- Diagenode
Contents
1. OFF Time OFF 30sec CYCLE Num 04 10 AS Press OK Modify ERA i y TIME TIME 1 ON 1 OFF 1 Cycle number reached iH in thi i CYCLE 4 cycles in this example START The display shows cycle 4 of 10 Waterbath will sonicate as shown Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 14 DIAGENODE BIORUPTOR USER MANUAL Digital Timer UCD 400 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 CYCLE Num 10 BIORUPTOR RUNNING FUT Time 30 KRKK KKK KK KK KKKKRE Bath 2 OFF CYCLE Num 04 10 Press OK Modify ON I l I Bath 1 OFF i Lerla y TIME TIME i 1 ON 4 OFF 1 Cycl b hed The display shows cycle 4 of 10 ne gt Leanne declan START Waterbath will icat h Overheat Shutdown for UCD 300 and UCD 400 A E e tee aetna The ultrasound source is sensitive to high temperatures which means that increases in temperature diminish the sonication efficiency and can damage the device The production of ultrasound generates heat which is transferred into the waterbath To avoid excessive overheating of the ultrasound source the Bioruptor Plus UCD 300 and Twin UCD 400 contains a temperature sensor We recommend that the water in the waterbath remain between 4 C 10 C 39 F 50 F for2. Level meter Digital timer Power button E Disruption unit Drain hose Output selector switch Stop button Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de l H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info diagenode com DIAGENODE BIORUPTOR USER MANUAL PAGE 13 Control Units a Intensity Multi Bioruptor UCD 200 Meter aes Multi timer Produces automatic ON and OFF cycles to preserve samples from overheating from ultrasound energy The green needle shows the OFF time and can iene be set by turning the external surface of the dial The red needle shows the ON time Setting toe Dial and can be set by turning the internal knob of the dial The time units min O sec can be modified by using a screw driver on the screws directly above the ON and OFF diagendde gioruPTOR Total analog timer The Bioruptor is activated by the clockwise rotation of this dial The maximum time is 15 minutes The time set will equal the sum of the ON and OFF cycles Alternatively turning the timer knob counterclockwise will set the Bioruptor on a permanent position always cycles ON and OFF To stop this process manually set the timer knob on to the vertical position Intensity setting dial 3 power settings are available for the sonication L Low 160W M Medium 200W and H High 320W Intensity level meter Al
3. diagengte Innovating Epigenetic Solutions ruptor Sonication System USER MANUAL VERSION 2 1 User Manual for the Bioruptor Family of Sonication Systems and Accessories UCD 200 Bioruptor Standard UCD 300 Bioruptor Plus UCD 400 Bioruptor Twin m UCD 500 Bioruptor XL 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 extrem
4. 90min without primer design and sequencing Untreated DNA and bisulphite treated DNA 40 Standard protocol 3 days optimized for Histones and their modifications Histones amp modified histones 10e5 3 days Cell fixation collection lysis Shearing IP DNA purification Included 18 Gives precise information on methylation status of single cytosines Sequencing Min 100 pg 6h 18h without primer design and sequencing Untreated DNA and bisulphite treated DNA 25 or 96 LowCell HighCell OneDay Transcription Histone Automated ChIP Kit ChIP Kit ChIP Kit ChIP Kit ChIP Kit ChIP Kit ll Use from 1 000 5 million cells per IP validated on SX 86 IP Star Automated System which ensures maximum reproducibility and time savings All DNA protein interaction 1 000 5 million 1 day IP DNA purification Included 16 or 48 Quality control using internal Fast method for transient and cyclical methylation study Linear amplification and genome wide analysis microarray sequencing 9 Ug 5h incubation time 1h or 4 h overnight incubation GST protein optional 90 Ordering information diagengte Description Reference Bioruptor Models Innovating Epigenetic Solutions UCD 200 TM 1 5 ml Bioruptor Standard UCD 200 TO 1 5 ml amp 15 ml UCD 200 TS 0 5 0 65 mJ UCD 300 TM 1 5 ml Bioruptor Plus UCD 300 TO 1 5 ml amp 15 ml Diagenode s a BELG
5. can accommodate up to 3 tubes The holding plates should price list for spare parts always be completely filled to guarantee homogeneity of shearing Sonication Protocols Sample Protocol for DNA Shearing Next Generation Sequencing Applications The following describes our in house protocol for DNA shearing for sequencing library preparation Samples Prior to sonication human DNA samples were O A Illumina Meda dissolved in a sonication buffer of TE 10 mM Tris Sequencer FLX Genome Analyzer SOLID 1mM EDTA pH 8 with a DNA concentration of 0 01 ug ul and a final volume of 100 ul Required fragment size post sonication 100 800 bp 100 500 bp 100 300 bp Costar 0 65 ml Low Binding Microcentrifuge Small genomes Tube Cat No COR 3206 and Tube holder for lesa Bacen 5 10 cycles 20 30 cycles 60 80 cycles 12 x 0 5 ml tubes Diagenode Cat No UCD pack Large genomes 1 L 4 l 0 1 l eg ua 30 40 cycles 80 100 cycles 0 5 All samples were vortexed and centrifuged before shearing in the Bioruptor sonication system Sonication Parameters As shown in the table sequencing libraries were prepared by sonicating genomic DNA to obtain optimal fragment size distributions to fit those recommended by the manufacturers of each of the commercial sequencing platforms Solexa SOLID and 454 platforms We established a set of sonication conditions that could be used to generate each of the required size distributions by varying on
6. 20 00005 20 Troubleshooting reir ea aa ada das Soe eee Ue sa eee ee dada 21 Bioruptor Chromatin Shearing FAQS 60 sice0nnsceuane sated a a a a cans 21 Bioruptor Packing Instructions sica eee ees eee e aes ee Waa a eee we wae Ged 22 Related ProdUCIS saring esni tiaa eed a bee coro ee ae Oe Eas eee eee Renewed 23 AUDI S ser doa dh be boos hoe bE EE nos CA Gos FOR dnd oe ee Bw 23 CU Ve oa oa a od tee gna wae eG oo dea EE aaa eo ee eee Zo IN PoC OR A co Mee Gg ob woke Aer ae ns wee eee oe we ee 23 Ordering Informa tON x cestas erstes cds re srta se ced det dee dehdo ee ds Back Cover Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 4 DIAGENODE BIORUPTOR USER MANUAL Warnings These instructions do not necessarily cover all the details of possible equipment variation installation or operation Trouble free and safe operation of the instrument is dependent on proper transport and installation by qualified personnel READ ALL THE FOLLOWING PRECAUTIONS BEFORE INSTALLING AND USING THE INSTRUMENT General warnings e Never use the instrument near flammable gases to avoid risk of fire Qu e Never use the instrument in an environment of extreme dust or FRAGILE e Do not place instrument in direct sunlight e Handle the waterbath component of the instrument with extreme caution The waterbath unit contains the ultrasound emitter which is composed of fragile mechanisms
