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PAGE 17 

DIAGENODE 

BIORUPTOR

® 

PICO 

USER MANUAL

Diagenode Inc. North America

 / Phone: +1 862 209-4680 // Fax: +1 862 209-4681 // Mail: orders.na

@

diagenode.com

Standard protocols for DNA shearing

Standard operating conditions

Sample volume:

 

100 µl

Tubes:

 

0.65 ml Bioruptor

®

 Microtubes (Cat. No. WA-005-0500)

Tube holder:

 

0.65 ml tube holder for Bioruptor

®

 Pico (Cat. No. B01200042) for 12 x 0.65 ml tubes

Sonication buffer:

 

TE (10 mM Tris, 1mM EDTA, pH 7.5 - 8.0)

DNA concentration:

  1-20 ng/µl (10 ng/µl recommended)

Samples are vortexed (5-10 sec) and centrifuged (10 sec) before shearing.

For optimal results samples should be stored on ice during 5-10 minutes prior to sonication.

Temperature:

 

 4°C – 

Water Cooler (Cat. No. BioAcc-Cool) & Single Cycle Valve (Cat. No. B02020004)

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.

125 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

® 

Pico

Figure  shows  different  DNA  size  distributions 
of sheared genomic DNA produced by varying 
the  duration  of  sonication.  The  different 
curves  depict  a  specific  Bioruptor

® 

Pico 

Next-Generation  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.

Summary of Contents for B01060001

Page 1: ...U S E R M A N U A L Version 1 1 Bioruptor Pico Cat No B01060001 Bioruptor Pico Sonication System ...

Page 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...

Page 3: ... Valve for Bioruptor Pico 8 Sonication bath 8 Motorized lid 9 Tube holders 9 Equipment Installation 10 Installation overview 10 Installing the Bioruptor Pico System with Water Cooler 11 Controlling the Sonication 14 Tube Holders and tubes 16 Standard protocol for DNA Shearing 17 Operating Conditions 17 Important comments about DNA shearing 20 Small Volume DNA Shearing for Bioruptor Pico 22 Operati...

Page 4: ...sensitive to the heat generated during a run Do not exceed 1 hour 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 ...

Page 5: ...ultrasound on biological samples The Bioruptor Pico sonication system uses ultrasound to create focused mechanical stress to shear chromatin or 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 energ...

Page 6: ...00 230V 50 60Hz 2 1A EU 4 2A US Ultrasonic wave frequency 20 60 kHz Ultrasonic wave output power 25 210 W Sonication unit dimensions 350 W x 245 D x 280 H mm Sonication bath volume 750 ml Timer Digital Possibility to control water flow via connector kit for water cooler Yes Tube holder Available for 0 1 0 65 1 5 or 15 ml tubes Total weight 7 90 kg Number of samples to be processed simultaneously 0...

Page 7: ...62 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com Getting to Know Your Bioruptor Pico System Bioruptor Pico Components Overview Water Cooler To learn more please visit www diagenode com Power Cable EU Power Cable US Sonication Unit Sonication bath Motorized lid Tube holder ...

Page 8: ...t 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 sonication unit 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 us...

Page 9: ...process Note You may permanently install the Bioruptor Pico 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 sonication bath during sonication When in motion do not hamper the rotation of the white gear p...

Page 10: ...e Bioruptor Pico 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 ...

Page 11: ...rical outlet 1 Open the boxes and unpack all components 2 Place the Bioruptor on a bench 3 Place the Water cooler below the Bioruptor 4 Place the Single Cycle Valve on top of the Water cooler as shown in the image Location Requirements The Water cooler must be located below the Bioruptor Pico minimum elevation difference 400 mm or 15 74 inch Important Note Please make sure that the Bioruptor Pico ...

Page 12: ...tion unit 8 Plug the power cord into the outlet of the Water cooler 6 Connect the Bioruptor Pico to the Water cooler with the long red and blue tubing by inserting them into the upper red and blue nozzle connectors of the single cycle valve box as shown in the image Respect the red and blue color codes Optional Cut the length you need for the output and input flow Make sure there is enough slack I...

Page 13: ... to the red line of the sticker 700 or 730 ml depending on the model with distilled water only do not use deionized water 11 Temperature can be set to 4 C by pushing the SET key and the arrow key of the control panel at the same time 12 Press Start Stop key to control the temperature Note See Water cooler manual for additional information Now you are ready to start 10 Press main switch on the fron...

