X-CLARITY™
Contents
1. Component Quantity X CLARITY ETC Chamber 1 ea X CLARITY ETC Controller 1 ea X CLARITY Pump 1 ea X CLARITY Reservoir 1 ea Multi Cable 1 ea Power Cord with AC Adapter 2 ea Snap Lock Connector Tube 1 ea Peristaltic Pump Tube 1 ea Container Holder for 1 Tissue Container 1 ea Tissue Container 5 ea Electrophoretic Tissue Clearing Solution 12x1L Upon receiving the product package please inspect its contents to ensure that all parts have been included and that no damage has occurred during shipping The warranty does not cover damage that may occur during shipping and handling Any damage claims must be filed with the carrier 1 3 Product Specifications 1 3 1 X CLARITY ETC Chamber Instrument Type Electrophoretic chamber Dimensions WxDxH 176 mm x 128 mm x 154 mm Internal chamber volume 57 mm x 30 mm x 93 mm Weight 2 8 kg Note The electric power to the X CLARITY ETC Chamber is provided by the X CLARITY ETC Controller via the multi cable 1 3 2 X CLARITY ETC Controller Instrument Type Power supply and control Dimensions WxDxH 180 mm x 340 mm x 200 mm Weight 5 1 kg Applicable Power AC100 240V 50 60 Hz Power Consumption 210 W including the X CLARITY ETC Chamber 1 3 3 X CLARITY Pump Instrument Type Peristaltic pump Dimensions WxDxH 232 mm x 142 mm x 149 mm Weight 2 4 kg Speed 0 1 100 0 rom Speed2. X CLARITY Tissue Clearing System User Manual Catalog No C10001 Revision Date April 9 2015 www logosbio com The contents of this document may be changed in the future without advance notice All copyrights of this manual are owned by Logos Biosystems The X CLARITY Tissue Clearing System is a laboratory electrical instrument for scientific research use only It is not a medical therapeutic or in vitro diagnostics device The WEEE Waste Electrical and Electronic Equipment symbol indicates that users of this instrument have the responsibility of returning and disposing of WEEE in an environmentally friendly manner Follow the waste ordinances of your region for proper disposal provisions The CE mark indicates that this instrument conforms to all applicable European Community provisions for which this marking is required Users must be aware of and follow the conditions described in this manual for operating the instrument The protection provided by the instrument may be impaired if the instrument is used in a manner not specified by this manual Protective earth Ground FCC This equipment has been tested and found to comply with the limits for a Class A digital device COMPLIANCE pursuant to part 15 of the FCC Rules These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment This equipment generates u
3. by circulation of the clearing solution Turn on the X CLARITY ETC Controller and set the values for current temperature and switching time To clear a whole adult mouse brain use the parameters in the following table To reduce time for the ETC process adjust the switching time to 60 600 min A shorter switching time usually means a shorter clearing time However it also means more burden to the tissue When using a short switching time a proper end point time should be determined Recommended Current 15A Temperature 37 45 C Switching time 0 Peristaltic pump speed 30 rpm Push the RUN STOP button on the X CLARITY ETC Controller to start the ETC process As the system runs you will observe bubbles coming from the outlet These bubbles are formed by the electrolysis of water Note 1 The X CLARITY ETC Controller provides maximum 60 V and 1 5 A In some cases the current may not initially reach 1 5 A despite being set at 1 5 A This can occur when the initial voltage exceeds 60 V However the current will stabilize to 1 5 A after a few hours of running Note 2 A significant amount of heat will be generated in the X CLARITY ETC Chamber during the ETC process To eliminate this heat a cooler has been integrated into the X CLARITY ETC Chamber However temperature control may not be efficient at a low setting value ex below 40 C or high external temperatures Cooling the Reservoir with an additional