7. 5 ml tube Check disrupted material on a 1 agarose gel 10 ul lane Run the gel slowly Gel electrophoresis of cross linked samples often gives smears on gel Also take several pictures of the gel to assure image quality The migration of large quantities of DNA on agarose gel can lead to poor quality pictures which do not reflect the real DNA fragmentation 1X TAE or TBE is preferred to 0 5X TAE which can lead to smears on gel Use a freshly prepared gel and fresh buffer DIAGENODE BIORUPTOR USER MANUAL Comments Correct formaldehyde concentration in fixation Is critical It is possible to fix for as little as 5 minutes depending on your protein of interest for subsequent ChIP assays Fixation can be performed at 4 C RT and 37 C Make sure you perform the fixation step at the right temperature The HighCell ChIP kit is compatible with cell numbers up to 10 million cells in small volumes Do not use a too high cell concentration Quality and quantity of detergent is important It is possible to shear from 5 30 minutes If 30 interrupt sonication after 15 minutes and centrifuge tubes briefly before proceeding with the remaining 10 Make sure waterbath Is kept cool Once optimal conditions are reached use for all assays to assure reproducibility Do not use a too big sample volume Reverse cross links from DNA afterphenol chloroform extraction before loading on gel To obtain cle
8. Disruption unit Drain hose unit reset timer Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 10 DIAGENODE BIORUPTOR USER MANUAL Installing the Bioruptor UCD 300 and UCD 400 1 Connect the power supply adapter to the 2 Connect the controller to the waterbath control unit with the power cable through the sound proof box Power supply adapter is only needed outside the U S 3 Remove the rubber cap from the back of the 4 The fitting will secure the cable to the sound proof sound proof box and feed the instrument cable through box Turn the front section counterclockwise to seal the upper left hole marked instrument cable Be sure there is enough slack in the cable red green 5 Connect the instrument cable to the waterbath NOTE The UCD 400 has dedicated connectors that are and place into the sound proof box colored red and green with corresponding receptacles Bioruptor UCD 300 Bioruptor UCD 400 Twin Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de U H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info diagenode com DIAGENODE BIORUPTOR USER MANUAL PAGE 11 Bioruptor UCD 300 0 5 ml 1 5 ml Ep microtube adaptor 10 ml 15 ml A tube adaptor 50 ml CA Cold Water tube adaptor Circulation System o MH o Sample tube holding plate a Small sized motor Nay Soundproof box Multit
9. Reagents Cell fixation collection lysis IP DNA purification Control Antibodies included amp Control Primers IP per kit 16 Standard cell numbers improved handling magnetic beads fast increased DNA yield All DNA protein Ready to use on large quantities of sheared Standard protocol 3 days optimized for transcription factors chromatin fast All DNA protein interaction interaction 10e6 10e7 1 5 2X 10e6 1 day 1 day Cell fixation IP DNA collection lysis IP estad DNA purification P Included Included 16 or 48 60 or 180 Features Applications Amount of DNA rxn Total Time of Assay Controls controls improved handling magnetic beads high specificity monoclonal 5 mec Ab fast qPCR linear amplification and genome wide analysis microarray sequencing 1 ug Manual MeDIP 3 days Automated MeDIP Robotic System IP Auto 20h Methylated and unmethylated BAC clones 16 or 48 Quality control using internal controls high specificity monoclonal 5 mec Ab fast qPCR linear amplification and genome wide analysis microarray sequencing 1 ug 3 days Methylated and unmethylated BAC clones 10 Transcription factors and co factors studies 10e6 3 days Cell fixation collection lysis Shearing IP DNA purification Included 18 Gives precise information on methylation status of single cytosines Sequencing Min 50 pg
10. U S Transformer 220 100V Dimensions 170w x 130d x 140h mm Internal Internal Internal Interval Timer 0 60 sec or min on off cycles 0 60 sec or min on off cycles 0 60 sec or min on off cycles 0 99 sec or min on off cycles Total Timer Max 15 min analog Max 15 min digital Max 15 min digital Max 15 min digital Total Weight 22 6Kg 20Kg 30Kg 32 0KG Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 6 DIAGENODE BIORUPTOR USER MANUAL Getting to Know Your Bioruptor Bioruptor Components Control Unit Waterbath Motor Lid Sound Proof Box Power Cable Control Unit Cable Accessory Example Power Supply Adaptor only outside the U S Waterbath The waterbath Is a critical component of the instrument The generators below the tank produce ultrasonic waves which are then transferred through water The waterbath requires special handling and care as described below Handling The waterbath must remain upright at all times especially when moved Tilting the waterbath or handling roughly may damage the fragile 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 leve
11. lo empty the water tank use the plastic pump provided with the instrument Do not move the unit to pour out the water e The water in the waterbath must be kept at 4 C 40 F Sonication transfers energy to the waterbath which leads to a temperature increase To retain the integrity of biological samples and to prevent the Bioruptor from damage change the water in the waterbath as frequently as possible OR purchase our optional water cooler cooling system Cat No BioAcc cool e Do not turn on the instrument without water This will damage the instrument e Do not leave the instrument unattended for more than 20 minutes at a time e Make sure water level is always at the level indicated within the waterbath Deviation may cause damage e Use the 15 ml adaptor with the aluminium O ring or scratches will occur on the tank bottom Use of Bioruptor by pregnant women Exposure to 20kHz 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 20kHz wave lengths for a long period of time Noise level measurements amp precautions CEE noise data is not applicable to the Bioruptor s ultrasound emitter as no tests have been conducted on similar devices to date See listed noise levels las measured in the Accredited Acoustics Laboratory and precautions for the Bioruptor Leg noise level in dBA 78 4 dB Lmax dB
