For 50 ml tubes, the sample holding plate can accommodate 
up to 3 tubes. The holding plates should always be completely filled to 
guarantee homogeneity of shearing.

Standard protocols

DNA shearing

 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

®

  0.5  ml  Microtubes  for  DNA  Shearing  (Cat.  No.  

WA-004-0500).

To use the tube holder, remove the lower part by turning counterclockwise. Then place microtubes into 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.

Operating conditions

Sample volume:

 

100 μl

Tubes:

 

Bioruptor

®

 0.5 ml Microtubes for DNA Shearing (Cat. No. WA-004-0500)

Tube holder:

 

0.5/0.65 ml tube holder (Cat. No. UCD-pack 0.5) for 12 x 0.5 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)

0.5/0.65 ml tube holder (Cat. 
No. UCD-pack 0.5)

Bioruptor

®

 0.5 ml 

Microtubes for DNA 
Shearing  
(Cat. No. WA-004-0500)

Содержание Bioruptor plus

Страница 1: ...U S E R M A N U A L Version 1 1 Bioruptor Plus Cat No UCD 300 Bioruptor Sonication System ...

Страница 2: ... 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 appro...

Страница 3: ...tions 6 Getting to Know Your Bioruptor System 7 Bioruptor Components Overview 7 Sonication bath 7 Motorized lid 8 Metallic soundproof box 9 Power Supply Adapter 9 Tube holders 9 Equipment Installation 10 Installation overview 10 Installing the Bioruptor Plus 12 Controlling the Sonication 13 Tube Holders Tubes 15 Standard protocols 16 DNA Shearing 16 Chromatin Shearing 19 Bacteria Cell Disruption 2...

Страница 4: ... 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 Plus DNA shearing 0 5 ml Bioruptor Microtubes for DNA Shearing Cat No WA 004 0500 Chromatin Shear...

Страница 5: ... 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 sonication bath is exposed to ultrasound allowing all th...

Страница 6: ...to be harmful to human health However we would recommend avoiding unnecessary exposure Diagenode recommends that pregnant women should not be exposed to 20 60 kHz wave lengths for a long period of time Bioruptor Technical Specifications Bioruptor Power Supply 115 V 4 2A US 230V 2 1A EU 50 60Hz Control unit dimensions 350 W x 260 D x 165 H mm Sonication unit dimensions sonication bath 175 W x 160 D...

Страница 7: ...he 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 Use only distilled water to fill the tank Do not use deionized water Replacement stickers can be obtained from Diagenode...

Страница 8: ... BioAcc Cool can be used in combination with the Standard Connector Kit continuous valve to guarantee the automatic temperature control of the sonication bath during the entire sonication process Figure 3 The water flow shouldn t exceed 500 ml min to allow optimal resonance The Water Cooler features two pumps and produces a regular water flow to maintain a constant water level in the tank An addit...

Страница 9: ...h the power button located on the back Tube Holders Several sizes of tubes can be used with the Bioruptor Plus The minimum and maximum sample volume to be used with each container is given in the table below The 0 5 ml and 1 5 ml tubes can be simply closed and installed in the rotor For the sonication of larger volumes 10 ml 15 ml and 50 ml tubes a stopper with a metallic bar has to be used to ref...

Страница 10: ...ider all hazards even though no particular hazards have been identified during installation Before starting installation work turn the main switch off back side of the control unit 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 Water Connector kit fo...

Страница 11: ...power inlet behind the power supply adapter shows the right voltage corresponding to your area Otherwise switch it using a narrow blade screwdriver This feature is not applicable for the Bioruptor Plus UCD 300 sold in the United States Attaching Cables When connecting cables always be sure pins are properly aligned Note the indexing pins on the control unit cables for precise mating alignment Keep...

Страница 12: ...onication bath into the soundproof box 2 Place sonication bath in front of the soundproof box 5 Place the motor lid on the top of the sonication bath and connect it Make sure that the cable of the motor lid is connected as shown in the image triangle have to match 8 Connect the power supply adapter to the control unit with the power cable Power supply adapter is only needed outside the U S 9 Place...

Страница 13: ...he display shows cycle 4 of 10 Bioruptor NGS will sonicate as shown CYCLE Num 10 Time ON 30sec Time OFF 30sec Press OK Modify Bath 1 ON OFF TIME ON TIME OFF CYCLE START Cycle number reached 4 cycles in this example 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 cy...