4. in the head of the peristaltic pump Attach the free end of the tube to the X CLARITY ETC Chamber inlet 10 Reservoir outlet Reservoir inlet Go D 0 X CLARITY ETC Chamber outlet X CLARITY METC Chamberinlet Figure 5 Connection of tubes Take the free end of the plastic snap lock connector tube and attach it to the inlet located on the cap of the X CLARITY Reservoir Make sure the X CLARITY ETC Chamber cap and safety cover are closed and then attach the snap lock connector to the X CLARITY ETC Chamber outlet Do not attempt to open or close the X CLARITY ETC Chamber safety cover when the snap lock connector tube is attached to the X CLARITY ETC Chamber outlet Make the connections as tight as possible to prevent buffer leakage and make sure the tubes do not vent Note Use the tubes provided by Logos Biosystems Connect the multi cable to their ports on the rear panels of the X CLARITY ETC Chamber and the X CLARITY ETC Controller Figure 6 Temperature probe port Multi cable port a D E 5 Multi cable port Figure 6 Cable ports Insert the temperature probe connector that projects from the cap of the X CLARITY Reservoir into the temperature probe port on the rear panel of the X CLARITY ETC Controller Connect the power cords to the X CLARITY ETC Controller and X CLARITY Pump 11 3 2 Start up Turn the power on by flipping the power switch on the r
5. C12104 Peristaltic Pump Tube 1 unit C12201 Power Cord with AC Adapter 1 unit C13001 Electrophoretic Tissue Clearing Solution 12x1L Solutions C13101 X CLARITY Mounting Solution 1x25 mL C13102 X CLARITY Mounting Solution Value Pack 10x25 mL 22 7 Purchaser Notification 7 1 Limited Use Label License Research Use Only The purchaser of this product should use this product only for research for the sole benefit of the purchaser By use of this product the purchaser agrees to be bound by the terms of this limited use statement whether the purchaser is a for profit or a not for profit entity If the purchaser is not willing to accept the conditions of this limited use statement and this product is unused the Company will accept return of the product with a full refund The purchaser cannot re sell or otherwise transfer a this product b its components or c materials made using this product or its components to a third party for Commercial Purposes Commercial Purposes mean any and all uses of this product and its components by a party for monetary or other consideration including but not limited to a product manufacture b providing a service information or data c therapeutic diagnostic or prophylactic purposes or d resale of this product or its components whether or not such product and its components are resold for use in research Logos Biosystems Inc Company will not claim any considerati
6. Precision 0 1 rpm Speed Adjusting Membrane keypad continuous adjusting Applicable Power AC100 240V 50 60 Hz Power Consumption 30 W Note Please see the separately supplied user manual for more information 1 3 4 X CLARITY Reservoir Material Glass or plastic Total Volume 2L Recommended Buffer Volume 1 2L 2 Product Description The X CLARITY Tissue Clearing System consists of 1 the X CLARITY ETC Chamber 2 X CLARITY ETC Controller 3 X CLARITYT Pump and 4 X CLARITY Reservoir Figure 1 Figure 1 Components of the X CLARITYT Tissue Clearing System 2 1 X CLARITY ETC Chamber The X CLARITY ETC Chamber is an electrophoretic device that applies an electric current to tissue samples placed in the chamber Figure 2 New and improved electrodes produce a uniform electric field for better clearing The X CLARITY ETC Chamber inlet and outlet allow for buffer circulation which eliminates the loss of buffering capacity during electrophoresis and reduces the risk of overheating The X CLARITY ETC Chamber also has an integrated cooling system to dissipate the heat generated during electrophoresis Safety Cover _______ Outlet Chamberca Window Inlet Figure 2 The X CLARITY ETC Chamber 7 2 2 X CLARITY ETC Controller The X CLARITYT ETC Controller is an integrated device that controls the power temperature and safety for the X CLARIT
7. Y ETC Chamber Figure 3 No external devices are needed to supply power or control temperature when using the X CLARITYT ETG Controller The X CLARITY ETC Chamber and the X CLARITY ETC Controller are connected with just one cable eliminating the need for dangerous and messy wiring Displays voltage current temperature switching time RUN STOP button SET UP DOWN buttons Figure 3 The X CLARITY ETC Controller The control panel on the front of the X CLARITY ETC Controller has buttons for adjusting the current temperature and switching time Displays show the values of the voltage current temperature and switching time Figure 3 The X CLARITY Tissue Clearing System only works in constant current mode and does not provide a constant voltage mode The X CLARITY ETC Controller ranges are Range Increment Voltage V Not adjustable max 60 N A Current A 0 2 1 5 0 1 Temperature C 35 60 1 Switching time min 0 600 10 2 3 X CLARITY Pump The X CLARITY Tissue Clearing System has the peristaltic X CLARITY Pump By circulating the buffer the X CLARITY Tissue Clearing System maintains consistent buffering capacity and controls the temperature in the X CLARITY ETC Chamber See the separately supplied pump user manual for more information 2 4 X CLARITY Reservoir During the ETG process it is important to circulate the Electrophoretic Tissue Clearing Solu