12. optimized your sonication parameters in 19 ml tubes the same sample concentration will not necessary be applicable to sonication in tubes Greater sample dilutions for the tubes should thus be tested Bioruptor Chromatin Shearing Example U20S cells are fixed with 1 formaldehyde 10 minutes at RT Analysis on an agarose gel of the sheared chromatin One million cells are resuspended per 30 ul of lysis buffer prior to chromatin shearing Each sample consists on 5x 10e6 cells per 1 5 ml tube Samples are sonicated for 15 cycles of 30 seconds ON 30 seconds OFF with the Bioruptor from Diagenode Cat No UCD 200 Samples 1 and 2 are duplicates The sheared chromatin is Submitted to a cross linking reversion DNA purification and RNase treatment Then the samples are analyzed on a 1 agarose gel Iwo amounts of sheared chromatin are analyzed 1 5 ul and 3 ul The 100 bp DNA molecular weight marker Is on lanes 1 and 4 1 2 3 4 5 6 Quick Overview Tips for Starting a Successful Sonication Water level up to the blue line Do not add too much water or too little O UES Never start the sonication without water in the tank It is best to pre cool the tank before starting the first round of sonication in Water temperature econo order to reduce the water heating due to thermal inertia if the tank is stored at in the tank P room temperature Use the automated cooling system as described on page 7 Alternatively manual tem
13. optimum sonication Note he sensor does not measure the water temperature inside the ultrasound bath where the samples are submerged Once a critical limit is reached a warning is displayed on the control screen Depending on the situation different screens pop up as described below 1 If START is pressed and the instrument stops after a couple of seconds showing the following screen blinking the instrument could not start a new run due to the ultrasound source s temperature Causes e Instrument has been used several times in a row recently without breaks e Instrument is stored in a place exposed to direct sun e Room temperature is too hot What to do e Store the instrument in another place if the current one does not meet the installation specific requirements e Allow for longer breaks between uses e Place crushed ice in waterbath to help the cool ultrasound source Machine too hot to start a new run See Manual 2 During a run if the instrument stops and the following screen pops up the critical temperature has been reached To protect the ultrasound source from damage the instrument has stopped and is standing by to be restarted after the ultrasound source has cooled Causes e Instrument has been running too long without breaks RISK OF DAMAGE Machine stoped at What to do Cycls XX XX See Manual e Store the instrument in another place if the current one does not meet the installation specific requiremen
14. same brand of tubes e The 2 ml polypropylene tubes thin walled should not be used with the Bioruptor 1 5 ml tubes in TPX plastic that provide better ultrasound transfer rates and more efficient sonication are available from Diagenode see price list These tubes should be used for chromatin shearing not DNA shearing e Any 0 5 ml or 1 5ml tube can be used although shearing efficiency is Increased by using the hard plastic tubes TPX hard plastic available from Diagenode See catalog numbers on price list e The complete adaptor including O ring can be sterilized in the autoclave After more than 20 autoclave sterilizations the O ring might need to be replaced see price list for spare parts F 13 293 WwW O 0 5 ml tube adaptor unit 1 5 ml tube adaptor unit 10 ml tube adaptor unit Cat No UCD pack 0 5 Cat No UCD pack 1 5 Cat No UCD pack 10 15 ml tube adaptor unit Cat No UCD pack 15 The adaptors for 15 ml tubes are available in blue Falcon tubes and orange Corning tubes If you use another brand of tubes use the one which fits in the holder the best When using the 15 ml tubes do not forget to insert the aluminium ring to ensure an optimal position of the tube during sonication 50 ml tube adaptor unit Cat No UCD pack 50 Three different models of adaptors for 50 ml tubes are available one for Nalgene and two for Falcon Nalgene These tubes offer the best efficiency in terms of transfer of the
15. ul of complete Shearing Buffer S1 RT to the cells Vortex until resuspension Incubate for 10 minutes on Ice e Use preferably the cooling system but if not fill the tank with cold water 4 C and supplement with 0 5 cm crushed Ice e Submit the samples to sonication to shear the chromatin using the Bioruptor for two run of 10 cycles 30 seconds ON 30 seconds OFF each e Spin and vortex between each run c Reverse cross links and analyze on gel 3 Notes This protocol is a starting point and the total time of sonication and or ON OFF cycling parameters should be modified The susceptibility of each chromatin can vary depending on the cell type or cell number So we suggest conducting a time course e g 10 15 cycles of 30 seconds ON 30 seconds OFF for Low cell number to determine optimal shearing time for your cell line or cell mass e LowCell ChIP Kit kch maglow A16 kch maglow G16 kch maglow A48 kch maglow G48 e HighCell ChIP kit kch mahigh A16 kch mahigh G16 e Transcription Factor ChIP kit old description Red ChIP kit kch redTBP 01 2 e Histone ChIP Kit old description Orange ChIP kit kch orgHIS 012 e OneDay ChIP Kit kch oneDIP 060 kch oneDIP 180 Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de l H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info diagenode com DIAGENODE BIORUPTOR USER MANUA
16. ultrasound energy and can be ordered directly from Diagenode Cat No 3015 0050 Falcon or Corning The adaptors for 50 ml tubes are available in blue Falcon tubes and orange Corning tubes If you use another brand of tubes use the one which fits in the holder the best Note The quality of the 50 ml Corning tube hard plastic polyethylene ref Corning 430304 can be used as well as soft plastic Polypropylene ref Corning 430290 but you should stick to one kind as transfer of ultrasonic waves is different for the different tube types hard plastic is more efficient For Falcon tubes only polypropylene tubes are available Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de l H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info diagenode com DIAGENODE BIORUPTOR USER MANUAL PAGE 17 Holding Plates BEG amp Gear Plates included with tube adaptor kits O rings for 10ml 15ml 50ml tube adaptor units The gear plates holding plates for 10 ml and 15 ml tubes Removing the black knob it is possible to replace the can accommodate up to 6 tubes for the UCD 200 UCD 300 O ring The complete resonance chip including O ring can AND UCD 400 and up to 12 tubes for the Bioruptor XL For be sterilized in the autoclave After more than 20 autoclave 90 ml tubes the sample holding plate is the NG 50 3 which sterilizations the O ring might need to be replaced see
