logos biosystems X-CLARITY TISSUE CLEARING SYSTEM User manual

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C10401 C10301 C10101 C10201
System Setup
Buffer Reservoir Pump X-CLARITY™ETC Chamber X-CLARITY™ ETC Controller
Quick
Start
Guide
X-CLARITY™TISSUE CLEARING SYSTEM
This Quick Start Guide provides instructions to install and use the X-CLARITY™ TISSUE CLEARING SYSTEM.
For detailed instructions, please refer to the user manual in the supplied USB drive.
Document No: C14002

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Accessories
Item
Quantity
Catalog #
Description
1
C12101
Multi-cable with two female ends to connect the X-CLARITY™ ETC
Controller and X-CLARITY™ ETC Chamber
2
-
Power cords for the X-CLARITY™ ETC Controller and pump
1
C12102
X-CLARITY™ reservoir cap with temperature probe
1
C12103
Snap-lock connector tube (clear tube)
1
C12104
Peristaltic pump tube (light yellow tube)
1
C12002
Container holder (holds the tissue container)
5
C12001
Tissue container (holds a whole adult mouse brain)
Not
included
in the
starter kit
C12003
C12004
C12005
Mouse Brain Slice Holder (Thickness: 2 mm)
Mouse Brain Slice Holder (Thickness: 4 mm)
Mouse Brain Slice Holder (Thickness: 6 mm)
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C13001
Electrophoretic Tissue Clearing Solution (1 L per bottle)
*note: pictures are not to scale

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Making the Connections
1. Connect the X-CLARITY™ ETC Controller and X-CLARITY™ ETC Chamber
a. Take the multi-cable and connect the ends to the ports on the rear panels of the X-CLARITY™
ETC Controller and X-CLARITY™ ETC Chamber. Check the orientation of the pins before
inserting the ends of the multi-cable into the X-CLARITY™ ETC Controller or X-CLARITY™
ETC Chamber. There are homing grooves on the ends to ensure proper orientation.
b. Fasten the nuts on tightly to ensure there is a tight connection. This controls the electric current
and temperature of the X-CLARITY™ Tissue Clearing System.
X-CLARITY™ ETC Controller-ETC Chamber Connection
Homing groove

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2. Buffer reservoir temperature control
a. Fill the buffer reservoir with 1.2 L of the Electrophoretic Tissue Clearing Solution.
b. Screw on the cap of the buffer reservoir making sure the temperature probe and buffer reservoir
outlet tube are both in the reservoir.
c. Insert the temperature probe connector that projects from the cap of the X-CLARITY™ buffer
reservoir into the temperature probe port on the rear panel of the X-CLARITY™ ETC Controller.
Check the home on the connector and the thickness of the two pins for proper orientation.
Reservoir outlet
Reservoir outlet tube
Temperature probe connector
Temperature probe
Reservoir inlet
Thick pin
Thin pin
Homing groove

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X-CLARITY™ ETC Controller-ETC Chamber-Buffer Reservoir Connection
3. Connecting the buffer reservoir to the X-CLARITY™ ETC Chamber
a. Take one end of a peristaltic pump tube and attach it to the X-CLARITY™ ETC Chamber inlet
located on the front panel of the X-CLARITY™ ETC Chamber. Make sure there is a tight seal to
prevent buffer leakage.
b. The buffer reservoir outlet protrudes from the buffer reservoir cap with tubing that extends into
the buffer reservoir alongside the temperature probe. Securely attach the other end of the
peristaltic pump tube to the reservoir outlet. Make sure there is a tight seal to prevent buffer
leakage. (You may find it helpful to label the outlet for faster identification for future
applications.)
Chamber inlet

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c. Open the pump head compression block by pulling the lever to the left.
d. Lift the clamps on both sides of the pump head. Load the middle of the tube into the pump head
between the rollers and the compression block.
Reservoir outlet
Chamber inlet
Pump head
Lever (to the left)
Clamp 1
Clamp 2
Tube

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e. Release the clamps.
f. Close the compression block by pulling the lever to the right. Make sure the tube is secure.
4. Sample insertion
a. Open the red safety cover of the X-CLARITY™ ETC Chamber.
b. Unscrew the cap to the X-CLARITY™ ETC Chamber.
Lever (to the right)
Safety cover
Chamber cap
Tissue container
Tissue container top
Container holder

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c. Use the appropriate holder for your sample. Insert the tissue container holder into the chamber
(upright).
Note: To ensure proper clearing, the sample should always be oriented in the SAME direction when you
take it out and place it back into the chamber.
d. Screw on the chamber cap TIGHTLY to prevent leakage. Make sure to keep the platform/stage
around the holder dry to prevent electric shortages and keep from damaging the chamber.
e. Carefully shut the red safety cover of the X-CLARITY™ ETC Chamber.
5. Connecting the X-CLARITY™ ETC Chamber to the buffer reservoir
a. ONLY after the safety cover has been closed, attach the plastic head of the snap-lock connector
tube to the buffer outlet protruding from the cap. You will feel and hear a click when it has been
attached properly.

