PIXUL™ Multi-Sample Sonicator
powered by Matchstick Technologies
PIXUL™ is sold under an exclusive license to patents owned by Matchstick Technologies Inc. and University ofWashington, specifically Matula, T.J.; Bomsztyk, K.; Darlington, G.P., Maxwell, A.D.; MacConaghy, B.E., Reed, J.
“Ultrasound system for shearing cellular material”. US Patent US10809166. European Patent EP3169451.

Catalog No. 53130(version A2)
Active Motif North America
1914 Palomar Oaks Way, Suite 150
Carlsbad, California 92008, USA
Toll free:877 222 9543
Telephone:
760 431 1263
Fax:
760 431 1351
Active Motif Europe
Waterloo Atrium
Drève Richelle 167 – boîte 4
BE-1410 Waterloo, Belgium
UK Free Phone:		
0800 169 31 47
France Free Phone:
0800 90 99 79
Germany Free Phone: 0800 181 99 10
Telephone:		+32 (0)2 653 0001
Fax:		
+32 (0)2 653 0050
Active Motif Japan
Azuma Bldg, 7th Floor
2-21 Ageba-Cho, Shinjuku-Ku
Tokyo, 162-0824, Japan
Telephone:+81 3 5225 3638
Fax:
+81 3 5261 8733
Active Motif China
787 Kangqiao Road
Building 10, Suite 202, Pudong District
Shanghai, 201315, China
Telephone:(86)-21-20926090
Hotline:400-018-8123
Copyright 2020 Active Motif, Inc.
www.activemotif.com

Active Motif Limited Warranty
Active Motif warrants that the PIXUL Multi-Sample Sonicator will be free from defects for 12 months fromthe date of delivery when used under normal working conditions and in accordance with manuals and otherdocuments. Any component that proves defective during this period will be repaired or replaced at no costto the purchaser. Active Motif will provide a shipping container and instructions for the customer to returnthe instrument for repair or replacement. All shipping charges during the warranty period will be paid by
Active Motif. In the event of a warrantable defect, please contact Active Motif for a return authorization andinstructions prior to returning any instrument or parts.
The warranty is void if failure of the instrument or parts, including all firmware or hardware, has resulted from
accidents, abuse, improper maintenance, usage, or repair, or misapplication by the customer. It is also void if
damage is cause by any unauthorized modifications made to the instrument.
The warranty is limited to repair or replacement only, is not transferable, and is available only to the original
purchaser.
The warranty is void if the instrument is run without Active Motif Coupling Fluid (cat. no. 53136) in the coolingreservoir. Coupling Fluid not only acts as the cooling liquid, but is also required for the transmission of energy
from the transducers to samples in the wells. Failure to run the instrument without Active Motif Coupling
Fluid will damage the transducers samples.
The warranty is void if the instrument is run without the proper plate (cat. no. 53139) or without liquid/water in every well of the columns in the 96-well plate that are being sonicated. Permanent damage to thetransducer and electronic circuits could result if the transducer is operated without liquid/water in every wellof the columns in the 96-well plate that are being sonicated.
Except as otherwise stated above, Active Motif’s standard Terms and Conditions apply. See www.activemotif.
com/terms-conditions for more information.
Information in this manual is subject to change without notice and does not constitute a commitment on thepart of Active Motif, Inc. It is supplied on an “as is” basis without any warranty of any kind, either explicit or
implied. Information may be changed or updated in this manual at any time.
This documentation may not be copied, transferred, reproduced, disclosed, or duplicated, in whole or in part,without the prior written consent of Active Motif, Inc. This documentation is proprietary information andprotected by the copyright laws of the United States and international treaties.
The manufacturer of this documentation is Active Motif, Inc.
© 2020 Active Motif, Inc., 1914 Palomar Oaks Way, Suite 150; Carlsbad, CA 92008. All rights reserved.
All trademarks, trade names, service marks or logos referenced herein belong to their respective companies.