17. 100 10 ml Tubes AS 900 15 ml TPX Tubes M UN 15 90 ml Nalgene Tubes 3103 0050 2010 Diagenode Inc All rights reserved The 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
18. IUM EUROPE UCD 300 TS 0 5 0 65 ml Avenue de l h pital 1 Bioruotor Twi UCD 400 TM 1 5 ml Tour GIGA 3rd Floor loru win P UCD 400 TO 1 5 ml amp 15 ml 4000 Li ge Belgium a XL TM 1 5 ml Tel 32 4 364 20 50 Bioruptor XL o XL TO 1 5 ml amp 15 ml ESO ON Sample Tube Adaptor Kits ordersediagenode com infoediagenode com 0 5 0 65 H tube holder for Bioruptor Standard UCD pack 0 5 g Bioruptor Plus 1 5 ml tube holder for Bioruptor Standard Date Me ds SORTI PUE amp Bioruptor Plus UCD pack 1 5 400 Morris Avenue Suite 101 Denville NJ 07834 USA 10 ml tube holder for Bioruptor Standard UCD pack 10 a a 8 Bioruptor Plus Fax 1 862 209 4681 15 ml tube holder for Bioruptor Standard UCD pack 15 orders naediagenode com 8 Bioruptor Plus info naediagenode com 90 ml tube holder for Bioruptor Standard UCD k 50 amp Bioruptor Plus a A For a complete listing of Diagenode s international distributors visit Bioruptor Water Cooler including standard http www diagenode com pages distributors html connectors for Bioruptor lo For rest of the world please contact Diagenode s a Cooling System Connectors Kit for Water Cooler CONN 7D1 Peristaltic Pump Including Connectors Kit TWI pump Valve Kits Connector kit for Water Cooler Bioruptor Plus VB 100 0001 Valve Kit for UCD 300 VB 101 000 Tubes 1 9 ml TPX Tubes M 50050 1 9 ml TPX Tubes M 50001 10 ml Tubes AS
19. L Optimal Sonication Parameters The Bioruptor brings flexibility and walk away parallel processing to sonication Different sonication parameters and protocols can be customized to your specific application sample type volume and desired size range Before starting a new application or using a new tissue sample type it is a good idea to carry out one or more preliminary test runs in order to empirically optimize the best instrument parameters for your particular research goals Consider varying the type of sample sample concentration volume instrument power and duration of sonication in order to identify the best parameters for your experiments Once run conditions are optimized the Bioruptor provides unparalleled reproducibility from sample to sample and run to run Critical Points Use these starting points as the sonication parameters to yield the best results for a number of applications e Water level in the tank Fill precisely to the blue line e Temperature Use the Diagenode Water Cooler Cat No BioAcc cool for automated temperature control e Power For chromatin shearing set the output selector switch on High H For DNA shearing e g Next Gen Sequencing applications set the output selector on Low L for small to medium size fragments 100 to 800bp or on Extra Low HL for large size fragments 1000 to 5000bp e Cycling parameters 30 seconds ON amp 30 seconds OFF e Tube adaptors and holders See Using Adaptor
20. Od HAO ee ee oh wea weed ee ode a es I Fguipment installati M secos osos aia ruta te ai a A A a dba 6 a ei 8 installing the Bloruptor UCU 200 6 32544 risas ey 8 ede ss ob ees a 9 installing the Bioruptar UCL 300 and UCDAU iron eS keds aa ees 10 Installing the BIOruptor AL rodearon ohne oe ot ee ee be ee ia 11 COME OL WS pate o En en Re A 13 UC DEZU e Bag teehee eed eho eee He Aone AEG eee BEE eee eee Eee eee Ee eee Be eo 13 WD SU0 UG nse has be Sere sehen SaaS an GPa Oe PRESS we 13 COntrollimg TNE SONICO erid teescus da deen eee de de bee ea y a 13 UE vec ede pods oo E athe gp oseye eowiey eee dae oop AA ha DNA DITA E permi edi ad ade oda ea 14 Overheat Shutdown for UCD 300 and UCD 400 2 0 o 14 o A aad okt ered ao sh dea nde eae eee Rok aod eed E ike Controlling the SONICATION sas se 0 0 00054 siatie Shae eevee aa Ee eee 15 Using Adaptors and Holding PlateS ccc ee eee eens 16 Pal OS MHI 5 we pate pte angie ose ob gee ame aa E eg ee E 16 lo a oe oa 8 ene pee rene O II be eee ee 17 Sonication Protocols currar oanss4t as oba aa a iaa aa ame od 17 Sample Protocol tor DNA SOSaTINd sceseesceus ace du oP ate ae oes dR ese aes Sas 17 BIO FUDLOr gt apple PrOLOCO Sos oe bey abra ee diran eee wore Ge ws eos 18 Optimal Sonication ParameterS o sumen rsrrdasreriea acierto criada ss urb menus 19 Bioruptor Chromatin Shearing Example 00 000 cc eee 20 Quick Overview Tips for Starting a Successful Sonication
21. Peak 87 6 dB 1 Exposure limit value The exposure limit value is the maximum amount of noise an employee may be exposed to on any single day 8 hours Exposure beyond this limit presents a high risk to the user LEXPOSURE 8h 87 dB A PPEAK 200 Pa 140 dBIC referring to 20 Pa 2 Upper exposure Action value The exposure action value Is the upper daily limit of noise exposure Exposure beyond this value requires employers to take action to limit user exposure LEXPOSURE 8h 85 dB A PPEAK 140 Pa 137 dBIC referring to 20 uPa 3 Lower exposure action value LEXPOSURE 8h 80 dB A PPEAK 112 Pa 135 dB C referring to 20 uPa Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de U H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info diagenode com DIAGENODE BIORUPTOR USER MANUAL PAGE 5 Introduction The Diagenode Bioruptor uses a gentle method of sonication to retain the integrity of DNA and or biological complexes including chromatin protein protein binding protein DNA complexes and other biochemical and biological assay systems The Bioruptor Sonication System uses a waterbath to generate these indirect sonication waves which emanate from an ultrasound element below the water tank Because the system is gentler than other sonicators many customers report better and more consistent results with the Bioruptor than with harsher sonication methods Multiple