8. cooling system is helpful in such cases Generally it has been known that efficient clearing occurs at temperatures of 37 60 C 17 Replace the Electrophoretic Tissue Clearing Solution every 24 hours To change the Electrophoretic Tissue Clearing Solution first stop the run by pushing the RUN STOP button on the X CLARITY ETC Controller Check to see that the voltage and current values are at 0 Reverse the direction of the pump CW to CCW OR CCW to CW The draining of the solution can be observed through the window of the X CLARITYTM ETC Chamber Note At this point if the values of voltage and current do not drop to 0 after pushing the RUN STOP button to stop the run turn the power off by flipping the main power switch of the X CLARITY ETC Controller If the system does not recover when you turn on the power back on please contact your local sales representative or Logos Biosystems The tube connecting the X CLARITY ETC Chamber outlet and the Reservoir outlet must be completely empty to prevent spilling when you disconnect the tube from the chamber outlet Stop the pump when the Electrophoretic Tissue Clearing Solution has been removed from the Chamber Remove the snap lock connecter tube from the X CLARITY ETC Chamber outlet open the safety cover and unscrew the chamber cap Rinse the chamber with fresh Electrophoretic Tissue Clearing Solution if necessary Note Dark particles may appear on the electrodes or surface of
9. e cent de die det deeded dle 16 5 Maintenance and Troubleshoo0tinQ cooccccnnnncconnneccconnnonccnno nono a aa cnn 19 lt A A OU A 19 9 2 Troubleshooinguu ri O Ta eee 20 5 3 Error Codes ci A A a E aS 21 6 Ordering Information setmana 22 7 Purchaser Not ICAO EEE 23 7 1 Limited Use Label License Research Use Only coonoocinccccncconoccononnnonnccnoncnnnnnnnno cnc cn nn rnn narcos 23 Safety Information Before using this instrument read this manual carefully to ensure that you know how to operate it safely and correctly Keep this manual in an easily accessible location for future reference For safe and risk free use of the X CLARITY Tissue Clearing System read the warnings and information provided Use the instrument as specified Avoid electric shock while operating the instruments Do not touch the components with wet hands Operate the instrument in the conditions described in the Environmental Conditions for Operation Wear proper personal protective equipment PPE when handling the Electrophoretic Tissue Clearing Solution to avoid exposure Use only components provided or authorized by Logos Biosystems Make sure that the input voltage is compatible with the X CLARITY ETC Controller power supply voltage before use Use the power cord and AC adapter provided Ensure that the power cord is firmly plugged into the X CLARITYTM ETC Controller and the power source Turn the X CLARITY ETC Controller on only after connectin
10. e container and put the top on Insert the tissue container into the hole of the container holder Figure 9 Tissue Container amp Container Holder Place the container holder into the X CLARITY ETC Chamber as shown in Figure 10 Figure 10 Insertion of the Container Holder into the X CLARITY ETC Chamber Note Do not fill the X CLARITY ETC Chamber to the brim prior to sample insertion This may cause the solution to overflow and potentially damage the X CLARITY ETC Chamber Start with just enough Electrophoretic Tissue Clearing Solution to cover the sample 16 Screw on the chamber cap tightly If the chamber cap has been fastened correctly the silicone ring inside the cap will create a tight seal preventing leaks In case of leakage please check the silicone ring inside the chamber cap Connect the snap lock connector end of the silicone tube to the chamber outlet NEVER open or close the X CLARITY ETC Chamber safety cover when the tube is still attached to the chamber outlet Disconnect the tube from the chamber outlet prior to opening or closing the safety cover by pressing the stainless steel button on the side of the snap lock connector Make sure all the tubes are connected securely and properly Turn on the peristaltic pump to 30 50 rpm to begin to circulate the Electrophoretic Tissue Clearing Solution Adjust the flow rate of the pump to 30 rpm when the X CLARITY ETC Chamber has been completely filled