www.activemotif.com

ii

TABLE OF CONTENTS

Page

General Warnings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . iv
Overview  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Introduction  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
PIXUL™ Multi-Sample Sonicator Exterior Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Installing the PIXUL Multi-Sample Sonicator  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Operating the PIXUL Multi-Sample Sonicator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4
Maintenance  .  .  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Touchscreen Messages and Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
References  .  .  .  .  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Appendix
Section A. PIXUL Sonication Parameters Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Section B. Troubleshooting Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9Technical Services  . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  10

www.activemotif.com

iii

General Warnings
Don’t run the PIXUL™ Multi-Sample Sonicator without PIXUL Coupling Fluid (Cat. No. 53136).
Tilting the PIXUL instrument can result in spillage of Coupling Fluid.
Do not unplug or power off the PIXUL instrument during a run. Loss of power to the instrument
while a file is open can result in corruption of the data file and operating system.
It is recommended to change the PIXUL Coupling Fluid every 2 months.
PIXUL Coupling Fluid temperature should be approximately 15°C at the start of the sonication run.
Don’t exceed a Coupling Fluid temperature of 35°C during sonication. If Coupling Fluid temperature
is maintained within this range, in-well thermal monitoring indicates that the temperature of thesample is within the normal range experienced by samples in all major sonication instruments(please see referenced publication on page 9).
Only use room temperature (not previously frozen) 96-Well PIXUL Plates (cat. no. 53139) with the
PIXUL instrument. Place plates with well A1 in the upper left corner. All wells in columns being
sonicated MUST be filled with fluid. Do not reuse plates from partial runs, as this can lead to issues
with shearing consistency and sample contamination.
Don’t lift the external lid during processing of samples. Lifting the external lid will stop the run,initiating drainage of Coupling Fluid from under the plate, necessitating re-circulation of Coupling
Fluid to start over from the beginning processing samples. The run will not resume from the point
in time it was interrupted.
Any technical modifications to the device are prohibited. Service works may be carried out only by
qualified personnel.

www.activemotif.com

iv

Overview
Active Motif’s PIXUL™ Multi-Sample Sonicator is a high-throughput instrument for mechanicalshearing of DNA, RNA, chromatin, or protein from purified samples, cells, or tissue. This systemutilizes ultrasound transducers to create focused ultrasonic waveforms, transmitted through
PIXUL Coupling Fluid, to a 96-well microplate (cat. no. 53139). This flexible system allows for up
to 12 unique sonication parameters (one for each column of wells) to be set in the 96-well plate,generating consistent and reproducible fragmentation profiles in just 1 to 30 minutes per plate,depending on sample type.
product
PIXUL™ Multi-Sample Sonicator

formatcatalog no.

1-96 samples

53130*The PIXUL™ Multi-Sample Sonicator is powered by Matchstick Technologies.
PIXUL™ is sold under an exclusive license to patents owned by Matchstick Technologies Inc. andUniversity of Washington, specifically Matula, T.J.; Bomsztyk, K.; Darlington, G.P., Maxwell, A.D.;
MacConaghy, B.E., Reed, J. “Ultrasound system for shearing cellular material”. US Patent US10809166.
European Patent EP3169451