22. agenode com Troubleshooting Bioruptor Chromatin Shearing FAQs Fixation Cell lysis Number of cells shearing buffer volume Shearing buffer Shearing step Checking for high quality shearing on an agarose gel What is the formaldehyde final concentration How long Is the fixation step What is the temperature to use for fixation Are the washes after fixation important How can achieve complete cell disruption What is the amount of cells per shearing trial to use What is the key buffer component How long is the shearing What is the optimal cycle What is the best temperature for shearing What is the best volume tube for shearing What kind of gel should use to determine size accuracy What do smears indicate How much DNA should load and is RNAse treatment necessary What should my running buffer concentration be Will using an old gel cause problems Answers 1 Fix for 10 minutes with a time course when needed Fix at room temperature Wash the fixed cells properly Make sure you get rid of ALL the formaldehyde Use glycine to stop the fixation Do not use too many cells in the cell lysis buffer Lyse about 5x 10e6 cells 1 ml 1x 10e6 10x 10e cells 300 ul 3x 106 30x 106 cells 1 ml Include detergent in buffer Perform a time course for chromatin shearing 30 seconds ON 30 seconds OFF LC 1 9 ml per 15 ml tube 200 ul per 1
23. arer image with accurate fragment size reversion of the crosslinking Is advised Do not load too much on a gel Do not load more than 5 ug lane Also treat the sample with RNAse Do not reuse an old gel PAGE 21 Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 22 DIAGENODE BIORUPTOR USER MANUAL Bioruptor Packing Instructions If you need to ship your Bioruptor for any reason it is important to follow these specific packing instructions as the Bioruptor is extremely fragile Please use our pre molded container and components for packing The box is composed of a double wall corrugated carton a foam base and a foam lid made of ultra shock absorbent foam Each part of Bioruptor has a designated area in the box las shown 1 Tank unit preparation A Place a scrap piece of corrugated cardboard over the top of the tank as shown B Tie packaging strap around the tank and cardboard C Tighten the strap as securely as possible due to extreme fragility of tank unit which is prone to damage during transit 2 Placement of components A The controller unit should be placed in the largest rectangular recessed area in the molded foam box with the fan toward the outer side of the box B The tank unit should be placed in the square recessed area in the molded foam box towards the inside of the box las shown Wedge a piece of cardboard in the space between t
24. ation tests For example a nuclear extract should be always produced with the same protocol and generated with a fixed number of cells Since the sample concentration is a key factor to calibrate sonication efficiency a serial dilution should be performed with the starting material For example 6 aliquots of the starting material could be diluted as follows 1X 5X 10X 20X 50X and 100X Sonicate the 6 tubes together using the sonication parameters of 30 seconds ON amp 30 seconds OFF If insufficient disruption occurs either perform a further serial dilution of the samples or increase the total time of sonication If excessive disruption occurs either concentrate samples or reduce the total time of sonication A fine tuning of the ON amp OFF cycles and of the other sonication parameters can be done once a satisfactory result has been obtained on a specific Sample concentration The optimal conditions should give excellent sonication reproducibility i e fragment size and preservation of the sonicated material without overheating PAGE 19 Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 20 DIAGENODE BIORUPTOR USER MANUAL Important note when testing different sonication vessels 15 ml and 50 ml tubes are sonicated in the Bioruptor with a metal bar which triggers the resonance effect and improves the sonication efficiency In other words if you
25. cations Fig 1 Propagation in 15ml 50ml tubes Ultrasonic Wave Frequency Bioruptor UCD 200 20kHz Bioruptor UCD 300 20kHz Bioruptor UCD 400 20kHz Bioruptor UCD 500 20kHz Ultrasonic Wave Output Power switchable 160 200 320W 160 320W 160 200 320W 130 200 250 300W Power Supply 100V 50 60Hz 4 24 100V 50 60Hz 4 2A 230V 50 60Hz 2 14 240V 50 60Hz 3 24 Control Unit Dimensions 150w x 300d x 195h mm 150w x 300d x 195h mm 150w x 300d x 195h mm 400w x 260d x 160h mm Sonication Unit Dimensions 117w x 190d x 300h mm 390w x 260d x 150h mm 350w x 260d x 150h mm 320w x 180d x 280h mm Noise Reduction Box Dimensions 200w x 260d x 360h mm 200w x 260d x 360h mm 200w x 260d x 360h mm 400w x 300d x 520h mm Waterbath Volume 800cc 800cc 800cc 1800cc Number of Samples Processed Simultaneously IZ 20a ml 6 am 6x Uml ex1 ml 3x50 ml 120 3 mil exar 6x10ml 6x15 ml 3x50 ml a UNA Lam 1210 mk 12x 15 mL 6 x 50 ml AS x 0 5 ml AXLI 24 10 ml 24x15 rml 12x50 ml Attachment Unit Avallable for 0 5 1 5 10 15 50 ml tubes Available for 0 5 1 5 10 15 amp 50 ml tubes Available for 0 5 1 5 10 15 50 ml tubes Available for 0 5 1 5 10 15 amp 50 ml tubes Power Supply Adapter 26 x16x 18 outside the U S 26x16x18 outside the U S 26x16x18 outside the U S 26x16x18 outside the
26. closed tubes can be sonicated together 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 What is the effect of ultrasound on biological samples The Bioruptor sonication system uses ultrasound to create focused mechanical stress to lyse cells or shear DNA or chromatin The ultrasound waves pass through the sample expanding and contracting liquid During expansion negative pressures pull the molecules away from one another and form a cavity or bubble in a process called cavitation The bubble continues to absorb energy until it can no longer sustain itself and then implodes producing intense focused shearing forces which disperses or breaks biomolecules Also the fragmentation of DNA takes place as a consequence of this mechanical stress or shear from the bubbles a E With the Bioruptor the entire volume of water present in the waterbath is exposed to ultrasound allowing the samples in the tubes to be efficiently sonicated For larger tubes 15 ml or 50 ml the transfer of the ultrasound to the tubes is facilitated by a metallic bar in contact with the sample This metallic bar is not a probe no corrosion problems but reflects the ultrasound originated from the waterbath and improves the sample sonication efficiency by a patented resonance system See Figure 1 Bioruptor Technical Specifi