11. e is on This may be caused by malfunction of the controller Other Please contact your local sales representative or Logos Biosystems 5 3 Error Codes Error code Possible Cause Solution Reboot your system If the error code persists please Malfunction due to a defect of E01 contact your local sales representative or Logos part Biosystems Overheating due to high Set up your system in a cooler environmental environmental temperature a temperature less than 35 C If the error code E02 malfunctioning controller or a persists please contact your local sales malfunctioning cooling system representative or Logos Biosystems 21 6 Ordering Information The following products can be ordered through your local sales representative or by contacting salesOlogosbio com Category Cat Product Unit Starter Kit C10001 X CLARITY Tissue Clearing System Starter Kit 1 unit C10101 X CLARITY ETC Chamber 1 unit Main C10201 X CLARITY ETC Controller 1 unit Components C10301 X CLARITYT Pump 1 unit C10401 X CLARITY Reservoir 1 unit C12001 Tissue Container 20 units 1 box Containers amp 012002 Container Holder for 1 Tissue Container 1 unit Holders C12004 Mouse Brain Slice Holder Chamber Height 4mm 1 unit C12007 Whole Rat Brain Holder 1 unit C12101 Multi Cable 1 unit C12102 X CLARITY Reservoir Cap with Temperature Probe 1 unit Replacements C12103 Snap Lock Connector Tube 1 unit
12. ear panel of the X CLARITY ETC Controller When the X CLARITYTM ETC Controller has been turned on red numbers will appear on the displays and the cooling fan within the X CLARITY ETC Chamber will begin to run If not check the power connection The front panel of the X CLARITY ETC Controller consists of four displays for 1 the voltage 2 current 3 temperature and 4 switching time Figure 7 Displays voltage current temperature switching time RUN STOP button Figure 7 The display on the front panel of X CLARITY ETC Controller A RUN STOP button is located below the display panel Figure 7 By pushing this button the user can start or stop the ETC process The X CLARITYTM ETC Chamber is equipped with a mechanical sensor to detect the opening and closing of the safety cover If the cover is open the bulb below the RUN STOP button will blink red and the X CLARITY ETC Controller will stop running Buttons for SET UP and DOWN are located on the lower half of the front panel Figure 7 12 3 3 Voltage Current Temperature and Switching Time Settings The X CLARITY Tissue Clearing System only works in constant current mode and not in constant voltage mode Note Many researchers and the original paper published in Nature have reported results obtained from using a constant voltage of 10 60 V However Logos Biosystems found that constant current mode leads to more consistent tissue clea
13. g the power cord to both the power source and the controller Always turn the X CLARITYTM ETC Controller off before disconnecting the power cord and or moving the instrument Turn the power off before opening the X CLARITY ETC Chamber Carefully monitor tube connections Replace tubes if leakage occurs Always use the pump to fill or drain the X CLARITY ETC Chamber Do not pour liquids in or out directly Use the recommended volume of Electrophoretic Clearing Solution with the provided X CLARITY TM Reservoir Bubbles may overflow during the run otherwise Do not use organic solvents other than the Electrophoretic Clearing Solution described in this manual Different solvents may cause permanent and irreparable damage If components emit smoke disconnect the power cord immediately from the outlet and contact a service representative or Logos Biosystems Do not disassemble the components in any event lf a device is malfunctioning or broken please contact a service representative or Logos Biosystems Disassembling the components invalidates the warranty Environmental Conditions for Operation Operating Power Frequency Installation Site Operating Temperature Maximum Relative Humidity Altitude Pollution Degree 100 120 VAC 2 2 A 200 240 VAC 1 1A 50 60 Hz Indoor use only 10 30 C 20 70 lt 2 000 m 2 1 Introduction 1 1 Product Overview In 2013 what many called one