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NOTE: To detach the snap-lock connector from the buffer outlet, press the stainless steel button on the
side to release the tube from the X-CLARITY™ ETC Chamber.
NEVER OPEN OR CLOSE THE CHAMBER SAFETY COVER WITH THE TUBE IN PLACE.
b. Attach the other end of the tube to the buffer reservoir inlet.
6. Connecting the power cords
a. Plug in the power cord to the pump. Connect to a power outlet.
b. Plug in the power cord to the X-CLARITY™ ETC Controller. Connect to a power outlet.
Reservoir inlet
Chamber outlet
Snap-lock
connector
Chamber outlet
Stainless steel button

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Buffer Flow
X-CLARITY™ buffer reservoir  buffer reservoir outlet  chamber inlet  X-CLARITY™ ETC Chamber
 chamber outlet  reservoir inlet  X-CLARITY™ buffer reservoir

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Ready, Set, Run!
1. Flip the power switch to the on position on the rear panel of the X-CLARITY™ ETC Controller. You will
know the machine is on when red numbers appear on the LED display on the X-CLARITY™ ETC
Controller. If not, check the power connection.
2. Push the SET button on the X-CLARITY™ ETC Controller to adjust values for current, temperature, or
timer.
a. Use the UP and DOWN buttons to adjust to the desired values.
b. Push the SET button again to complete the setting.
c. Voltage settings cannot be manipulated. The X-CLARITY™ ETC Controller supports constant
current mode only.
d. For more details, please refer to the user manual.
3. Turn on the power for the pump.
4. Set up the pump’s settings.
a. Set to 30-50 rpm to begin circulating the Electrophoretic Tissue Clearing Solution.
b. Adjust to 30 rpm when the X-CLARITY™ETC Chamber has been completely filled.
c. For more details, please refer to the user manual.
5. Start the pump. Make sure the buffer is flowing in the right direction:
X-CLARITY™ buffer reservoir buffer reservoir outlet chamber inlet X-CLARITY™ ETC
Chamber chamber outlet reservoir inlet X-CLARITY™ buffer reservoir
6. Run the experiment by pushing the RUN/STOP button on the X-CLARITY™ ETC Controller. A red halo
will appear around the button when the instrument is running.

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CAUTION!!!
1. DO NOT open the red safety cover of the X-CLARITY™ETC Chamber while the snap-lock connector
tube is attached as shown below. This can damage the tube.
THE TUBE IS STILL ATTACHED!
2. DO NOT attach the snap-lock connector tube before closing the safety cover.
THE SAFETY COVER HAS NOT BEEN CLOSED!
3. DO NOT pour liquids directly into the X-CLARITY™ETC Chamber. Always use the X-CLARITY™pump
to fill or drain the X-CLARITY™ETC Chamber. See the user manual for more details.
4. BEWARE of electric shock. Keep the X-CLARITY™Tissue Clearing System as dry as possible.
If buffer spills or leaks occur, immediately turn off the power. Clean up the liquid as quickly as
possible with a clean, dry cloth to prevent damage to the electric wiring inside the X-CLARITY™
ETC Chamber.
Pay careful attention to the mechanical sensor near the safety cover hinges as this is where the
X-CLARITY™ETC Chamber is the most vulnerable to buffer leakage. In case of spills or leaks,
dry this area first!

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The magnetic sensor detects whether the safety cover is open or closed. The X-CLARITY™
Tissue Clearing System will not run if the safety cover is open even if you push the RUN/STOP
button. No electric current will enter the chamber if the safety cover is not closed.
5. DRAIN the X-CLARITY™ETC Chamber and tube attached to its outlet before you open it again.
Turn the power off via the X-CLARITY™ ETC Controller.
Change the direction of the pump to pump counterclockwise.
The tube connecting the X-CLARITY™ETC Chamber outlet and the buffer reservoir outlet will
begin to empty into the X-CLARITY™ETC Chamber. ****Make sure this tube is completely
empty to prevent buffer spilling when you disconnect the tube from the chamber outlet.****
The buffer will flow out of the chamber inlet back into the reservoir. You can watch the buffer
level drop through the window of the X-CLARITY™ETC Chamber.
When the X-CLARITY™ETC Chamber is sufficiently drained, turn off the pump. Disconnect the
snap-lock connector tube from the chamber outlet. Open the safety cover. Unscrew the
chamber cap. Check your sample.
Magnetic sensor

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Intentionally Left Blank
Logos Biosystems, Inc.
STE 930 Doosan Venture Digm; 415 Heungan-daero, Dongan-Gu; Anyang-Si, Gyeonggi-Do 431-755; Republic of Korea
∙Tel: [phone] ∙Fax: [phone] ∙Email: [e-mail] ∙Website: www.logosbio.com