27. d 400 can also be used 2 Sonication parameters a Set Bioruptor on High Power setting H b Add 130 ul of complete Buffer B RT to the cells Vortex until resuspension Incubate for 5 minutes on Ice e Use preferably the cooling system but if not fill the tank with cold water 4 C and supplement with 0 5 cm crushed Ice e Submit the samples to sonication to shear the chromatin using the Bioruptor for 12 cycles of 30 seconds ON 30 seconds OFF each c Reverse cross links and analyze on gel 3 Notes e Protocol for quick analysis of shearing is given in the additional protocol section of the kit manual ChIP kit references including Buffer B e AUTO ChIP KIT AB Auto01 0016 AB Auto01 0100 High Eukaryotic Cell Number Protocol to obtain 300 500 bp chromatin fragments 1 Starting material e Nucleus from 1 000 000 to 10 000 000 fixed cells e Use preferably 1 5 ml TPX tubes Cat No M 50050 but can be optimized with all kind of tubes e Shearing Buffer B from the Diagenode s ChIP kits for the complete list of ChIP kits containing Buffer B please refer to the list provided at the end of this protocol As an alternative the reagents and protocols provided with the Shearing Optimization kit ref kch shchro 040 or with the Shearing ChIP kit kch redmod 100 kch redmod 400 can also be used 2 Sonication parameters a Set Bioruptor on High Power setting H b Add 200
28. e temperatures cnemical solvents or acids We strongly recommend that maintenance or repairs of Diagenodes products are performed by our approved Diagenode service center Improper or Incorrectly performed maintenance or repairs will void the warranty Technical Assistance Ordering Information Phone 32 0 4 364 20 69 niagenndeee Diagenode Inc Fax 32 0 4 364 20 51 Europe Asia amp Australia North America info diagenode com CHU Tour GIGA B34 3rd Floor 400 Morris Avenue Suite 101 Diagenode Avenue de l H pital n 1 Denville NJ 07834 USA CHU B34 are ney A Phone 1 862 209 4680 Tour GIGA 3eme tage Fax 1 862 209 4681 e Unopital 1 Phone 32 0 4 364 20 50 Email orders naAdiagenode com 4000 Liege Fax 32 0 4 364 20 51 Belgium Email info diagenode com DIAGENODE BIORUPTOR USER MANUAL PAGE 3 ontents E PA o RI es oedema een ee eeenetabben erate ener a eesonean ee 4 MOTE OG OW fete ate Hae te noe on Gn a A de erie de GA ee ene ee aA one a a E 5 Bior ptor lechnical SUCCIIICAIONS asistir 5 Getting to Know Your BIOFUDIOl cc cri aia ds sele ad ana ole tard dolar dra e te ooh ahh woes kiteko dd oe 6 Bioruptor CO MPOn ents sss iai ati ohne a dica E oda eee ee ls dl oe eee da ese nat 6 WORD AU seems ee ce iaa PER eee oR eee eee ee sd Ree eee eae 6 Moon o Ws 4 4 doa ote bE Sa hoe bbe he Ca PA es Ee a oe Be BE ee 7 TUC OEO erara eee ke Hk ee EE EE BS ee Oe ee ee ees 7 o AS i Fower Uppy Ad E der ogee creo 1 eG
29. he housing and the foam to keep the tank in place C The motor plate should be placed in the slotted area in the molded foam with the motor towards the inside of the box las shown Tuck the cable into the foam in the middle of the circle of the motor plate to block its movement D Roll the grey cable up and place it in the circular recessed area in the molded foam box Place the other accessories in the same circular area E For UCD 200 The transformer 220V 100V unit should be placed in the remaining rectangular recessed area in the molded foam box with the cable between the foam and housing Note The transformer is not used in every area of the world 3 Placement of foam lid and seal box A For UCD 200 Place foam lid on the top so that the protrusion in the lid is over the transformers area The protrusion helps to keep things in place during transit B The carton box should be easy to close otherwise you might have to shift the Bioruptor parts and wires slightly C Close the box and seal securely with wide tape Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de l H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info diagenode com Low cell numbers improved handling magnetic beads fast increased DNA yield Features Optimized for All DNA protein interaction Amount of cells IP 10e3 10e5 Time from cell 1d ay collection to PCR Buffers amp
30. imer Level meter Power cord TT Stop button Disruption unit Drain hose Intensity setting button Start button Bioruptor UCD 400 Twin 0 5 ml 1 5 ml ji microtube adaptor 10 ml 15 ml Th tube adaptor 50 ml coo Cold Water tube adaptor Circulation System o Mm gt rn Sample tube holding plate Small sized motor ARA ail NA Y C 7A Water Soundproof box a Es Multitimer Level meter Power cord da A Stop button Disruption unit Drain hose Intensity setting button Start button Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 12 DIAGENODE BIORUPTOR USER MANUAL Installing the Bioruptor XL Note Control unit connector has two different plugs one Is for the control unit and the other is for the waterbath Turn the connector 90 to secure the connection 1 Connect the power supply adapter to the 2 Connect the waterbath and rotor control unit with the power cable Rotate the black cap to secure the connection Power Supply Adapter is only needed outside the U S 3 Add the accessory and place the waterbath 4 Connect the waterbath and control unit into the sound proof box You are ready to work 0 5 ml 1 5 ml i microtube adaptor Top case 10 ml 15 ml tube adaptor 50 ml Hn Cold Water tube adaptor Circulation System o MH lt ae Sample tube holding plate Small sized motor Soundproof box Start button
31. l and quality The level of the water has been optimized and should always reach the blue line sticker on the wall of the tank Tap water or distilled water can be used to fill the tank Waterbath Water temperature The water in the waterbath must be kept at 4 C 40 F Ultrasonic waves produced by the Bioruptor generate heat To ensure preservation of the samples and to prevent damage to the instrument it is necessary to start the sonication process with cold water Diagenode suggests maintaining the waterbath temperature during sonication by either adding ice throughout the run manual temperature control or by connecting the system to a circulating water cooling system Cat No BioAcc cool for automatic temperature control Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de l H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info diagenode com DIAGENODE BIORUPTOR USER MANUAL PAGE 7 Manual temperature control A pre cooling of the Bioruptor s tank 15 minutes before starting the first round of sonication is advised This prevents the water from heating too quickly due to thermal inertia i e when the tank and the ultrasound generating elements are stored at room temperature To pre cool simply add crushed ice and then fill with cold water up to the indicated level blue line or sticker The crushed ice floating in the water should not exceed 0 5cm and the total water