Page 14: ...one 32 4 364 20 50 Mail info diagenode com Controlling the Sonication 1 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 2 Start Button A Begins sonication 3 Stop Button B Cancels sonication Switch on power switch back side of sonication unit 1 2 3 ...

Page 15: ...ll be opened during a run the sonication will automatically pause Once the cover is again closed the machine continues with the sonication process As shown in Figure 5 the Break Cycle screen shows the information when the run stopped In the example Figure 5 the machine stopped during the second sonication cycle after 30 sec of TIME ON and 8 sec of TIME OFF If the sonication process worked properly...

Page 16: ...pty spaces with tubes containing the same volume of distilled water 1 5 ml tube holder for Bioruptor Pico Cat No B01200040 15 ml sonication accessories for Bioruptor Pico Cat No B01200016 15 ml Bioruptor tubes sonication beads recommended for chromatin not recommended for DNA shearing Cat No C01020031 0 65 ml tube holder for Bioruptor Pico Cat No B01200042 0 1 ml tube holder tube adaptor for Bioru...

Page 17: ...sonication Temperature 4 C Water Cooler Cat No BioAcc Cool Single Cycle Valve Cat No B02020004 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 125 bp 135 bp 183 bp 200 bp 234 bp 319 bp 476 bp 696 bp 848 bp 1036 bp 1230 bp Programmable DNA size distribut...

Page 18: ...300 and 400 bp based on the standard Ion Torrent standard sample preparation size requirements Figure B shows different DNA size distributions of sheared genomic DNA produced by varying the duration of sonication The different lanes depict a specific Bioruptor Pico run optimized to produce specific mean sizes and size ranges for Next Generation DNA sequencing Panel A peak electropherogram view Lan...

Page 19: ...ith Ion Torrent standard sample preparation protocols 150 200 300 and 400 bp Panel A 30 cycles 30 sec ON 30 sec OFF cycles Expected fragment size 150 bp observed average fragment size is 150 6 bp CV 2 07 Panel B 13 cycles 30 sec ON 30 sec OFF cycles Expected fragment size 200 bp observed average fragment size is 202 2 bp CV 4 7 Panel C 6 cycles 15 sec ON 90 sec OFF cycles Expected fragment size 30...

Page 20: ...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...

Page 21: ...tion 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 pu...

Page 22: ...ty spaces with tubes containing the same volume of distilled water Standard operating conditions Sample volume 10 µl Tubes 0 1 ml Bioruptor Microtubes Cat No C30010015 Tube holder 0 1 ml tube holder tube adaptor for Bioruptor Pico Cat No B01200041 for 12 x 0 1 ml tubes Sonication buffer TE 10 mM Tris 1 mM EDTA pH 7 5 8 0 DNA concentration 10 ng μl recommended Samples are vortexed 10 15 sec and cen...

Page 23: ...commended 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 s...

Page 24: ...sing 0 1 ml Bioruptor Microtubes Panel A B and C show DNA size distributions of sheared human genomic DNA using standard operating conditions Panel A 200 bp after 20 cycles 30 sec ON OFF Average size 215 bp CV 6 6 Panel B 300 bp after 13 cycles 30 sec ON OFF Short centrifugation after 4 and 8 cycles added Average size 316 bp CV 4 5 Panel C 550 600 bp after 7 cycles 15 sec ON 90 sec OFF Short centr...

Page 25: ...erefore 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 ...

Page 26: ...A 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 a...

Page 27: ...t No C30010015 Panel B 100 µl volume Chromatin samples are sheared for 10 cycles of 30 sec ON 30 sec OFF with the Bioruptor Pico using 0 65 ml Bioruptor Microtubes Cat No WA 005 0500 Panel C 200 300 µl volume Chromatin samples are sheared for 10 20 and 30 cycles of 30 sec ON 30 sec OFF with the Bioruptor Pico using using 1 5 ml Bioruptor Microtubes Cat No C30010016 Prior to de crosslinking samples...

Page 28: ...he content of this document cannot be reproduced without prior permission of the authors Bioruptor and IP Star are registered trademarks of Diagenode Inc Bioanalyzer is a registered trademark of Agilent MA Picoruptor V1 1_12_03_13 Description Cat No Bioruptor Pico Bioruptor Pico sonication device for 0 65 ml tubes B01060001 Cooling System Single Cycle Valve for Bioruptor Pico B02020004 Water coole...

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