14. ide from insufficient buffer changes may cause an adverse reaction causing dark particles to precipitate in the tissue and or electrodes Note Longer incubation times in Electrophoretic Tissue Clearing Solution may reduce the time required for the ETC process 4 2 Electrophoretic Tissue Clearing Solution The Electrophoretic Tissue Clearing Solution Cat No C13001 is made up of 200 mM boric acid 4 wt vol SDS pH 8 5 Do not reuse Electrophoretic Tissue Clearing Solution Reused clearing solution may have lowered buffering capacity which reduces clearing efficiency Electrophoretic Tissue Clearing Solution should be replaced daily while the tissue is being cleared Prolonged use of Electrophoretic Tissue Clearing Solution may cause electrolysis of the extracted lipids turning the tissue yellow In general the amount of Electrophoretic Tissue Clearing Solution needed for the X CLARITY Tissue Clearing System is 1 2 L per adult mouse brain per day Since it takes about 48 hours to clear a whole adult mouse brain with the X CLARITY Tissue Clearing System the total volume of Electrophoretic Tissue Clearing Solution needed is 2 4 L 15 4 3 ETC Running Use the X CLARITY pump to fill the X CLARITY ETC Chamber about half full with the Electrophoretic Tissue Clearing Solution Always use the pump to fill or drain the X CLARITY ETC Chamber Do not pour the solution in directly Place the tissue sample into the tissu
15. ill the reservoir with 1 L of deionized water and run the pump as you would during the ETG process Press the prime button maximum speed to accelerate washing Use lint free wipes to remove any residual particles after washing Put a little water on the wipes and gently wipe the interior of the X CLARITY ETC Chamber Wipe gently Rough and excessive handling may damage the X CLARITY ETC Chamber Dry the X CLARITY ETC Chamber thoroughly When cleaning the surfaces of the X CLARITY ETC Chamber do not use excessive amounts of water Do not allow liquid to enter the device as this may cause electric damage If liquid enters the device do not turn the device on Contact your local sales representative or Logos Biosystems 19 5 2 Troubleshooting Symptom Possible Cause Solution Tissue is not clear Inappropriate voltage and or current applied Check the voltage and current If 40 V at 1 5 A is observed it will take about 48 hours to clear a whole adult mouse brain Low temperature Set the temperature to 37 50 C Short clearing time Run the system for longer Inappropriate clearing solution Use fresh Electrophoretic Tissue Clearing Solution Incorrect pH Use fresh Electrophoretic Tissue Clearing Solution do not adjust the pH Tissue is dark Insufficient polymerization of hydrogel Perform polymerization of hydrogel with nitrogen under vacuum Ti
16. of the most important advances for neuroanatomy was published in the journal Nature CLARITY a new method developed by scientists at Stanford University was found to produce structurally sound and transparent tissues that are ready for multiple rounds of antibody labeling and imaging With the CLARITY method the biomolecules in intact tissues are covalently linked to a sturdy hydrogel network preserving molecular information and structural integrity Lipid bilayers are broken up through electrophoresis in the presence of ionic detergents leaving behind a stable and transparent tissue hydrogel hybrid that is chemically accessible for molecular phenotyping The CLARITY method has opened up a world of possibilities from tracing neural circuitry to exploring the relationship between structure and function with a global perspective The original electrophoretic tissue clearing ETC chamber used platinum wires as electrodes and controlled the temperature of the chamber by using a water circulator with a high flow rate Many researchers have since discussed the low efficiency of clearing in the original design in an online forum Scientists trying to clear their own tissue samples have run into difficulties that range from constructing their own DIY clearing chamber to poor tissue clearing Time resources and samples have been wasted Logos Biosystems has since licensed and independently developed the CLARITY technology to make significant improvemen