Страница 14: ...in a row recently without breaks Instrument is stored in a place exposed to direct sun Room temperature is too hot What to do Store the instrument in another place if the current one does not meet the installation specific requirements Allow for longer breaks between uses Place crushed ice in sonication bath to help the cool ultrasound source 2 During a run if the instrument stops and the followin...

Страница 15: ... 10 ml tube holder Cat No UCD pack 10 Tube holders tubes Tube holders Available for 0 5 0 65 ml 1 5 ml 10 ml 15 ml and 50 ml To use adaptor tube unit remove the lower part of the microtube holder by turning counterclockwise Then place microtubes in the unit Attach the lower part to the upper part of the adaptor To guarantee homogeneity of chromatin shearing the tube holders should always be comple...

Страница 16: ...ring 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 0 5 ml Microtubes for DNA Shearing Cat No WA 004 0500 To use the tube holder remove the lower part by turning counterclockwise Then place microtubes into the unit Attach the lower part to the upper part of the adaptor To guarantee homogeneity of DNA shearing th...

Страница 17: ...itions On Off times in sec Number of cycles 1250 bp 15 90 2 cycles 950 bp 15 90 4 cycles 750 bp 30 90 3 cycles 550 bp 30 90 5 cycles 400 bp 30 90 6 cycles 350 bp 30 90 8 cycles 300 bp 30 90 10 cycles 250 bp 30 90 15 cycles 200 bp 30 90 30 cycles 150 bp 30 30 70 cycles recommended to use a lab timer to set time precisely The protocol settings listed above are recommended guidelines and actual resul...

Страница 18: ...NA preparation might generate a biased fragment distribution profile on microfluidics based platform eg 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 ...

Страница 19: ...er sonication effiency Chromatin shearing Critical points for chromatin shearing Chromatin shearing efficiency varies on cell type Each cell type might need additional protocol optimization The extent of cross linking is critical for the efficient disruption of fixed cells and also affects DNA yield and average size of chromatin fragments Over cross linked chromatin will not produce small fragment...

Страница 20: ...l lines Note Cells growing in suspension culture are known to be difficult to shear Nuclei extraction is recommended before sonication Do not use very dense cell suspension for sonication 1 Cross link chromatin with 1 fresh formaldehyde for 8 10 min at RT 2 Stop the cross linking reaction by adding glycine to the final concentration 0 125 M for 5 min at RT with gentle rotation 3 Wash cells 3 times...

Страница 21: ...hed ice Power setting H position High Sonication cycle 30 sec ON 30 sec OFF Total sonication time 10 min for UCD200 300 15 min for Bioruptor XL Note Please note that additional optimization might be required depending on the bacterial strain and growth phase Gram positive bacteria are more resistant to sonication than Gram negative bacteria because of the rigid cell wall Cells in log phase are les...

Страница 22: ...cells with intact membranes and discrimination from cells with damaged membranes Thus efficient cell disruption is observed after 5 10 minutes of sonication Figure 1 Effect of sonication on cell disruption The number of intact cells after sonication was determined by measuring optical density at 600 nm Optical density of the cell culture before sonication 0 min is arbitrarily set to 100 Sheared DN...

Страница 23: ...ing step How long is the shearing Perform a time course for chromatin shearing It is possible to shear from 5 30 minutes If 30 interrupt sonication after every 10 minutes and centrifuge tubes briefly before proceeding with the remaining time What is the optimal cycle 30 seconds ON 30 seconds OFF What is the best temperature for shearing 4 C Make sure sonication bath is kept cool Once optimal condi...

Страница 24: ...ard UCD 200 TM 1 5 ml UCD 200 TO 1 5 ml 15 ml UCD 200 TS 0 5 0 65 ml Bioruptor Plus UCD 300 TM 1 5 ml UCD 300 TO 1 5 ml 15 ml UCD 300 TS 0 5 0 65 ml Bioruptor Pico B01060001 Cooling System Water Cooler including continuous valve for Bioruptor BioAcc cool Consumables 1 5 ml TPX Microtubes M 50001 1 5 ml TPX Microtubes M 50050 15 ml TPX Microtubes M UN 15 0 5 ml Bioruptor Microtubes for DNA Shearing...

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