Introduction
PIXUL™ Multi-Sample Sonicator
Next-generation sequencing applications, such as ChIP-Seq, RNA-Seq, RIP-Seq, exome, and wholegenome sequencing, require precise sample fragmentation (200-600 bp) for compatibility withshort read sequencing platforms. Shearing by mechanical sonication, as opposed to enzymatic
methods, is preferred for its unbiased nature and ability to produce a relatively narrow fragmentation profile. However, the currently available sonication systems can be incompatible withhigh-throughput sample processing. The PIXUL Multi-Sample Sonicator provides a flexible andreproducible shearing profile for up to 96 samples processed in parallel.
Furthermore, high-throughput sonication on other platforms is currently limited by the cost of
consumables (tubes, plates, and reagents). However, the low cost, round-bottom plates (cat. no.
53139) used in the PIXUL instrument are compatible with cell culture and shearing, eliminating
sample transfer steps that are inconvenient and can lead to loss of sample. Furthermore, the PIXUL
Coupling Fluid does not require lengthy degassing and can be adequately circulated and ready forsonication in approximately 15 minutes.
Sonication of the samples is quick and easy. Using the touchscreen user interface, researchers
are able to specify unique sonication parameters for each column of the 96-well plate, enablingprocessing of many sample types for many different applications in the same microplate.
Most runs are complete within 10-30 minutes, ensuring that sample sonication will not be thebottleneck for your high-throughput applications.
www.activemotif.com

1Technical Specifications:
Dimensions (h, d, w)

45 cm x 59 cm x 34 cm (17.7 in x 23 in x 13 in)

Weight23 kg (50.7 lbs)

Power Requirements

100-240 VAC, 50-60Hz, 6 A max. at 115 VAC

Operating Environment

15°C to 25°C (59°F to 77°F), max. 85% relative humidity

Storage Temperature

5°C to 25°C (41°F to 77°F)

EMC

Complies with EN IEC 61326-1, “Electrical equipment
for measurement, control and laboratory use - EMC
requirements - Part 1: General requirements”, Class A.
Complies with FCC Part 15 Class A radio emissions
requirements for the USA and ICES-001 for Industry Canada.
Complies with EU EMC Directive 2014/30/E.

Safety Certification

UL Listing - certified to comply with UL 61010-1, 3rd Edition
cUL Listing - certified to comply with CAN/CSA C222.2
No. 61010-1-12, 3rd edition
CE Mark - complies with EN/IEC 60601-1 3rd edition

Operating System

User interface, software and processors are fully integrated
into the instrument

Chiller

Chiller is fully integrated into the instrument

Sample Processing Capacity

Sample processing uses round bottom 96-well microplates(Corning Cat. No. 3799), 200 µL per well

Recommended Batch Size

1 to 96

Applications

DNA Shearing
RNA Shearing
Chromatin Shearing
Protein Extraction

Included Accessories:

a. Drain tube
www.activemotif.com

b. Shipping cap
2

PIXUL™ Multi-Sample Sonicator Exterior Components
1
2
3
4
5
6
7

1.

Main Power Button: Press to turn on the PIXUL instrument. Power switch on back side of the
PIXUL instrument must be turned on first.

2.

Touchscreen User Interface: Will initiate once main power button is pressed. Use thetouchscreen to circulate the PIXUL Coupling Fluid, select sonication parameters, monitor
Coupling Fluid temperature, and monitor the time remaining for the run.

3.

Exterior Lid: Lift to install sample plate. Lid must remain down during sonication run.

4.

Pressure Distribution Plate Cover: Sits directly on top of the sample plate and is secured downwith the plate-securing rods.

5.

Plate-Securing Rods: Once the sample plate has been placed with well A1 in the upper left
corner and covered with the pressure distribution lid, clip these rods down to secure the plateprior to closing the exterior lid.

6.

Coupling Fluid Reservoir: Lift cap to fill reservoir with PIXUL Coupling Fluid (approximately
0.5 L capacity). Add Coupling Fluid periodically to maintain the minimum level (about one inch
below the top of the reservoir). It is recommended to drain old Coupling Fluid and add new
Coupling Fluid every two months.

7.