17. on against the purchaser of infringement of patents owned or controlled by the Company that cover the product based on the manufacture use or sale of a therapeutic clinical diagnostic vaccine or prophylactic product developed in research by the purchaser in which this product or its components were employed provided that neither this product nor any of its components were used in the manufacture of such product For any use other than this limited use label license of research use only please contact the Company or email info logosbio com for more information CLARITY T is the registered trademark of Stanford University X CLARITY is the registered trademark of Logos Biosystems Inc Patent pending 23 7 2 Instrument Warranty Logos Biosystems Inc Company warrants to the original purchaser Purchaser that the instrument Instrument if properly used and installed will be free from defects in materials and workmanship and will conform to the product specifications for a period of one 1 year Warranty Period from the date of purchase If the Instrument under this limited warranty fails during the Warranty Period the Company at its sole responsibility will 1 within and up to 30 calendar days of purchase refund the purchase price of the Instrument to the Purchaser if the Instrument is in original conditions or 2 after 30 calendar days of purchase only replace or repair the Instrument for u
18. p to the Warranty Period without issuing a credit In no event shall the Company accept any returned instrument including its components that might have been used or contaminated in some labs including but not limited to HIV or other infectious disease or blood handling labs This limited warranty does not cover refund replacement and repair incurred by accident abuse misuse neglect unauthorized repair or modification of the Instrument This limited warranty will be invalid if the Instrument is disassembled or repaired by the Purchaser In case that the Company decides to repair the Instrument not to replace this limited warranty includes replacement parts and labor for the Instrument This limited warranty does not include shipment of the Instrument to and from service location or travel cost of service engineer the costs of which shall be borne by the Purchaser Every effort has been made to ensure that all the information contained in this document is correct at its publication However the Company makes no warranty of any kind regarding the contents of any publications or documentation as unintended or unexpected errors including occasional typographies or other kinds are inevitable In addition the Company reserves the right to make any changes necessary without notice as part of ongoing product development If you discover an error in any of our publications please report it to your local supplier or the Company The Company shall ha
19. ring results The recommended constant current value is 1 5 A Changing the current value may affect the time and or efficiency of clearing and require further optimization A built in electric switching system allows users to change the direction of the electric current at pre defined time periods To adjust values for current temperature or switching time push the SET button located on the front panel of the X CLARITY ETC Controller The activated display will blink on in the following order when you continue to push the SET button Current gt Temperature gt Switching time Use the UP and DOWN buttons to adjust to the desired values Push the SET button again to complete the setting The ranges provided by the X CLARITY ETC Controller are Range Increment Voltage V Not adjustable max 60 N A Current A 0 2 1 5 0 1 Temperature C 35 60 1 Switching time min 0 600 10 The following are the recommended values to clear a whole adult mouse brain At these settings it takes about 48 hours to clear a whole adult mouse brain Recommended Current 15A Temperature 37 45 C Switching time 0 Peristaltic pump speed 30 rpm Note 1 The current and voltage are dependent on the resistance of the buffer Depending on the condition of the Electrophoretic Tissue Clearing Solution the initial current value may be lower than 1 5 A due to the voltage limit 60 V If the X CLARITY Tissue Clearing System doe