32. level water and ice should be exactly at the indicated water level We advise keeping a 4 C stock of water for the process At the end of a typical sonication time 10 minutes cycles of 30 seconds ON and 30 seconds OFF the temperature in the waterbath should be below 10 C Note You may permanently install the Bioruptor in a cold room though this is not sufficient to avoid the temperature increases during sonication The cold room would only eliminate the need for the pre cooling step described above Automatic temperature control A refrigerated circulation bath can be used to guarantee the automatic temperature control of the waterbath during the entire sonication process The optional Diagenode Water Cooler circulation bath Cat No BioAcc cool features two pumps IN and OUT and produces a regular water flow to maintain a constant water level in the tank An additional regulating valve the Connectors Kit for Water Cooler should be installed into the water circuit from the refrigerating unit to the Bioruptor to ensure that the water flows at an optimal level The water flow must not exceed 500 ml min to allow optimal resonance The Water Cooler can be ordered directly through Diagenode with all the required tubing see price list The Water Cooler is not available to North American customers Motorized Lid The motorized lid along with the blue gear plate accessory keeps the sample tubes In cons
33. lows visualization of sonication intensity Bioruptor UCD 300 and UCD 400 Controlling the Sonication CYCLE NUMBER TIME ON and TIME OFF are the parameters controlling the sonication First press UP or DOWN depending on the value to be modified The four flashing black squares move up or down Once the selected values are chosen to be modified press OK The four flashing black squares disappear and 2 digits start flashing The digits can be changed by pressing UP or DOWN To select and save the correct number press OK to confirm or ESC to escape without saving the change Digital Timer Allows the user to easily program the sonication of samples ON OFF pulse time amp total time See use of digital timer in next section below Stop Button Ends sonication Intensity Setting Button Adjusts intensity of the Intensity Level Meter ultrasonic waves generated Indicates the sonication Start Button o ES a intensity Begins sonication Power Switch Turns Bioruptor on and off Once all parameters are selected and confirmed press START Once the run is started BIORUPTOR RUNNING is displayed on the control screen UCD 300 Digital Timer After the introductory message the control screen shows the main sonication parameters in the first three lines CYCLE Number Time ON Time OFF and summary of actions in the last line see example below CYCLE Num 10 BIORUPTOR RUNNING Time ON 30sec PROS Bath 1
34. ly the duration of sonication ie the number of cycles and leaving the buffer concentrations power and other parameters identical between runs These conditions were e Low power 1 min sonication cycles 30 sec ON 30 sec OFF and number of cycles based on desired DNA size The temperature was kept at 4 C using the Diagenode Water cooler Cat No BioAcc Cool for optimal shearing results e For the larger fragments 1 5 kb and higher the Bioruptor was set on 50 of the Low power setting and samples were kept at room temperature Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 18 DIAGENODE BIORUPTOR USER MANUAL Bioruptor Sample Protocols Chromatin Shearing for ChIP Assays from Eukaryotic cells adherent or suspension cell lines with ionic detergent buffers Low Eukaryotic Cell Number Protocol to obtain 300 500 bp chromatin fragments 1 Starting material e 100 000 to 1 000 000 fixed cells e Use preferably 1 5 ml TPX tubes Cat No M 50050 or 0 5 ml tube but can be optimized with all kind of tubes e Shearing Buffer B from the Diagenode s ChIP kits for the complete list of ChIP kits containing Buffer B please refer to the list provided at the end of this protocol As an alternative the reagents and protocols provided with the Shearing Optimization kit ref kch shchro 040 or with the Shearing ChIP kit kch redmod 100 kch redmo
35. perature control protocols may also be used 10 pl In 0 5 ml tubes de 100 ul In 1 5 ml tubes volume per tube for 900 ul In 15 ml tubes each sonication trial r In 50 ml 1ml In 50 ml 100 ul In 0 5 ml tubes 300 ul In 1 5 ml tubes Maximum sample volume per tube for 2 ml each sonication trial 20 ml In 50 ml In 15 ml tubes 8 ml In 50 ml Polystyrene or polyethylene clear tube in hard plastic is much more efficient for the transfer of ultrasonic waves for chromatin shearing Do not use TPX tubes for DNA shearing as prolonged shearing times may damage the DNA Quality of the 15 ml fhe Falcon or Corning Sonicating in 15 ml tubes Sonication process Optimization of sonication cycling time Do not forget to insert the aluminum ring Sonicate by cycles Cycles dependent on the sample volumes and type of tubes The ring is essential to ensure an optimal position of the tube during sonication Cycles of 30 seconds ON amp 30 seconds OFF are advised for chromatin shearing and DNA shearing Cycles depend on the application chromatin shearing DNA shearing RNA shearing obtention of bacteria lysates or tissue lysates For 0 5 and 1 5 ml tubes we have optimized with Sarstedt Costar Eppendorf Fisher Bioblock Scientific and Diagenode tubes Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de l H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info di
36. pply adapter shows the right voltage corresponding to your area Otherwise switch it using a narrow blade screwdriver When connecting cables always be sure pins are Keep dot facing up Once plugged in secure properly aligned Note the indexing pins on the control by turning 90 clockwise unit cables for precise mating alignment until a click is heard Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de l H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info diagenode com DIAGENODE BIORUPTOR USER MANUAL PAGE 9 Installing the Bioruptor UCD 200 Note Control unit connector has two different plugs one is for the control unit and the other is for the waterbath Turn the connector 90 to secure the connection 1 Connect the power supply adapter to the 2 Connect the waterbath and control unit control unit with the power cable using the control unit cable Power supply adapter is only needed outside the U S 3 Connect the rotor Rotate the black cap 4 Place the waterbath into the sound proof box to secure the connection and add the accessory You are ready to work 0 5 ml 1 5 ml it microtube adaptor Top case 10ml 15ml n l tube adaptor 50 ml A Cold Water tube adaptor Circulation System o HN lt Sample tube holding plate AS Small sized motor Soundproof box Multitimer Level meter Output selector swich Power cord Mechanical