Drain: To drain PIXUL Coupling Fluid from the Coupling Fluid reservoir, ensure that no plate is
installed. Then, connect the drainage tubing to the drain. Coupling Fluid should begin to flow.

www.activemotif.com

3Installing the PIXUL Multi-Sample Sonicator
The following instructions detail the installation procedure for the PIXUL Multi-Sample Sonicator.
Only attempt to install this instrument after reading these instructions.
No special tools are required for installation.
The PIXUL instrument is intended for indoor use, and the power plug must be grounded.
Place the PIXUL instrument on a level, non-slip surface with sufficient load bearing capacity. Do
not place anything heavy on the PIXUL instrument.
Do not cover the ventilation openings. Provide at least 20 cm of clearance to allow proper airflow.
Toxic vapors can be produced depending on the type of operation. Ensure sufficient extraction of
the vapors.
1.

Open the boxes and cut the shipping straps. Remove the molded styrofoam packaging,protective clear wrapping, and any tape securing moving parts. Inspect the instrument andaccessories immediately after delivery for completeness and transport damage.

2.

Place the PIXUL instrument on a bench. Always make sure the PIXUL is on a level surface.

3.

Fill the reservoir of the PIXUL instrument with approximately 0.5 liters of PIXUL Coupling
Fluid. The fluid level should reach about an inch below the reservoir top. If you accidentally
overfill the reservoir, wipe up any spilled Coupling Fluid and suction Coupling Fluid out ofreservoir until it reaches the appropriate level.

4.

Plug the power cord into the back side of the PIXUL instrument and the wall outlet.

Operating the PIXUL Multi-Sample Sonicator
Warning: A 96-Well PIXUL Plate (cat. no. 53139) should be mounted and secured prior toattempting to circulate the PIXUL Coupling Fluid. Load your samples into the 96-Well PIXUL Platein the same orientation as will be indicated on the instrument touchscreen. Any wells lacking
sample in the columns being sonicated MUST be filled with liquid (water or buffer).

48Be sure to seal the plate well with an adhesive plate seal to prevent the samples from spilling.
Coupling Fluid should be circulated and allowed to cool to approximately 15°C prior to initiating
sample processing.
1.

Ensure that the PIXUL Coupling Fluid level is about an inch (2.5 cm) below the reservoir top.
Do not overfill.

2.

Switch on the power switch on the back side of the PIXUL instrument.
www.activemotif.com

4

3.

Press the main power button on the front side of the PIXUL instrument. The touchscreen
will start initializing.

4.

Load a sample-containing 96-Well PIXUL Plate (cat. no. 53139) into the PIXUL instrument.
Lift the external lid, place the plate with well A1 in the upper left corner, secure down thepressure distribution lid on top of the plate with plate-securing rods, and close the externallid.

Timer appears
when running

00:00

23.3 C®

Enabling Epigenetics Research

Columns

Column selector(step 6)

1

2

3

4

5

6

7

< <
< <

9

10

11

12

Pulse
[N]

PRF
[kHz]

ProcessTime

Columns50

1.00

30:00 20:00

Columns Not Selected

50

1.00

30:00 20:00

Process

Preset selectors(step 7)8

1,2,3,4,5,6,7,8,9,10,11,12

Add/Delete buttons(step 7)

Powered by
Matchstick
Technologies

CIRCULATE

Burst
Rate[Hz]

Coupling Buffertemperature(step 5)START

Sonication
parameters(step 7)
Start
button(step 8)Circulate button(step 5)

5.

On the touchscreen, press Circulate to initiate PIXUL Coupling Fluid cooling. You cannot start
the sonication run with out circulation active. You can monitor Coupling Fluid temperature in
the upper right hand corner of the touchscreen.

6.

On the touchscreen, select the plate columns for which you would like to set sonication
parameters. Columns selected together will be outlined in the same color, and be processedwith the same parameters.

7.

On the left side of the touchscreen, you can use the left and right arrows to select fromsaved presets of sonication parameters. You can also use the add and delete buttons to add
or remove a row of process settings.