20. s not reach 1 5 A after a few hours please check the buffer Note 2 The tissue container holder design can also affect the resistance which may lead to a decreased current value Use the container holder provided 13 3 4 X CLARITY Pump Settings The peristaltic pump included in the X CLARITY Tissue Clearing System has a control panel as shown below Speed rpm Up Counter Clockwise indicator Prime max speed Clockwise indicator Start Stop External control indicator Reverse direction Down Figure 8 Control panel of X CLARITY Pump When the X CLARITY Tissue Clearing System is assembled run the pump to supply buffer to the X CLARITY ETC Chamber Depending on how the pump has been oriented in relation to the X CLARITY ETC Chamber run the pump in a clockwise CW or counterclockwise CCW direction to either supply or drain the chamber Start the pump at 30 50 rpm to begin circulating the Electrophoretic Tissue Clearing Solution Press the PRIME fast forward button to run the pump at maximum speed Set to 30 rpm when the X CLARITY ETC Chamber has been completely filled At 30 rom the pump moves about 200 mL per minute See the separately supplied pump manual for more details 14 4 Running 4 1 Sample Preparation To clear tissue samples the hydrogel polymerized tissue should be incubated in Electrophoretic Tissue Clearing Solution for at least 24 hours prior to the run Residual acrylam
21. ses and can radiate radio frequency energy and if not installed and used in accordance with the instruction manual may cause harmful interference to radio communications Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at the user s own expense www logosbio com Table of Contents Table of Contents musea ce dada 1 Safety Information orar a A AA ev a ade ees 2 Environmental Conditions for Operation ooooocnncccnnncconnncnnnccnonccnnn vnr nana cnc 3 Aige STN 4 1 1 Product Over Wester a ai ri 4 1 2 Product Contents irritada 5 1 3 Product Specifications cinco irc O dadas hs 6 2 Product Descrip ae 7 21 X GLARITYT ETG Chamber Ad dad 7 22 X GLARITYT ETG Controller cocido dd ici oda e a EAEAN 8 23 X CLARITY M PUMP ica a de 9 2 4 CLARITA Reservo liar 9 3 Setting Up aasuaammienikaam a ds dic dates 10 A PE o E E A E eet 10 02 Stata a daa te tat kb hd sept da aa 12 3 3 Voltage Current Temperature and Switching Time SettingS ccccccceeeeeeseeseeeeseeeeeseeeeeeeeee 13 3 4 X CLARITY Pump Settings cimil dto 14 O ented a ence 15 4 1 Sample Preparation askuuirnumeiseideisuniiejsrnmnnfetisuniddisntdkedseduidelinsddasaded smidde 15 4 2 Electrophoretic Tissue Clearing Solution ccccccceeceeeeeeeeeeeeeeeeeaeeseceeecaeeesaaeseeneeseaeeesaeeeeaesseeees 15 4 3 ETG RUNNING uxsmuessumsmbemdade pietet at
22. ssue is yellow Reused clearing solution More than one whole adult mouse brain per chamber Change the Electrophoretic Tissue Clearing Solution with a cycle of 1 2 L day for a whole adult mouse brain Reused tissue container Use a new tissue container Tissue is distorted and or deformed Over clearing Reduce the time or current for the ETC process Displayed and set temperature are different This is not unusual This is not unusual In some cases the displayed temperature may be above the setting value Contact Logos Biosystems when the difference is more than 10 C High temperatures in the tube attached to the chamber outlet Convection Convection is a normal phenomenon The temperature of the clearing solution in the tube will be 5 C higher than indicated on the display 20 Symptom Possible Cause Solution Leaking from the chamber cap Improperly or loosely screwed on chamber cap Screw on the chamber cap tightly The silicone ring inside will prevent leaks Aging of or damage to the chamber cap silicone ring Replace the chamber cap Please contact your local sales representative or Logos Biosystems Voltage and current values are 0 despite the settings Open chamber safety cover Close the cover RUN STOP button not Push the RUN STOP button A red halo around the pushed button means the devic
23. the X CLARITY ETC Chamber These dark particles are carbon aggregates that are generated by electrolysis of organic materials Use lint free wipes to remove these particles as prolonged absorption of these particles may cause irreversible damage of electrodes Refill the X CLARITY ETC Chamber with the Electrophoretic Tissue Clearing Solution and continue the ETC process as described in pages 20 21 Note The X CLARITY ETC Chamber is equipped with a mechanical sensor to detect the opening and closing of the safety cover If the cover is open the X CLARITY ETC Controller will stop running 18 5 Maintenance and Troubleshooting 5 1 Cleaning Clean the X CLARITY ETC Chamber after every run The ETC process produces various byproducts such as tissue debris and carbonized particles Wash the X CLARITY ETC Chamber interior with fresh Electrophoretic Tissue Clearing Solution followed by deionized water after each run Note Always use the pump to fill or drain the X CLARITY ETC Chamber Do not pour liquids into the X CLARITY ETC Chamber directly Using the pump fill the X CLARITY ETC Chamber with 500 mL fresh Electrophoretic Tissue Clearing Solution Adjust the switching time of the X CLARITY ETC Controller to CL Set the temperature of the X CLARITY ETC Controller to 37 C Set the current to 1 5 A Run the X CLARITY Tissue Clearing system for 1 2 hours Stop the system and drain the buffer F