37. r Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 8 DIAGENODE BIORUPTOR USER MANUAL Equipment Installation The following pages contain information on installing your particular Bioruptor model In the interest of safety this equipment must only be installed by competent 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 e Indoor use e Power plug must be grounded e Altitude up to 2 000 meters e POLLUTION DEGREE 2 Normally only non conductive e Operating external temperature 0 C to 25 C pollution occurs However occasionally a temporary e Maximum relative humidity 80 conductivity caused by condensation is expected e Never install this equipment in a place where environmental conditions and warnings mentioned above are infringed e Transient overvoltage typically present on the MAINS supply e Degree of protection IP20 Power Supply Adapter The power supply adapter must be plugged into the power grid An IEC lead is provided IMPORTANT WARNING Ensure that your power inlet behind the power su
38. s and Holding Plates on page 16 for optimal tube recommendations Make sure holding plates are completely full for best results e Tube preparation All samples should be vortexed and centrifuged briefly le g 10 20 seconds before shearing in the Bioruptor sonication system Optimization Test Chromatin Shearing Optimization is required to obtain reproducible sonication results Various factors influence the outcome such as e Complexity of the mixture Cell lysis extracts DNA solutions or liposome suspensions are complex mixtures of molecules The ability to disrupt biological materials by sonication depends on the individual molecule concentration and on the presence of contaminants oe The aliquot volume in each tube should be fixed e The viscosity of the solution is another factor that can affect and correspond to the chosen tube the sonication efficiency as the cavitation process is dependent on the viscosity coefficient of the solution e The fixation step percentage of formaldehyde duration and 0 5 ml 100 ul 10 ul pelea for assay ne is a key factor that can Gaal 300 ul 100 ul attect the cnromatin shearing efficiency 15 ml 2 ml 500 ul The best way to start optimization tests with the Bioruptor is to 50 ml 20 ml 3 ml collect a large quantity of the biological material to be sonicated 50 ml 8 ml 1 ml This material should be well characterized easily attainable and avallable in sufficient quantities for repeat optimiz
39. seconds showing the following screen blinking the instrument could not start a new run due to the ultrasound source s temperature A LATS Bath 1 ES y TIME TIME A 1 ON 4 OFF 1 Cycle number reached ene A 4 cycles in this example START 2 To enter Time Settings go down to PARAMETER 3 After you get into PARAMETER select T1 Select and Press OK Please disregard the manufacturer 11 go left and go up and down to choose the total settings Password Stop Run Info sonication time in minutes and seconds And then Attention Do not change the password push OK Do not change the 12 12 must be 0 4 ON and OFF Cycles The control unit allows the automatic production of ON amp OFF cycles to preserve the samples from rapid heating due to ultrasonic waves ON cycle Select T2 Repeat as for T1 PAGE 15 Diagenode Inc North America Phone 1 862 209 4680 Fax 1 862 209 4681 Mail orders na diagenode com PAGE 16 DIAGENODE BIORUPTOR USER MANUAL Using Adaptors amp Holding Plates Adaptor Tube Units Available in 0 5 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 completely filled with tubes To ensure reproducibility always use the
40. tant rotation and ensures optimal Sound Proof Box A plastic sound proof box is available for the UCD 200 The metal sound proof box for the UCD 300 UCD 400 and Bioruptor XL is very efficient in absorbing the position in the waterbath iaa noise generated by the ultrasonic during sonication When in NS waterbath which is placed inside motion do not hamper the rotation of the blue gear plate this box Sound Proof Box Avoid the immersion of the motor into the water Power Supply Adapter Tube Holders PPly p A power supply adapter is needed when operating the Several sizes of tubes can be used with the Bioruptor Bioruptor outside the U S with a voltage other than 110V The maximum and minimum sample volume to be used This unit provides the instrument with several signals with each container is given in the table below The 0 5 ml used at the different stages during operation The power and 1 5 ml tubes can be simply closed and installed in the supply adapter is the heaviest part of the apparatus and rotor For the sonication of larger volumes 10 ml 15 ml needs particular handling caution and 50 ml tubes a stopper with a metallic bar has to be used to reflect sound waves to produce a better resonance The power supply adapter for the UCD 300 UCD 400 and efficiency Bioruptor XL is switched on with the power button located on the back The UCD 200 does not need to be switched on Tube Holders 90 ml Power Supply Adapte
41. ts e Allow for longer breaks between uses e Place crushed ce in waterbath to help the cool ultrasound source B ESC 6096 6 3 If the warning message appears at the bottom of the BIORUPTOR RUNNING screen see below it means that the critical temperature is about to be reached Causes e Instrument has been running too long without breaks What to do e Reduce the number of consecutive cycles or split protocols into two runs separated by a break e Keep cold water in the sonication bath while running to help keep the ultrasound source at low temperature BIORUPTOR RUNNING kkkkkkkkkkkkkkkkk CYCLE Num xx xx WARNING gets hot B ESC 6096 0 Europe Diagenode sa CHU Tour GIGA B34 3 tage Avenue de l H pital 1 4000 Li ge Sart Tilman Belgium Phone 32 4 364 20 50 Mail info diagenode com DIAGENODE BIORUPTOR USER MANUAL Bioruptor XL Sant amp Intensity Level Meter e diagengde Digital Timer tom J J POWER Start Stop Button E Power Switch k BIORUPTOR x Power Settings Controlling the Sonication First switch on the Bioruptor with the POWER button Next set the intensity level L 130W M1 200W M2 250W and H1 300W Next use the digital timer as described in the following steps note the parameters CYCLE NUMBER TIME ON and TIME OFF control the sonication 1 If START is pressed and the instrument stops after a couple of
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