		Adjust the following parameters (See Appendix, Section A for further details):		

Pulse: The number of cycles per pulse		

PRF: Pulse Repetition Frequency; the kHz frequency of pulse repetitions

		Process Time: Time a given column is actively processed. Process timers for all columns 		
run simultaneously, so the total run time for the entire plate is equal to the time of thecolumn(s) chosen to have the longest process time. For example, a plate with the fol-		
lowing column-associated process times will take a total of 21 minutes:

			Columns		

Process Time			1, 2 and 4		

18 minutes			

3, 6, 9, 10 and 12

12 minutes			5, 7 and 8		

21 minutes

			

11		

0 minutes

www.activemotif.com

5

Burst Rate: The frequency with which the burst (a set of pulses) transitions from one
column to the next; this parameter is always the same for all columns. We recommend
using the following parameter specifications as a starting point, and adjusting Process
Time to optimize for your specific sample and application:
Note: The software will not allow settings that could damage the transducers and theupper limits are a maximum Pulse of 50 or a maximum PRF of 1.00. We recommend aminimum Burst Rate of 20.00. Varying the Process Time is typically the only parameterthat needs adjusting, with longer Time needed for difficult samples such as adipose
tissue.
Sonication Parameter
Pulse [N]DNA**
(Cells & Tissue)

Chromatin**(Cells & Tissue)

DNA/RNA**(Purified)Protein**(Cells & Tissue)

50

50

50

50

PRF [kHz]

1.00

1.00

1.00

1.00

Process Time

30:00

30:00

10:00-30:00

1.00 - 2.00

Burst Rate [Hz]

20.00

20.00

20.00

20

*Labile marks, like phosphorylated epitopes, may be preserved better by discontinuous
sonication (e.g. rather than 30 minutes, 4 rounds of 4-6 minutes each, where the PIXUL
Coupling Fluid is allowed to circulate and cool between runs).
**Please see our Quick Guides for additional details on sonication recommendations.

8.

Once the PIXUL Coupling Fluid has reached approximately 15°C, press Start on thetouchscreen. The time to completion will appear in the top left hand corner of thetouchscreen.

9.

Once the run has completed, open the external lid. PIXUL Coupling Fluid will drain fromunderneath the sample plate for the next few seconds.

10. Unload the sample plate.
11.

To turn off the PIXUL instrument, press the main power button on the front side of the
PIXUL instrument and switch the power switch off on the back side of the PIXUL instrument

Maintenance•

Before all maintenance work, you should ensure that decontamination of the device has
been performed if it came into contact with hazardous materials.

•

Ensure all components of the PIXUL instrument are at room temperature before touching them.

•

Before and after each use, wipe down the plate loading area with a damp cloth, and thendry. You may remove the external lid to aid in this cleaning.

•

At daily intervals, inspect the drain plug by visual inspection from the outside.		
www.activemotif.com

6•

At monthly intervals, inspect the PIXUL instrument, and clean the touchscreen with waterand detergent. Do not use acetone or solvents as these may cause damage.

•At bimonthly intervals, it is recommended to drain and replace PIXUL Coupling Fluid. To drain
Coupling Fluid, attach the drain hose to the drain on the front of the instrument and ensurethat no plate is loaded into the instrument. Once the hose is attached, the Coupling Fluid
will begin to flow. Be ready to capture draining Fluid in a waste collection container or sink.
Be ready to capture draining Fluid in a waste collection container or sink.

•

To ship the PIXUL, the Coupling Fluid must be drained, and the Shipping Cap that came with
the instrument must be used as the cover for the Coupling Fluid Reservoir. There also must
be a microplate in place and secured with the Pressure Distribution Cover and Plate-Securing
Rods.