24. tion to maintain buffering capacity control buffer temperature and remove bubbles from the X CLARITY ETC Chamber The X CLARITYT Tissue Clearing System comes with a 2 L bottle as a Reservoir Due to water electrolysis and the presence of a detergent in the buffer bubbles will come out of the chamber outlet Start the process with 1 2 L of Electrophoretic Tissue Clearing Solution in the reservoir to maintain buffering capacity and prevent an overflow of bubbles The temperature probe attached to the reservoir cap is inserted into the reservoir and connected to the X CLARITY ETC Controller The temperature of the clearing solution is displayed on the X CLARITY ETC Controller 3 Setting Up 3 1 Installation Place the components of the X CLARITY Tissue Clearing System on a clean and flat surface devoid of vibration Leave sufficient space around the X CLARITY ETC Chamber for the cooling fan to work properly Connect all tubes before running the system Note The tubes have a tubing life of 3000 hours Reservoir inlet connected ta the chamber outlet A Reservoir outlet connected to the chamber inlet Temperature probe Temperature probe connecter connected to the controller Figure 4 Diagram of the X CLARITY Reservoir Cap Take the tube with two plain ends and connect one end to the reservoir outlet located on the cap of the X CLARITYT Reservoir Run the middle of the tube
25. ts for tissue clearing efficiency and reproducibility The X CLARITYT Tissue Clearing System is an all in one easy to use solution for electrophoretic tissue clearing lts unique design accelerates the removal of lipids from tissues in a highly efficient manner The X CLARITY ETC Controller works as both a power supply and temperature controller for the X CLARITY ETC Chamber Improved electrodes generate a uniform electric field that eliminates uneven voltages and currents A built in electric switching system allows users to change the direction of the electric current at pre defined time periods An active cooling system minimizes the probability of artifacts arising due to poor temperature control A clearing buffer is continually circulated through the chamber for consistent buffering capacity temperature control and the elimination of electrophoretic byproducts This advanced system ensures that tissue clearing occurs efficiently and rapidly The X CLARITY Tissue Clearing System is easy to setup and easy to use Complicated electrical and communicating wires are combined into a single cable in an integrated system for power supply and control By simply pushing a few buttons researchers can easily operate the X CLARITY Tissue Clearing System Specifically designed consumables make the process even more convenient 1 2 Product Contents The X CLARITY Tissue Clearing System product package contains the following components
26. ve no responsibility or liability for any special incidental indirect or consequential loss or damage resulting from the use or malfunction of the Instrument This limited warranty is sole and exclusive The Company makes no other representations or warranties of any kind either express or implied including for merchantability or fitness for a particular purpose with regards to this Instrument To obtain service during the Warranty Period contact your local supplier or the Company s Technical Support team Out of Warranty Service Please contact your local supplier or the Company s technical support team in order to obtain out of warranty service If necessary repair service will be charged for replacement parts and labor hours incurred to repair the Instrument In addition the Purchaser is responsible for the cost of shipping the Instrument to and from the service facility and if necessary the travel cost of a service engineer 24 Contact Information For more information or technical support please contact us Our regional suppliers are listed on our website www logosbio com Logos Biosystems Inc Doosan Venture Digm STE 930 415 Heungan daero Dongan Gu Anyang Si Gyeonggi Do 431 755 Republic of Korea Tel 82 31 478 4185 Fax 82 31 478 4184 Email sales logosbio com 25
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