Touchscreen Messages and Errors
Checking for microplate/No microplate detected - The PIXUL instrument ensures that a plate isloaded prior to commencing Coupling Fluid circulation or sonication run.
Removing fluid from microplate area - The PIXUL instrument automatically drains Coupling Fluid
when the external lid is opened.
Unable to start processing. No columns are enabled. - The PIXUL instrument requires the Pulse, PRF,
Process Time, and Burst Rate to be set for at least one column before the sonication run will initiate.
Circulation must be enabled before starting process. - On the touchscreen, Circulate must bepressed and the Coupling Fluid allowed to circulate and cool before processing will initiate.
Lid is open. Please close lid to continue. - The external lid must be shut before processing will initiate.
Low pressure - The pressure of the Coupling Fluid is insufficient to initiate a sonication run. Pleasebe sure that Coupling Fluid is filled to the appropriate level.
Error messages:•

Unable to start processing. No columns are enabled.

•

Circulation must be enabled before starting process.

•Unable to communicate with device. Power off and on the system.

•

Lid is open. Close lid to continue.

•

Input parameter was invalid. Nearest valid value will be automatically selected.

•

Power off and on the system.

•

Checking for microplate.

•

Removing fluid from microplate area.

•

Low Pressure. pressure1 = 123 pressure2 = 123•

No microplate detected pressure1 = 123, pressure 2 = 123

www.activemotif.com

7

References
1.

Bomsztyk, K., et al. (2019) Nucleic Acids Research 47(12): e69.

Appendix
Section A. PIXUL Sonication Parameters Guide

www.activemotif.com

8Section B. Troubleshooting Guide
Problem/question

Possible cause

Recommendation

Instrument will notturn onNo power is being
supplied to the unit

Check that the power cord is securely plugged into both the
PIXUL instrument and wall plug.

Unit hasn’t been
properly turned on

Ensure that both the power switch on the back side and themain power switch on the front side of the PIXUL instrument
are both turned on.

Sonication run will not
start

Coupling Fluid is not
circulating

Check to make sure that the Coupling Fluid has started
circulating

Samples do not sonicate
as expected

Plate is installed
incorrectly

Ensure well A1 of the plate is placed in the upper left cornerSamples areoverheating

Monitor the Coupling Fluid temperature and ensure that it
does not exceed 35°C during sonication. Reduce the Pulse and/or PRF values if necessary.

Samples are notdiluted in appropriate
sonication buffer

Ensure that your sample is diluted in the recommended
sonication buffer, as specified in Quick Guides and User
Manuals. Consider running a positive control sample, available
from Active Motif.

Incorrect microplate
used

Ensure that the proper microplate is used, Corning Cat. No.
3799.

www.activemotif.com

9Technical Services
If you need assistance at any time, please call Active Motif Technical Service at one of thenumbers listed below.
Active Motif North America
1914 Palomar Oaks Way, Suite 150
Carlsbad, CA 92008, USA
E-mail: tech_service@activemotif.com
Active Motif Europe
Waterloo Atrium
Drève Richelle 167 – boîte 4
BE-1410 Waterloo, Belgium
E-mail: eurotech@activemotif.com

Active Motif Japan
Azuma Bldg, 7th Floor
2-21 Ageba-Cho, Shinjuku-Ku
Tokyo, 162-0824, Japan
Active Motif China
787 Kangqiao Road
Building 10, Suite 202
Pudong District
Shanghai, 201315, China

Toll Free: 877 222 9543
Direct: 760 431 1263
Fax: 760 431 1351

Germany Free Phone: 0800 181 99 10
France Free Phone: 0800 90 99 79
UK Free Phone: 0800 169 31 47
Direct: +32 (0)2 653 0001
Fax: +32 (0)2 653 0050

Direct: +81 3 5225 3638
Fax: +81 3 5261 8733
E-mail: japantech@activemotif.com

Direct: (86)-21-20926090
Hotline: 400-018-8123
E-mail: techchina@activemotif.com

Visit Active Motif online at http://www.activemotif.com
At this site:• Read about who we are, where we are, and what we do• Review data supporting our products and the latest updates• Share your ideas and results with us• View our job opportunities
Don’t forget to bookmark our site for easy reference!

www.activemotif.com

10